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finalmigrate.patch
commit 11e5c88f620fa352d31440b86fe4a304e9d9785d
Author: Dannon Baker <dannon.baker@gmail.com>
Date: Tue Nov 22 09:47:44 2016 -0500
Final update
diff --git a/Admin/API/index.md b/Admin/API/index.md
index 1d5b6a1..b10968f 100644
--- a/Admin/API/index.md
+++ b/Admin/API/index.md
@@ -3,8 +3,6 @@ autotoc: true
----
PLACEHOLDER_INCLUDE(../LinkBox)
-PLACEHOLDER_INCLUDE(/Under Construction)
-
Galaxy has an [Applications Programming Interface (API)](/Learn/API) that enables access to Galaxy from scripts. This page describes the [administrative](/Admin) aspects of the API. See [/Learn/API](/Learn/API) for information on using the [Galaxy API](/Learn/API).
diff --git a/Admin/CapacityPlanning/index.md b/Admin/CapacityPlanning/index.md
index e1dca18..a41d3d6 100644
--- a/Admin/CapacityPlanning/index.md
+++ b/Admin/CapacityPlanning/index.md
@@ -1,8 +1,6 @@
----
pagetitle: Galaxy Capacity Planning
----
-PLACEHOLDER_INCLUDE(/Under Construction)
-
PLACEHOLDER_INCLUDE(/Admin/LinkBox)
@@ -23,4 +21,4 @@ See the [Cloud page](/Cloud) for information on getting started with the cloud.
## See Also
* [/Cloud](/Cloud) - Galaxy on the cloud options
-* [/Public Galaxy Servers](/Public Galaxy Servers) - a list of known, publicly accessible, Galaxy servers.
+* [Public Galaxy Servers](/PublicGalaxyServers) - a list of known, publicly accessible, Galaxy servers.
diff --git a/Admin/Config/Performance/ProductionServer/index.md b/Admin/Config/Performance/ProductionServer/index.md
index a1120a2..b8c5f10 100644
--- a/Admin/Config/Performance/ProductionServer/index.md
+++ b/Admin/Config/Performance/ProductionServer/index.md
@@ -75,7 +75,7 @@ During deployment, you may run into problems with failed jobs. By default, Gala
The most important recommendation is to switch to an actual database server. By default, Galaxy will use [SQLite](http://www.sqlite.org/), which is a serverless simple file database engine. Since it's serverless, all of the database processing occurs in the Galaxy process itself. This has two downsides: it occupies the aforementioned GIL (meaning that the process is not free to do other tasks), and it is not nearly as efficient as a dedicated database server. There are other drawbacks, too. When load increases with multiple users, the risk of transactional locks also increases. Locks will cause (among other things) timeouts and job errors. If you start with SQLite and then later realize a need for a database server, you'll need to migrate your database or start over. Galaxy does not provide an internal method to migrate data from SQLite, and although free conversion tools are available on the web, this process is non-trivial.
-<div class='right'>[{{Images/Logos/PostgreSQLLogo160.png|PostgreSQL}}](http://www.postgresql.org/)</div>
+<div class='right'><a href='http://www.postgresql.org/'><img src='/Images/Logos/PostgreSQLLogo160.png' alt='PostgreSQL' /></a></div>
For this reason, Galaxy also supports [PostgreSQL](http://www.postgresql.org/) and [MySQL](http://dev.mysql.com/). *PostgreSQL is much preferred since we've found it works better with our DB abstraction layer, [SQLAlchemy](http://www.sqlalchemy.org).*
@@ -83,7 +83,7 @@ To use an external database, you'll need to set one up. That process is outside
Once installed, create a new database user and new database which the new user is the owner of. No further setup is required, since Galaxy manages its own schema. If you are using a UNIX socket to connect the application to the database (this is the standard case if Galaxy and the database are on the same system), you'll want to name the database user the same as the system user under which you run the Galaxy process.
-To configure Galaxy, set `database_connection` in Galaxy's config file, `config/galaxy.ini`. The syntax for a database URL is explained in the [SQLAlchemy documentation](http://sqlalchemy.readthedocs.org/en/rel_0_5/dbengine.html).
+To configure Galaxy, set `database_connection` in Galaxy's config file, `config/galaxy.ini`. The syntax for a database URL is explained in the [SQLAlchemy documentation](http://docs.sqlalchemy.org/en/latest/core/engines.html).
Here follow two example database URLs with username and password:
diff --git a/Admin/GetGalaxy/index.md b/Admin/GetGalaxy/index.md
index 4f2c0fc..c256960 100644
--- a/Admin/GetGalaxy/index.md
+++ b/Admin/GetGalaxy/index.md
@@ -54,7 +54,7 @@ If you are getting Galaxy for development, you want to use the default branch af
```
#!highlight sh
-$ git clone https://github.com/galaxyproject/galaxy/galaxy.git
+$ git clone https://github.com/galaxyproject/galaxy.git
```
diff --git a/BigPicture/Choices/index.md b/BigPicture/Choices/index.md
index 4f0824c..1363c80 100644
--- a/BigPicture/Choices/index.md
+++ b/BigPicture/Choices/index.md
@@ -28,11 +28,11 @@ Your choices depends upon your needs. Here are the options depending on what yo
| | [/Main](/Main) | [Local](/Admin/GetGalaxy) | [/Cloud](/Cloud) | [Appliance](http://www.bioteam.net/slipstream/galaxy-edition) | [Other](/PublicGalaxyServers) |
| | --------------- | -------------------------- | ----------------- | -------------------------------------------------------------- | ------------------------------ |
-| Your data sets are moderately sized | Yes | Yes | Yes | Yes | [?](/Public Galaxy Servers) |
-| Your computational requirements are moderate | Yes | Yes | Yes | Yes | [?](/Public Galaxy Servers) |
-| You want to share your Galaxy objects with others | Yes | Yes | Yes | Yes | [?](/Public Galaxy Servers) |
-| All needed [/Tools](/Tools) are [installed on Main](/Admin/Tools/Tool Dependencies). | Yes | ? | Yes | Yes | [?](/Public Galaxy Servers) |
-| Your data sets are very large | No | ? | Yes | Yes | [?](/Public Galaxy Servers) |
-| Your computational requirements are very large | No | ? | Yes | Yes | [?](/Public Galaxy Servers) |
-| You have absolute data security requirements | No | Yes | Yes | Yes | [?](/Public Galaxy Servers) |
+| Your data sets are moderately sized | Yes | Yes | Yes | Yes | [?](/PublicGalaxyServers) |
+| Your computational requirements are moderate | Yes | Yes | Yes | Yes | [?](/PublicGalaxyServers) |
+| You want to share your Galaxy objects with others | Yes | Yes | Yes | Yes | [?](/PublicGalaxyServers) |
+| All needed [/Tools](/Tools) are [installed on Main](/Admin/Tools/Tool Dependencies). | Yes | ? | Yes | Yes | [?](/PublicGalaxyServers) |
+| Your data sets are very large | No | ? | Yes | Yes | [?](/PublicGalaxyServers) |
+| Your computational requirements are very large | No | ? | Yes | Yes | [?](/PublicGalaxyServers) |
+| You have absolute data security requirements | No | Yes | Yes | Yes | [?](/PublicGalaxyServers) |
| No network transfer of data | No | Yes | No | Yes | No |
diff --git a/BigPicture/Terminology/index.md b/BigPicture/Terminology/index.md
index b5921ea..bf73ea0 100644
--- a/BigPicture/Terminology/index.md
+++ b/BigPicture/Terminology/index.md
@@ -3,7 +3,6 @@ autotoc: true
pagetitle: Galaxy Terminology
----
-PLACEHOLDER_INCLUDE(/Under Construction)
<div class='right'></div>
New to Galaxy? Trying to figure out the difference between a *workflow* and a *history?* This page attempts to be a glossary of Galaxy terminology.
diff --git a/CitingGalaxy/index.md b/CitingGalaxy/index.md
index baeecaa..23e61d0 100644
--- a/CitingGalaxy/index.md
+++ b/CitingGalaxy/index.md
@@ -153,9 +153,9 @@ Papers about or using Galaxy with [core team members](/GalaxyTeam) as authors.
1. [Anton Nekrutenko](/anton) & [James Taylor](/JamesTaylor), "[Next-generation sequencing data interpretation: enhancing reproducibility and accessibility](http://www.nature.com/nrg/journal/v13/n9/abs/nrg3305.html)." *[Nature Reviews Genetics](http://www.nature.com/nrg/index.html)*. 13, 667-672 (September 2012).
-1. [Enis Afgan](/EnisAfgan), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/JamesTaylor), ["Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html). *[Current Protocols in Bioinformatics](http://onlinelibrary.wiley.com/book/10.1002/0471250953)*. 2012 June: Unit 11.9.
+1. [Enis Afgan](/EnisAfgan), Brad Chapman, Margita Jadan, Vedran Franke, [James Taylor](/JamesTaylor), "[Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1109.html)." *[Current Protocols in Bioinformatics](http://onlinelibrary.wiley.com/book/10.1002/0471250953)*. 2012 June: Unit 11.9.
-1. [Jennifer Hillman-Jackson](/JenniferJackson), [Dave Clements](/DaveClements), [Daniel Blankenberg](/Dan), [James Taylor](/JamesTaylor), [Anton Nekrutenko](/anton), [Galaxy Team](/GalaxyTeam), ["Using Galaxy to Perform Large-Scale Interactive Data Analyses"](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html). *[Current Protocols in Bioinformatics](http://onlinelibrary.wiley.com/book/10.1002/0471250953)*. 2012 June: Unit 10.5.
+1. [Jennifer Hillman-Jackson](/JenniferJackson), [Dave Clements](/DaveClements), [Daniel Blankenberg](/Dan), [James Taylor](/JamesTaylor), [Anton Nekrutenko](/anton), [Galaxy Team](/GalaxyTeam), "[Using Galaxy to Perform Large-Scale Interactive Data Analyses](http://cda.currentprotocols.com/WileyCDA/CPUnit/refId-bi1005.html)." *[Current Protocols in Bioinformatics](http://onlinelibrary.wiley.com/book/10.1002/0471250953)*. 2012 June: Unit 10.5.
### 2011
@@ -175,13 +175,13 @@ Papers about or using Galaxy with [core team members](/GalaxyTeam) as authors.
### 2010
-1. [Blankenberg D](/Dan), [Von Kuster G](/greg_vonkuster), [Coraor N](/nate), [Ananda G](/GuruAnanda), [Lazarus R](/fubar), Mangan M, [Nekrutenko A](/anton), [Taylor J](/JamesTaylor). ["Galaxy: a web-based genome analysis tool for experimentalists"](http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb1910s89/abstract). *Current Protocols in Molecular Biology*. 2010 Jan; Chapter 19:Unit 19.10.1-21.
+1. [Blankenberg D](/Dan), [Von Kuster G](/greg_vonkuster), [Coraor N](/nate), [Ananda G](/GuruAnanda), [Lazarus R](/fubar), Mangan M, [Nekrutenko A](/anton), [Taylor J](/JamesTaylor). "[Galaxy: a web-based genome analysis tool for experimentalists](http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb1910s89/abstract)". *Current Protocols in Molecular Biology*. 2010 Jan; Chapter 19:Unit 19.10.1-21.
1. [Goecks, J](/JeremyGoecks), [Nekrutenko, A](/anton), [Taylor, J](/JamesTaylor) and The [Galaxy Team](/GalaxyTeam). [Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences](http://genomebiology.com/2010/11/8/R86). *Genome Biol.* 2010 Aug 25;11(8):R86.
1. [Afgan E](/EnisAfgan), [Baker D](/DannonBaker), [Coraor N](/nate), Chapman B, [Nekrutenko A](/anton), [Taylor J](/JamesTaylor). "[Galaxy CloudMan: Delivering Cloud Compute Clusters](http://www.biomedcentral.com/1471-2105/11/S12/S4)". *BMC Bioinformatics*. 2010 Dec 21. 11(Suppl 12):S4.
-1. [Blankenberg D](/Dan), Gordon A, [Von Kuster G](/greg_vonkuster), [Coraor N](/nate), [Taylor J](/JamesTaylor), [Nekrutenko A](/anton) and The [Galaxy Team](/GalaxyTeam). ["Manipulation of FASTQ data with Galaxy"](http://www.ncbi.nlm.nih.gov/pubmed/20562416). *Bioinformatics*. 2010 Jul 15;26(14):1783-5.
+1. [Blankenberg D](/Dan), Gordon A, [Von Kuster G](/greg_vonkuster), [Coraor N](/nate), [Taylor J](/JamesTaylor), [Nekrutenko A](/anton) and The [Galaxy Team](/GalaxyTeam). "[Manipulation of FASTQ data with Galaxy](http://www.ncbi.nlm.nih.gov/pubmed/20562416)." *Bioinformatics*. 2010 Jul 15;26(14):1783-5.
1. Bock C, [Von Kuster G](/greg_vonkuster), Halachev K, [Taylor J](/JamesTaylor), [Nekrutenko A](/anton), Lengauer T. "[Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy](http://www.ncbi.nlm.nih.gov/pubmed/20238087)". In "Methods in Molecular Biology: Genetic Variation: Methods And Protocols" (ed. M.R. Barnes and G. Breen). Humana Press, Towata, NJ. 2010 Feb.
@@ -199,9 +199,9 @@ Papers about or using Galaxy with [core team members](/GalaxyTeam) as authors.
1. Miller W, Rosenbloom K, Hardison RC, Hou M, [Taylor J](/JamesTaylor), Raney B, Burhans R, King DC, Baertsch R, [Blankenberg D](/Dan), et al. "[28-Way vertebrate alignment and conservation track in the UCSC Genome Browser](http://www.ncbi.nlm.nih.gov/pubmed/17984227)". *Genome Research*. 2007 Dec; 17(12):1797-808.
-1. [Taylor J](/JamesTaylor), Schenk I, [Blankenberg D](/Dan), and [Nekrutenko, A](/anton). ["Using Galaxy to Perform Large-Scale Interactive Data Analysis"](http://www.ncbi.nlm.nih.gov/pubmed/18428782). *[Current Protocols in Bioinformatics](http://onlinelibrary.wiley.com/book/10.1002/0471250953)*. 2007 Sep; 19:10.5.1-10.5.25.
+1. [Taylor J](/JamesTaylor), Schenk I, [Blankenberg D](/Dan), and [Nekrutenko, A](/anton). "[Using Galaxy to Perform Large-Scale Interactive Data Analysis](http://www.ncbi.nlm.nih.gov/pubmed/18428782)." *[Current Protocols in Bioinformatics](http://onlinelibrary.wiley.com/book/10.1002/0471250953)*. 2007 Sep; 19:10.5.1-10.5.25.
-1. [Blankenberg D](/Dan), [Taylor J](/JamesTaylor), Schenk I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova K, Hardison RC, [Nekrutenko A](/anton). ["A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly"](http://www.ncbi.nlm.nih.gov/pubmed/17568012). *Genome Research*. 2007 Jun; 17(6):960-4.
+1. [Blankenberg D](/Dan), [Taylor J](/JamesTaylor), Schenk I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova K, Hardison RC, [Nekrutenko A](/anton). "[A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly](http://www.ncbi.nlm.nih.gov/pubmed/17568012)." *Genome Research*. 2007 Jun; 17(6):960-4.
### 2005
diff --git a/Cloud/Jetstream/FAQ/index.md b/Cloud/Jetstream/FAQ/index.md
index 3b8d3af..d6d8592 100644
--- a/Cloud/Jetstream/FAQ/index.md
+++ b/Cloud/Jetstream/FAQ/index.md
@@ -22,7 +22,7 @@ Galaxy server can be restarted from the Jetstream's web interface, Atmosphere. D
## Where are Galaxy's log files?
Log files are available for problem diagnosis. Each launched server will have their respective logs in the same locations, which are as follows:
-<div class='center'>
+
| Log path | Description |
| -------- | ------------ |
| */opt/galaxy/logs/galaxy_web0.log* | This is the main Galaxy process server log. |
@@ -32,4 +32,3 @@ Log files are available for problem diagnosis. Each launched server will have th
| */var/log/supervisor/* | This directory contains log files for Supervisor process, which is used to manage Galaxy and several other Galaxy-related processes running on this server. |
| */var/log/postgresql/* | This directory contains log files for the PostgreSQL database process used by Galaxy. |
| */var/log/proftpd/* | This directory contains log files for the ProFTPd process used to upload data to Galaxy via FPT. |
-</div>
diff --git a/Cloud/Jetstream/Troubleshooting/index.md b/Cloud/Jetstream/Troubleshooting/index.md
index 71fdbbe..59cf596 100644
--- a/Cloud/Jetstream/Troubleshooting/index.md
+++ b/Cloud/Jetstream/Troubleshooting/index.md
@@ -11,7 +11,7 @@ PLACEHOLDER_INCLUDE(/Cloud/Jetstream/LinkBox)
----
## Galaxy does not run jobs
-There could be many reasons so if the following method does not help, please [|contact us](https://biostar.usegalaxy.org/).
+There could be many reasons so if the following method does not help, please [contact us](https://biostar.usegalaxy.org/).
There's a bug in Jetstream's configuration for instance's hostname, and our automated workaround does not always apply. If you queue jobs on your instance, but Galaxy won't actually execute any, try the following:
diff --git a/Cloud/Jetstream/index.md b/Cloud/Jetstream/index.md
index 51bcbd3..dcf6a44 100644
--- a/Cloud/Jetstream/index.md
+++ b/Cloud/Jetstream/index.md
@@ -21,14 +21,15 @@ After you have your XSEDE account and an active allocation:
* Once logged in *select* **Launch an instance**
[{{attachment:jetstream_GettingStarted.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLjetstream_GettingStarted.png)<br /><br />
-* Browse the available images and choose *Galaxy 16.01 Standalone*
- [{{attachment:jetstream_SelectGalaxy.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLjetstream_SelectGalaxy.png)<br /><br />
+* Browse the available images and choose a Galaxy image (see [Released versions](/Cloud/Jetstream#released_versions) below for the available options)
+ [{{http://i.imgur.com/OCA45pA.png||width="75%"}}|&do=get,target="_blank"](http://i.imgur.com/OCA45pA.png) <br /><br />
* Launch a Galaxy instance:
- [{{attachment:jetstream_LaunchGalaxy.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLjetstream_LaunchGalaxy.png)<br /><br />
+ [{{http://i.imgur.com/AQIeZyl.png?1||width="75%"}}|&do=get,target="_blank"](http://i.imgur.com/AQIeZyl.png?1)
+ <br /><br />
* Set basic parameters of the instance:
- [{{attachment:jetstream_LaunchGalaxyBasic.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLjetstream_LaunchGalaxyBasic.png)<br /><br />
+ [{{http://i.imgur.com/TSOUMJd.png?1||width="75%"}}|&do=get,target="_blank"](http://i.imgur.com/TSOUMJd.png?1)<br /><br />
* Select the provider: TACC or Indiana University.
* Select the instance size: This must be **large** or larger.
* And then click **Launch**
@@ -37,11 +38,17 @@ After you have your XSEDE account and an active allocation:
[{{attachment:jetstream_LaunchProject.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLjetstream_LaunchProject.png)<br /><br />
* The instance will be built and then launched. After a few minutes the instance will be **Active** and ready to use:
- [{{attachment:jetstream_GalaxyActive.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLjetstream_GalaxyActive.png)<br /><br />
+ [{{http://i.imgur.com/Z9GDeru.png||width="75%"}}|&do=get,target="_blank"](http://i.imgur.com/Z9GDeru.png)<br /><br />
* In less than 5 minutes, you should have your own, fully configured Galaxy server - just copy the new server IP address to a new browser window.
[{{attachment:galaxy_landing.png||width="75%"}}|&do=get,target="_blank"](ATTACHMENT_URLgalaxy_landing.png)<br /><br />
+## Released versions
+
+Each Galaxy server is based on a virtual machine image that has been preconfigured with Galaxy application, tools, data and configurations that are all ready for use. The following are versions of the image that have been made available on the Jetstream cloud:
+* **Galaxy 16.07 Standalone**: this image contains Galaxy 16.07 release with a toolset that closely matches that of the public Galaxy server available at [usegalaxy.org](https://usegalaxy.org/) as well as a complete set of reference genomes available on that same server. Availability of the reference data was realized by enabling a connection to a (CVMFS-based) replica server that offers access to approximately 3TB of reference data (vs. ~50GB in the previous version of the image). An additional benefit of such integration is that the reference data is no longer stored on the machine image, reducing the size of that image to about 10GB, leaving more space for the analysis data. The base operating system is Ubuntu 14.04. The image was built using the *cloud_setup* flavor of the [GalaxyKickStart](https://github.com/ARTbio/GalaxyKickStart) [Ansible](https://www.ansible.com/) playbook.
+* **Galaxy 16.01 Standalone**: the initial release of Galaxy on Jetstream. This image includes Galaxy 16.01 release and comes preconfigured with numerous tools as well as about 50GB of reference data. The base operating system is Ubuntu 14.04.
+
## What is Jetstream cloud?
<div class='right'>![](https://www.nsf.gov/news/mmg/media/images/jetstream_logo_f_fe60185c-962f-4c1f-99bf-e6ec82d54c21.jpg)</div>
diff --git a/Cloud/index.md b/Cloud/index.md
index 1644bbf..e528429 100644
--- a/Cloud/index.md
+++ b/Cloud/index.md
@@ -13,14 +13,18 @@ The *cloud* provides another option for this situation that can be cost-effectiv
Cloud infrastructures are just [one of the many ways that Galaxy is available](/BigPicture/Choices).
-## CloudMan
+## Galaxy CloudMan
-<div class='left'><a href='/CloudMan'><img src='/Images/Logos/CloudManWideBlackLogo.png' alt='CloudMan' width="250" /></a></div>
+<div class='left'><a href='/CloudMan'><img src='/Images/GalaxyLogos/cloudman-logo.jpg' alt='CloudMan' width="250" /></a></div>
-CloudMan is a software package that abstracts the interface to cloud infrastructure, allowing users to take advantage of the power of cloud infrastructure without having to learn much of the underlying details of any particular infrastructure. CloudMan supports elastic, dynamic resource scaling and works with Galaxy out of the box. It is also integrated with [CloudBioLinux](http://cloudbiolinux.org/). CloudMan works with multiple cloud infrastructures including [Amazon Web Services](http://aws.amazon.com), [OpenStack](http://www.openstack.org/), and [OpenNebula](http://opennebula.org).
+!CloudMan is a software package that abstracts the interface to cloud infrastructure, allowing users to take advantage of the power of cloud infrastructure without having to learn much of the underlying details of any particular infrastructure. !CloudMan supports elastic, dynamic resource scaling and works with Galaxy out of the box. !CloudMan works with multiple cloud infrastructures including [Amazon Web Services](http://aws.amazon.com), [OpenStack](http://www.openstack.org/), and [OpenNebula](http://opennebula.org).
See the CloudMan page for more.
+## Galaxy Standalone image(s)
+
+Some cloud providers have not yet been integrated with !CloudMan. Instead, standalone Galaxy images have been built that come pre-configured with the same configurations as the !CloudMan-backed images but without the option to scale into a virtual cluster. Images on the [NSF Jetstream cloud](/Cloud/Jetstream) and Google Compute Engine cloud exist.
+
## Globus Genomics
<div class='right'><a href='http://www.globus.org/genomics'><img src='/Images/Logos/GlobusGenomics.png' alt='Globus Genomics' width="200" /></a></div>
diff --git a/CloudMan/CapacityPlanning/index.md b/CloudMan/CapacityPlanning/index.md
index 9e90ff5..00fdf33 100644
--- a/CloudMan/CapacityPlanning/index.md
+++ b/CloudMan/CapacityPlanning/index.md
@@ -13,7 +13,7 @@ This page offers advice on how much cloud infrastructure you will need to run yo
There are many reasons why you may want to run Galaxy on the cloud. This page attempts to address these three general scenarios.
## Scenario 1: Light usage
-Scenario 1 is characterized by **light usage paired with the desire to avoid system administration.** In this case you want to use Galaxy for relatively lightweight processing tasks, but you don't want to use a [shared Galaxy server](/Public Galaxy Servers), or install your own copy. Galaxy's cloud images come with more tools and datasets preinstalled than does [/Main](/Main), and far more than a [locally installed Galaxy](/Admin/GetGalaxy). You may also not want to put your data on a public server.
+Scenario 1 is characterized by **light usage paired with the desire to avoid system administration.** In this case you want to use Galaxy for relatively lightweight processing tasks, but you don't want to use a [shared Galaxy server](/PublicGalaxyServers), or install your own copy. Galaxy's cloud images come with more tools and datasets preinstalled than does [/Main](/Main), and far more than a [locally installed Galaxy](/Admin/GetGalaxy). You may also not want to put your data on a public server.
## Scenario 2: Occasional but heavy usage
Scenario 2 is the canonical case for cloud computing: **You need heavy-duty computing, but you don't need it all the time, and you don't have access to your own compute cluster.** In this case, you would only bring up a Galaxy on the cloud on those occasions when you have new datasets to analyze. Once your analysis is done, you would offload your results and delete the instance.
diff --git a/Community/Arabic/index.md b/Community/Arabic/index.md
new file mode 100644
index 0000000..8084873
--- /dev/null
+++ b/Community/Arabic/index.md
@@ -0,0 +1,24 @@
+<div class='left'>![Galaxy Arabic Speaking Community](/GalaxyArabic400.png)</div>
+
+## Galaxy Arabic Speaking Community (العربية Galaxy)
+
+<table>
+ <tr>
+ <td style=" text-align: right; border:none;"> هذا مجتمع عربي لمستخدمي جالاكسي يضم أنشطة الجالاكسي كالدورات التدريبيه والنقاشات في المجتمع العربي والمناطق الناطقة<br />بالعربية في العالم كله إذا كنت تتكلم العربية أو تعيش في الوطن العربي يمكنك متابعتنا على تويتر والفيس بوك واشترك في القائمة<br />البريدية</td>
+ </tr>
+</table>
+
+
+----
+
+The **Galaxy Arabic speaking community** supports Galaxy activity for the Arabic speaking community and Arabic speaking regions of the world.
+
+If you speak Arabic or live in Arabic speaking regions, please consider
+
+* Following [@Galaxy_Arabic on Twitter](http://twitter.com/galaxy_arabic)
+* Joining the [Galaxy Arabic mailing list](https://lists.galaxyproject.org/listinfo/galaxy-arabic)
+* Joining the [Galaxy Arabic Facebook group](http://bit.ly/2ek7fTh)
+
+## Other Resources
+
+* Introduction to Galaxy Project presentation in Arabic ([PowerPoint](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.pptx), [PDF](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.PDF))
diff --git a/Community/Cistrome/index.md b/Community/Cistrome/index.md
index b8ba9b1..ab34410 100644
--- a/Community/Cistrome/index.md
+++ b/Community/Cistrome/index.md
@@ -2,7 +2,7 @@
The [Cistrome Analysis Pipeline](http://cistrome.org/ap/) has the standard Galaxy tools, plus 29 additional ChIP-chip and ChIP-seq specific tools, including preliminary peak calling and correlation analyses, downstream genome feature association, gene expression analyses, and motif discovery.
-Cistrome is a free [public Galaxy server](/Public Galaxy Servers), but does require you to create a login.
+Cistrome is a free [public Galaxy server](/PublicGalaxyServers), but does require you to create a login.
## See Also
* [Cistrome.org](http://cistrome.org) - Cistrome project
diff --git a/Community/Deployment/GalaxyAtUIowa/index.md b/Community/Deployment/GalaxyAtUIowa/index.md
index d2f9290..04020f3 100644
--- a/Community/Deployment/GalaxyAtUIowa/index.md
+++ b/Community/Deployment/GalaxyAtUIowa/index.md
@@ -40,7 +40,7 @@ This instances of Galaxy runs on a local [HPC cluster](http://hpc.uiowa.edu/reso
### Compute
[3600 cores](http://hpc.uiowa.edu/resources/compute), SGE DRM.
### Storage
-[|NFS, FhGFS](http://hpc.uiowa.edu/resources/storage).
+[NFS, FhGFS](http://hpc.uiowa.edu/resources/storage).
### Network
Ethernet and Infiniband.
## User Management
diff --git a/Community/Log/2015/BioJS2Galaxy/index.md b/Community/Log/2015/BioJS2Galaxy/index.md
index d22b14a..6ec6660 100644
--- a/Community/Log/2015/BioJS2Galaxy/index.md
+++ b/Community/Log/2015/BioJS2Galaxy/index.md
@@ -20,7 +20,7 @@ pagetitle: 2015, /, 07, :, , [BioJS2Galaxy - A step by step guide](http://www.b
From [the guide](http://www.benjamenwhite.com/2015/07/biojs2galaxy-a-step-by-step-guide/):
<div class='indent'>
-To encourage the use of [BioJavaScript (BioJS)](http://biojs.net/) visualisations in [Galaxy](https://galaxyproject.org/) we decided to create this simple step by step guide on how to use [@MrGreenify](https://twitter.com/MrGreenify)’s application, [biojs2galaxy](https://github.com/biojs/biojs2galaxy), which he introduced at the [Galaxy Community Conference 2015 in Norwich](http://gcc2015.tsl.ac.uk/abstracts/#BioJS2Galaxy_Automatic_Conversion_of_BioJS_Visualisation_Components_into_Galaxy_Plugins). As an example, we will use the [Multiple Sequence Alignment (MSA)](http://biojs.io/d/msa) viewer BioJS component (which was also written by [@MrGreenify](https://twitter.com/MrGreenify)).
+To encourage the use of [BioJavaScript (BioJS)](http://biojs.net/) visualisations in [Galaxy](https://galaxyproject.org/) we decided to create this simple step by step guide on how to use @[MrGreenify](https://twitter.com/MrGreenify)’s application, [biojs2galaxy](https://github.com/biojs/biojs2galaxy), which he introduced at the [Galaxy Community Conference 2015 in Norwich](http://gcc2015.tsl.ac.uk/abstracts/#BioJS2Galaxy_Automatic_Conversion_of_BioJS_Visualisation_Components_into_Galaxy_Plugins). As an example, we will use the [Multiple Sequence Alignment (MSA)](http://biojs.io/d/msa) viewer BioJS component (which was also written by @[MrGreenify](https://twitter.com/MrGreenify)).
To use biojs2galaxy you need to have [node](https://nodejs.org/) and [npm](https://www.npmjs.com/) installed. If you have never heard of node or npm it’s about time! You can find all the information you need in the [npm documentation](https://docs.npmjs.com/getting-started/what-is-npm).
</div>
diff --git a/Community/NBIC/index.md b/Community/NBIC/index.md
index 9a0152b..845dc5c 100644
--- a/Community/NBIC/index.md
+++ b/Community/NBIC/index.md
@@ -6,7 +6,7 @@ The [Netherlands Bioinformatics Centre (NBIC)](http://www/nbic.nl) is power user
## Links
* [NBIC home page](http://www.nbic.nl)
-* [Sombrero](http://galaxy.nbic.nl) - NBIC's test Galaxy server. This is [open to the public](/Public Galaxy Servers).
+* [Sombrero](http://galaxy.nbic.nl) - NBIC's test Galaxy server. This is [open to the public](/PublicGalaxyServers).
* [NBIC Hackathon April 2011](https://wiki.nbic.nl/index.php/NBIC_Hackathon_April_2011)
* [Galaxy related pages](https://wiki.nbic.nl/index.php/Category:NBIC_Galaxy) at NBIC's [BioAssist Wiki](https://wiki.nbic.nl/).
* Running Taverna Workflows in Galaxy
diff --git a/Community/index.md b/Community/index.md
index a8cd10d..3043b96 100644
--- a/Community/index.md
+++ b/Community/index.md
@@ -27,11 +27,18 @@ In short, the Galaxy community includes anyone who works with Galaxy in any capa
# By Geography / Language
+## Arabic
+
+ **[Galaxy Arabic](/Community/Arabic):**
+* Arabic speaking Galaxy community
+* @[Galaxy_Arabic on Twitter](http://twitter.com/galaxy_arabic)
+* [Galaxy Arabic mailing list](https://lists.galaxyproject.org/listinfo/galaxy-arabic)
+
## Australia
**[Galaxy Australia](https://www.embl-abr.org.au/galaxyaustralia/):**
* Australian Galaxy community
-* [@GalaxyAustralia on Twitter](http://twitter.com/galaxyaustralia)
+* @[GalaxyAustralia on Twitter](http://twitter.com/galaxyaustralia)
* Hosts [Galaxy Australasia Meeting (GAMe)](https://www.embl-abr.org.au/game2017/)
## France & French
@@ -46,7 +53,7 @@ In short, the Galaxy community includes anyone who works with Galaxy in any capa
**[Pitagora Galaxy](http://www.pitagora-galaxy.org/)**
* This community features Galaxy VMs, instances, [monthly meetups](http://wiki.pitagora-galaxy.org/wiki/index.php/Events#Meetup_2), and an [annual workshop in Tokyo](http://wiki.pitagora-galaxy.org/wiki/index.php/Galaxy_Workshop_Tokyo_2016).
-* [#usegalaxyjp on Twitter](https://twitter.com/hashtag/usegalaxyjp)
+* #[usegalaxyjp on Twitter](https://twitter.com/hashtag/usegalaxyjp)
## Spain & Spanish
@@ -57,7 +64,7 @@ In short, the Galaxy community includes anyone who works with Galaxy in any capa
**[Galaxy UK](http://galaxy-community.org.uk/)**
* Galaxy in the United Kingdom.
-* [@GalaxyUKFriends on Twitter](http://twitter.com/galaxyukfriends)
+* @[GalaxyUKFriends on Twitter](http://twitter.com/galaxyukfriends)
# Resources
diff --git a/Datafiles/Mouse%20ChIP-Seq%20Data/index.md b/Datafiles/Mouse%20ChIP-Seq%20Data/index.md
index 690d32e..92ae679 100644
--- a/Datafiles/Mouse%20ChIP-Seq%20Data/index.md
+++ b/Datafiles/Mouse%20ChIP-Seq%20Data/index.md
@@ -1,4 +1,3 @@
-PLACEHOLDER_INCLUDE(/Under Construction)
# Datafiles used in various teaching exercises using Mouse mm9 chr19
* Used in ***Using Galaxy to Perform Large-Scale Interactive Data Analysis: A live supplement*** June 2012 Update published in *Current Protocols in Bioinformatics* (pending release)
diff --git a/DevNewsBriefs/2010_11_24/index.md b/DevNewsBriefs/2010_11_24/index.md
index 774c7bb..bc8ff4f 100644
--- a/DevNewsBriefs/2010_11_24/index.md
+++ b/DevNewsBriefs/2010_11_24/index.md
@@ -12,7 +12,7 @@ Here are the highlights of the following upgrade:
## What's New
### Galaxy's FTP Server New Data Upload Option
-* User how-to: [/wiki/UploadViaFTP](http://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP)
+* User how-to: [UploadViaFTP](/Admin/Config/UploadviaFTP)
* Configuration instructions for local installs: [wiki/Config/UploadViaFTP](http://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP)
### OpenID Login
diff --git a/DevNewsBriefs/2011_08_30/index.md b/DevNewsBriefs/2011_08_30/index.md
index d0d5137..fd9f48d 100644
--- a/DevNewsBriefs/2011_08_30/index.md
+++ b/DevNewsBriefs/2011_08_30/index.md
@@ -21,9 +21,9 @@ Slides for several [Galaxy](http://galaxyproject.org) related talks from this ye
### Recent Publications
-Blankenberg D, Taylor J, Nekrutenko A, The Galaxy Team. ["Making whole genome multiple alignments usable for biologists."](http://www.ncbi.nlm.nih.gov/pubmed/21775304 ) *Bioinformatics*. 2011 Jul 19. [Epub ahead of print]
+Blankenberg D, Taylor J, Nekrutenko A, The Galaxy Team. "[Making whole genome multiple alignments usable for biologists](http://www.ncbi.nlm.nih.gov/pubmed/21775304 )." *Bioinformatics*. 2011 Jul 19. [Epub ahead of print]
-Afgan, E., Baker, D., Team, t. G., Nekrutenko, A. and Taylor, J. (2011). ["A reference model for deploying applications in virtualized environments."](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/abstract ) *Concurrency and Computation: Practice and Experience*. doi: 10.1002/cpe.1836
+Afgan, E., Baker, D., Team, t. G., Nekrutenko, A. and Taylor, J. (2011). "[A reference model for deploying applications in virtualized environments](http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/abstract)" *Concurrency and Computation: Practice and Experience*. doi: 10.1002/cpe.1836
<div class='right'>![](/Images/Screenshots/GalaxyProjectOrg.png)</div>
### GalaxyProject.org
@@ -142,7 +142,7 @@ And there is now an updated [Galaxy](http://galaxyproject.org) article on Wikipe
See API run_as for more details.
* Expose workflows shared with the user in /workflows list of the API
* Addition of a case sensitivity notice for login not found error.
-* Enhancements to handling format="input" in workflows, fixes [#582 ](http://bitbucket.org/galaxy/galaxy-central/issue/583 )
+* Enhancements to handling format="input" in workflows, fixes #[582](http://bitbucket.org/galaxy/galaxy-central/issue/583)
* Added the ability for a user to use the API as another user via the setting 'api_allow_run_as' in the config file (thanks John Duddy!)
* Added the ability to create histories, delete histories, and create new history items from library items (thanks again John Duddy!)
diff --git a/Develop/ResourcesTools/index.md b/Develop/ResourcesTools/index.md
index c2d3108..129cb66 100644
--- a/Develop/ResourcesTools/index.md
+++ b/Develop/ResourcesTools/index.md
@@ -2,7 +2,7 @@
* [A somewhat complete description](/Admin/Tools/ToolConfigSyntax) of tags used for in tool XML files.
* A place to share your tools with the community: the [Galaxy Tool Shed](http://toolshed.g2.bx.psu.edu/) - more information on [publishing tools to the ToolShed](/ToolShed).
-* [Planemo|](https://planemo.readthedocs.org/en/latest/) a CLI tool to assist tool developer - easily lint, test, and preview your tools. ([Quick Start](https://planemo.readthedocs.org/en/latest/readme.html#quick-start), [Planemo on Github](https://github.com/galaxyproject/planemo))
+* [Planemo](https://planemo.readthedocs.org/en/latest/) a CLI tool to assist tool developer - easily lint, test, and preview your tools. ([Quick Start](https://planemo.readthedocs.org/en/latest/readme.html#quick-start), [Planemo on Github](https://github.com/galaxyproject/planemo))
* [Tool Development Training Materials](https://github.com/Public-Health-Bioinformatics/galaxy-tool-tutorials) - from Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control.
* [Tool Development Slides (PDF)](https://github.com/Public-Health-Bioinformatics/galaxy-tool-tutorials/blob/master/Galaxy%20Tool%20Development.pdf?raw=true)
* [Tool Versioning Slides (PDF)](https://github.com/Public-Health-Bioinformatics/galaxy-tool-tutorials/raw/76e1511413202122fbb3a758510744442b2726b7/Galaxy%20Tool%20Versioning.pdf)
diff --git a/Events/AdminTraining2016/AdvancedSession/index.md b/Events/AdminTraining2016/AdvancedSession/index.md
index 62f1c78..ed70631 100644
--- a/Events/AdminTraining2016/AdvancedSession/index.md
+++ b/Events/AdminTraining2016/AdvancedSession/index.md
@@ -22,9 +22,9 @@ We will use compute resources from the [University of Utah Center for High Perfo
<br />
-<span style="font-size: larger;"> 1. All prerequisites from the [Basic Topics workshop](/Events/AdminTraining2016/BasicsSession) </span>
+<span style="font-size: larger;"> 1. [All prerequisites](/Events/AdminTraining2016/BasicsSession#prerequisites) for the [Basic Topics workshop](/Events/AdminTraining2016/BasicsSession) </span>
-You need to have a solid grasp of the, Linux command line, a text editor, and Linux package management.
+You need to have a solid grasp of the Linux command line, a text editor, and Linux package management.
<br />
@@ -37,221 +37,9 @@ You can get this by
## Schedule
-*This is a draft schedule and is a work in progress. Topic order and specific start and end times are likely to change.*
+The Advanced Session starts at 9:00am on Wednesday, Thursday and Friday morning. Checkin and coffee opens at 8:30am. The sessions break for lunch and dinner (as well as morning and afternoon breaks). All 3 nights wrap up around 8:30pm.
-### Tuesday
-
-**Galaxy Architecture Session, Tuesday evening, November 7**
-
-The [basics section](/Events/AdminTraining2016/BasicsSession) will end on Tuesday evening with an overview of Galaxy's architecture. All participants in the advanced session are also welcome to attend this session at the [Salt Lake City Library](/Events/AdminTraining2016/BasicsSession#venue).
-
-<table>
- <tr class="th" >
- <th> Time </th>
- <th style=" width: 90%;"> Topic </th>
- </tr>
- <tr>
- <th style=" text-align: right;"> &nbsp;&nbsp;7:00pm </th>
- <td> Introduction to Galaxy Architecture <span style="font-size: smaller;"> (Joint session with the <a href='/Events/AdminTraining2016/BasicsSession'>Basics Topics session</a>) </span> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:20pm </th>
- <td> Wrap-up </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30pm </th>
- <td style=" text-align: center;"> </strong>Done<strong> </td>
- </tr>
-</table>
-
-
-
-### Wednesday
-
-Starting on Wednesday the advanced session will be held at the [Commanders House](http://www.universityguesthouse.com/Commanders-House) on the [University of Utah](http://utah.edu/) campus. This is a short walk from the [University Guest House](http://www.universityguesthouse.com/University-Guest-House), where participants are staying.
-
-<table>
- <tr class="th" >
- <th> Time </th>
- <th style=" width: 90%;"> Topic </th>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30am </th>
- <td style=" text-align: center;"> </strong>Checkin and Coffee<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:00am </th>
- <td> Welcome and intro</td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:20am </th>
- <td> Server setup <div class='indent'>Get a copy of the workshop server up and running.</div> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:50am </th>
- <td> Updating tools and supporting multiple versions of tools </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:30am </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:50am </th>
- <td> Server monitoring and maintenance<div class='indent'>Admin UI, Log files, Direct database queries, Command line & scripts, What to backup and how</div> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 12:20pm </th>
- <td style=" text-align: center;"> </strong>Lunch Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 1:20pm </th>
- <td> Upgrading to a new Galaxy release </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 2:50pm </th>
- <td> Introduction to <a href='https://www.ansible.com/'>Ansible</a> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:20pm </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:40pm </th>
- <td> Using Ansible to deploy Galaxy </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 5:40pm </th>
- <td style=" text-align: center;"> </strong>Dinner Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 7:00pm </th>
- <td> Advanced Tool Definition: Adding tests </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30pm </th>
- <td style=" text-align: center;"> </strong>Done<strong> </td>
- </tr>
-</table>
-
-
-### Thursday
-
-<table>
- <tr class="th" >
- <th> Time </th>
- <th style=" width: 90%;"> Topic </th>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30am </th>
- <td style=" text-align: center;"> </strong>Coffee<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:00am </th>
- <td> Welcome, Questions </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:20am </th>
- <td> Using and configuring external authentication services </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:30am </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:50am </th>
- <td> Connecting Galaxy to a compute cluster I </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 12:20pm </th>
- <td style=" text-align: center;"> </strong>Lunch Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 1:20pm </th>
- <td> Connecting Galaxy to a compute cluster 2 </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:20pm </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:40pm </th>
- <td> Using public and private cloud compute resources </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 5:40pm </th>
- <td style=" text-align: center;"> </strong>Dinner Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 7:00pm </th>
- <td> Using Heterogeneous compute resources </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30pm </th>
- <td style=" text-align: center;"> </strong>Done<strong> </td>
- </tr>
-</table>
-
-
-### Friday
-
-<table>
- <tr class="th" >
- <th> Time </th>
- <th style=" width: 90%;"> Topic </th>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30am </th>
- <td style=" text-align: center;"> </strong>Coffee<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:00am </th>
- <td> Welcome, Questions </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:20am </th>
- <td> Advanced Tool Definitions: Collections </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:30am </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:50am </th>
- <td> Advanced Tool Definitions: Error Handling </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 12:20pm </th>
- <td style=" text-align: center;"> </strong>Lunch Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 1:20pm </th>
- <td> Storage management and using heterogeneous storage services </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:20pm </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:40pm </th>
- <td> Advanced tool definition: data types and data sources</div> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 5:30pm </th>
- <td style=" text-align: center;"> </strong>Dinner Break<strong>* </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 6:50pm </th>
- <td> Participant selected topics and open questions.* Could include <div class='indent'>Advanced tool definition: visualizations, data managers<br /> Customizing and extending your Galaxy code<br /> Interactive environments: development and deployment</div> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:20pm </th>
- <td> Wrap-up </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30pm </th>
- <td style=" text-align: center;"> </strong>Done<strong> </td>
- </tr>
-</table>
+A [complete schedule](https://github.com/martenson/dagobah-training#advanced-sessions) and topics list (with resource links) are available on the workshop's [GitHub page](https://github.com/martenson/dagobah-training).
<div class='center'> <span style="font-size: smaller;"> * *We are exploring combining the final dinner and the open questions sessions into a single informal and pizza-fueled open discussion session.* </span> </div>
diff --git a/Events/AdminTraining2016/BasicsSession/index.md b/Events/AdminTraining2016/BasicsSession/index.md
index f639217..1dbf5f1 100644
--- a/Events/AdminTraining2016/BasicsSession/index.md
+++ b/Events/AdminTraining2016/BasicsSession/index.md
@@ -58,155 +58,35 @@ All participants should bring a wifi-enabled laptop with
## Topics
-This two day workshop will cover the big picture, and installation, configuration, and customization basics. We'll present these topics by exploring several specific examples in detail. Participants will finish this workshop with a solid understanding of how to set up and customize a Galaxy instance running on a desktop or standalone server.
+This two day workshop [will cover the big picture, and installation, configuration, and customization basics](https://github.com/martenson/dagobah-training#basic-sessions). We'll present these topics by exploring several specific examples in detail. Participants will finish this workshop with a solid understanding of how to set up and customize a Galaxy instance running on a desktop or standalone server.
* Deployment platform options
-* Installing a basic Galaxy server
-* Database choices and configuration (SQLite & PostgreSQL)
-* Web server choices and configuration (NGINX & Apache)
-* Identifying and installing well-defined tools from the Galaxy Tool Shed
+* Installing a basic Galaxy server
+* Database choices and configuration (SQLite & PostgreSQL)
+* Web server choices and configuration (NGINX & Apache)
+* Galaxy Tool Shed and Tool Installation
+ * Tool Shed intro
+ * Tool Installation
+ * Tool Management
+ * Advanced Tool Management
* Importing and defining reference genomes
-* Defining users, groups, and quotas
-* Basics of Tool Definition
-* Enabling extensions: FTP & SMTP
+* Extending the installation
+* Users, groups, and quotas
+* Basics of Tool Definition & Planemo
+* Upgrading Release
+* Basic Troubleshooting
* Introduction to Galaxy Architecture
-## Schedule
-
-*This is a draft schedule and is a work in progress. Topic order and specific start and end times are likely to change.*
-
-### Monday
-
-<table>
- <tr class="th" >
- <th> Time </th>
- <th> Topic </th>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:15am </th>
- <td style=" text-align: center;"> </strong>Checkin and Coffee<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:30am </th>
- <td> Welcome and intro</td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:00am </th>
- <td> Deployment and platform options </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 10:20am </th>
- <td> Get a basic Galaxy server up and running. </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 11:00am </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 11:20am </th>
- <td> Database choices and configuration. Introduction to <a href='https://www.postgresql.org/'>PostgreSQL</a>. </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 12:30pm </th>
- <td style=" text-align: center;"> </strong>Lunch Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 1:30pm </th>
- <td> Web server choices and configuration. Introduction to <a href='https://nginx.org/en/'>NGINX</a>. </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:20pm </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:40pm </th>
- <td> Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools. </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 4:50pm </th>
- <td> Defining and importing genomes </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 5:40pm </th>
- <td style=" text-align: center;"> </strong>Dinner Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 7:00pm </th>
- <td> Defining and importing genomes, cont.; Data Managers </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30pm </th>
- <td style=" text-align: center;"> </strong>Done<strong> </td>
- </tr>
-</table>
-
-
-### Tuesday
-
-<table>
- <tr class="th" >
- <th> Time </th>
- <th> Topic </th>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:15am </th>
- <td style=" text-align: center;"> </strong>Coffee<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:30am </th>
- <td> Welcome, Questions </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 9:45am </th>
- <td> Extending your installation: Enabling FTP & SMTP </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 11:00am </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 11:20am </th>
- <td> Users, Groups, and Quotas </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 12:20pm </th>
- <td style=" text-align: center;"> </strong>Lunch Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 1:20pm </th>
- <td> Tool Definition Basics & Planemo </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:20pm </th>
- <td style=" text-align: center;"> </strong>Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 3:40pm </th>
- <td> Tool Definition Basics & Planemo, cont. </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 5:40pm </th>
- <td style=" text-align: center;"> </strong>Dinner Break<strong> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 7:00pm </th>
- <td> Introduction to Galaxy Architecture <span style="font-size: smaller;"> (Joint session with the <a href='/Events/AdminTraining2016/AdvancedSession'>Advanced Topics session</a>) </span> </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:20pm </th>
- <td> Wrap-up </td>
- </tr>
- <tr>
- <th style=" text-align: right;"> 8:30pm </th>
- <td style=" text-align: center;"> </strong>Done<strong> </td>
- </tr>
-</table>
+See the [event GitHub page](https://github.com/martenson/dagobah-training#basic-sessions) for details and resource links.
+## Schedule
+The Basics Session starts at 9:30am on Monday and Tuesday morning. Checkin and coffee opens at 9:15am. The sessions break for lunch and dinner (as well as morning and afternoon breaks). They wrap up both nights around 8:30pm.
+A [complete schedule is available on the workshop's GitHub pages](https://github.com/martenson/dagobah-training#basic-sessions).
<div class='right'><br />
-<a href='http://www.slcpl.lib.ut.us/branches/view/Main+Library'><img src='/Events/AdminTraining2016/SLCLibrary1.jpg' alt='alt Lake City Main Public Library, the venue for the introduction workshop' /></a>
+<a href='http://www.slcpl.lib.ut.us/branches/view/Main+Library'><img src='/Events/AdminTraining2016/SLCLibrary1.jpg' alt='alt Lake City Main Public Library, the venue for the introduction workshop' width="170" /></a>
</div>
## Venue
diff --git a/Events/AdminTraining2016/Header/index.md b/Events/AdminTraining2016/Header/index.md
index 4363424..fbbb0ff 100644
--- a/Events/AdminTraining2016/Header/index.md
+++ b/Events/AdminTraining2016/Header/index.md
@@ -2,7 +2,7 @@
<tr>
<td style=" border: none;"> <a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width=200" /></a> </td>
<td style=" border: none; width: 5%;"> </td>
- <td style=" border: none;"> <div class='title'><a href='/Events/AdminTraining2016'>Galaxy Admin Training</a></div> <span style="font-size: larger;">November 7-11, 2016<br />University of Utah<br />Salt Lake City, Utah<br />United States<br /><br /> </strong><a href='/Events/AdminTraining2016/Registration'>Register by October 16</a><strong> </span><br /><a href='/Events/AdminTraining2016/Logistics#lodging'>Lodging released October 6</a> </td>
+ <td style=" border: none;"> <div class='title'><a href='/Events/AdminTraining2016'>Galaxy Admin Training</a></div> <span style="font-size: larger;">November 7-11, 2016<br />University of Utah<br />Salt Lake City, Utah<br />United States<br /><br /> </td>
</tr>
</table>
diff --git a/Events/AdminTraining2016/Logistics/index.md b/Events/AdminTraining2016/Logistics/index.md
index f263fc8..c133647 100644
--- a/Events/AdminTraining2016/Logistics/index.md
+++ b/Events/AdminTraining2016/Logistics/index.md
@@ -105,7 +105,7 @@ See the [event map for details](https://drive.google.com/open?id=1vC6J8BdrMDQo_c
The **[Basics Session](../BasicsSession)** will be held at the **[Salt Lake City Main Public Library](http://www.slcpl.lib.ut.us/branches/view/Main+Library).** This [stunning venue](https://www.google.com/search?tbm=isch&q=salt+lake+city+library) is located in downtown Salt Lake City at [210 East 400 South](https://drive.google.com/open?id=1vC6J8BdrMDQo_cIJvTr9pjUGGcA&usp=sharing), and is a stop on the [UTA TRAX Red Line](https://www.rideuta.com/Rider-Tools/Schedules-and-Maps/703-Red-Line) and just [5 stops from conference housing](https://drive.google.com/open?id=1vC6J8BdrMDQo_cIJvTr9pjUGGcA&usp=sharing). We'll be meeting in [Conference Room 4](http://www.slcpl.lib.ut.us/rooms/)
-The **[Advanced Session](../AdvancedSession)** will be held at the [Commanders House](http://www.universityguesthouse.com/Commanders-House) on the [University of Utah](http://utah.edu/) campus**. This is a short walk from the [University Guest House](#lodging), where participants are staying.
+The **[Advanced Session](../AdvancedSession)** will be held at the **[Commanders House](http://www.universityguesthouse.com/Commanders-House) on the [University of Utah](http://utah.edu/) campus**. This is a short walk from the [University Guest House](#lodging), where participants are staying.
<div class='left'>
<a href='http://ucgd.genetics.utah.edu/'><img src='/Images/Logos/USTAR-UCGD-Logo.jpg' alt='USTAR Center for Genetic Discovery (UCGD)' width="280" /></a></div>
diff --git a/Events/AdminTraining2016/index.md b/Events/AdminTraining2016/index.md
index 420b8f8..08579a1 100644
--- a/Events/AdminTraining2016/index.md
+++ b/Events/AdminTraining2016/index.md
@@ -70,7 +70,8 @@ See the [Advanced Session](/Events/AdminTraining2016/AdvancedSession) page for d
# Instructors
Instructors are from the [Galaxy Project Team](/GalaxyTeam) and the Galaxy Community:
-* [Nate Coraor](/nate), lead sys admin and a software engineer for the Galaxy Project
+* [Dan Blankenberg](/Dan). senior software engineer for the Galaxy Project.
+* [Nate Coraor](/nate), lead sys admin and a software engineer for the Galaxy Project.
* [Martin Čech](/Marten), software engineer and frequent sys admin for the Galaxy Project.
* [Simon Gladman](https://www.vlsci.org.au/researcher/sgladman), software engineer and bioinformatician with [VLSCI](https://www.vlsci.org.au/) and has done extensive work with the [Genomics Virtual Lab](https://www.genome.edu.au/).
@@ -85,6 +86,16 @@ See the [Registration](/Events/AdminTraining2016/Registration) page for dates, r
For information on event lodging, arriving in Salt Lake, and getting around, see the [Event Logistics](/Events/AdminTraining2016/Logistics) page. Lodging, the airport, and all training events are on the University of Utah campus or in downtown Salt Lake City, and all are easily accessible using [TRAX](http://www.rideuta.com/), Salt Lake's light rail network
+# Can't make it to Salt Lake or on another continent?
+
+<div class='right'><div class='right'><a href='https://www.embl-abr.org.au/game2017/training-for-admin-workshop/'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="80" /></a> </div><br />
+<a href='/Events/egdw2017'><img src='/Images/Logos/IFBGalaxyWG.png' alt='European Galaxy Developer workshop 2017' width="100" /></a></div>
+
+This is one of three comprehensive Galaxy admin and developer training events between November and February. They are:
+
+* **Galaxy Admin Training 2016**, Nov 7-11, Salt Lake City, Utah, United States
+* **[European Galaxy Developer workshop 2017](/Events/egdw2017)**, Jan 16-20, Strasbourg, France
+* **[Galaxy Administrator Training](https://www.embl-abr.org.au/game2017/training-for-admin-workshop/)**, Feb 6-9, Melbourne, Australia
# Hosts
diff --git a/Events/Archive/index.md b/Events/Archive/index.md
index 83fc7d3..f37897b 100644
--- a/Events/Archive/index.md
+++ b/Events/Archive/index.md
@@ -1161,7 +1161,7 @@ Listing of Galaxy events from previous years. See the main [/Events](/Events) pa
<a href='/Events/SG2014'><img src='/Images/Logos/SG2014Logo400.png' alt='2014 Swiss German Galaxy Tour' height="90" /></a>
<a href='http://wiki.data.dtls.nl/index.php/DTL_Programmers_Meeting'><img src='/Images/Logos/DTLLogo150.png' alt='iReport - A tool to create flexible, scalable Galaxy tool interface, presented at the DTL Programmers Meeting' height="90" /></a>
<a href='http://galaxy4bioinformatics.sb-roscoff.fr/'><img src='/Images/Logos/SB-RoscoffBig.JPG' alt='Des bonnes pratiques d'intégration d'outils sous Galaxy' height="60" /></a> &nbsp;
-[{{attachment:Images/Logos/GenoToulLogo.png|Galaxy Training Days|height="60"}}|Galaxy training days](http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=62) &nbsp;
+<a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=62'><img src='/Images/Logos/GenoToulLogo.png' alt='Galaxy Training Days' height="60" /></a> &nbsp;
<a href='http://web.ornl.gov/sci/knowledgediscovery/CloudComputing/PDAC-SC14/'><img src='/Images/Logos/SC14.png' alt='Deciphering Big Data Stacks: An Overview of Big Data Tools, Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC-14)]], Supercomputing 2014' width="150" /></a>
<a href='http://www.bioinformatica.crs4.it/next_generation_sequencing_course_with_galaxy_november_2014'><img src='/Images/Logos/CRS4Logo.jpg' alt='Analisi dati Next Generation Sequencing in Galaxy' width="140" /></a> &nbsp;
<a href='http://www.qfab.org/event/workshop-extended-rna-seq-analysis-1920-november-brisbane/'><img src='/Images/Logos/QFABLogo.png' alt='Workshop: Extended RNA-Seq analysis' height="80" /></a>
diff --git a/Events/Cornell2016/index.md b/Events/Cornell2016/index.md
index b0058c0..5f63c62 100644
--- a/Events/Cornell2016/index.md
+++ b/Events/Cornell2016/index.md
@@ -94,7 +94,7 @@ No programming or Linux command line experience is required.
## Support
-This workshop is generously supported by an [AWS in Education](http://aws.amazon.com/education/) research grant award, the [Boyce Thompson Institute|](http://bti.cornell.edu/), [Cornell University|](http://cornell.edu/), and the [National Institutes of Health (NIH)](http://www.nih.gov/).
+This workshop is generously supported by an [AWS in Education](http://aws.amazon.com/education/) research grant award, the [Boyce Thompson Institute](http://bti.cornell.edu/), [Cornell University](http://cornell.edu/), and the [National Institutes of Health (NIH)](http://www.nih.gov/).
## Slides
diff --git a/Events/GCC2012/Logistics/index.md b/Events/GCC2012/Logistics/index.md
index 7c2e2b0..ee78eab 100644
--- a/Events/GCC2012/Logistics/index.md
+++ b/Events/GCC2012/Logistics/index.md
@@ -3,8 +3,6 @@ pagetitle: Logistics
----
PLACEHOLDER_INCLUDE(/Events/GCC2012/PageHeader)
-PLACEHOLDER_INCLUDE(/Under Construction)
-
PLACEHOLDER_INCLUDE(../LinkBox)
diff --git a/Events/GCC2012/Program/index.md b/Events/GCC2012/Program/index.md
index b547344..f3354bf 100644
--- a/Events/GCC2012/Program/index.md
+++ b/Events/GCC2012/Program/index.md
@@ -4,8 +4,6 @@ pagetitle: Program
----
PLACEHOLDER_INCLUDE(/Events/GCC2012/PageHeader)
-PLACEHOLDER_INCLUDE(/Under Construction)
-
PLACEHOLDER_INCLUDE(../LinkBox)
diff --git a/Events/GMODSummerSchool2014/index.md b/Events/GMODSummerSchool2014/index.md
index e20b034..2e153a5 100644
--- a/Events/GMODSummerSchool2014/index.md
+++ b/Events/GMODSummerSchool2014/index.md
@@ -662,7 +662,7 @@ do that and try them out on some isolate data from a library. Also, it's best to
much as possible so we'll convert this trial run (if it worked) into a workflow (AKA pipeline) that will reduce this
process to a two click operation.
-Using the procedure in [#installing-a-tool-from-a-tool-shed](#installing-a-tool-from-a-tool-shed), search for and install the following tools:
+Using the procedure in [Installing a tool from a Tool Shed](#installing-a-tool-from-a-tool-shed), search for and install the following tools:
1. `fastq_paired_end_joiner`:
* search with the tool name 'fastq joiner'
* The owner is 'devteam' and
diff --git a/Events/Germany2016/index.md b/Events/Germany2016/index.md
index 10169d6..f93ecfc 100644
--- a/Events/Germany2016/index.md
+++ b/Events/Germany2016/index.md
@@ -14,6 +14,11 @@ On the second day of the [Swiss German Galaxy Days 2016](/Events/SG2016), we wil
The developer day will be held at the Universität of Freiburg
+## Schedule
+
+We will start at 9:30 on Friday as well. There will be no fixed schedule,
+but we expect to finish between 5 and 6pm.
+
## Ideas
The second day is the traditional developers day and we are planning to
diff --git a/Events/PAG2017/index.md b/Events/PAG2017/index.md
new file mode 100644
index 0000000..4acc098
--- /dev/null
+++ b/Events/PAG2017/index.md
@@ -0,0 +1,80 @@
+----
+pagetitle: Galaxy , @, , [PAG 2017](http://www.intlpag.org/)
+----
+<div class='center'><a href='http://www.intlpag.org/'><img src='/Images/Logos/PAGLogo300.png' alt='Galaxy @ Plant and Animal Genome XXV (PAG 2017)' height="100" /></a>
+</div>
+
+
+
+Galaxy will be at [Plant and Animal Genome XXV (PAG 2017)](http://www.intlpag.org/), being held in San Diego, California, United States, January 14-18. Galaxy related presentations will be added to this page as they are scheduled. If you know of something that isn't on this page, then [outreach AT galaxyproject DOT org](please tell us about it).
+
+<table>
+ <tr class="th" >
+ <th> Date </th>
+ <th> Time </th>
+ <th> Topic </th>
+ <th> Session </th>
+ <th> Links </th>
+ <th> Contact </th>
+ </tr>
+ <tr>
+ <th> Saturday<br />January 14 </th>
+ <td style=" text-align: center;"> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th colspan=6> </th>
+ </tr>
+ <tr>
+ <th> Sunday<br />January 15 </th>
+ <td style=" text-align: center;"> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th colspan=6> </th>
+ </tr>
+ <tr>
+ <th rowspan=2> Monday<br />January 16 </th>
+ <td rowspan=1> 10:00-11:30 </td>
+ <td> </td>
+ <td> Poster Session: Even numbers </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td rowspan=1> 3:00-4:30 </td>
+ <td> </td>
+ <td> Poster Session: Odd numbers </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th colspan=6> </th>
+ </tr>
+ <tr>
+ <th> Tuesday<br />January 17 </th>
+ <td style=" text-align: center;"> 4:00-6:10</td>
+ <td> <a href='https://pag.confex.com/pag/xxv/meetingapp.cgi/Session/4217'>Genome Annotation with Galaxy</a> </td>
+ <td> Workshop, California Room </td>
+ <td> </td>
+ <td> <a href='/JeremyGoecks'>Jeremy Goecks</a> </td>
+ </tr>
+ <tr>
+ <th colspan=6> </th>
+ </tr>
+ <tr>
+ <th> Wednesday<br />January 18 </th>
+ <td style=" text-align: center;"> 10:30-2:30 </td>
+ <td> </em>TBA<em> </td>
+ <td> <a href='https://pag.confex.com/pag/xxv/meetingapp.cgi/Session/4229'>GMOD</a>, Golden West </td>
+ <td> </td>
+ <td> <a href='/DaveClements'>Dave Clements</a> </td>
+ </tr>
+</table>
+
diff --git a/Events/SG2016/index.md b/Events/SG2016/index.md
index 93136cf..ff44cbf 100644
--- a/Events/SG2016/index.md
+++ b/Events/SG2016/index.md
@@ -10,12 +10,27 @@ PLACEHOLDER_INCLUDE(/Events/SG2016/LinkBox)
There will be a *Swiss-German Galaxy Tour* this fall featuring a range of events over 2 days in Freiburg (Germany) .
-## Registration
+## Wednesday Evening
+
+For those of you who arrive on Wednesday, we will meet at [bar brasil](http://www.brasil-freiburg.de/) for food and drinks starting at 7PM
+
+
+## Thursday Evening
+
+We have a reservation at [Ganter Brauereiausschank](http://www.ganter-brauereiausschank.de) at 7PM. The place is next to the cathedral ([google maps](http://tinyurl.com/hq88h2d))
+
-Registration is free, but space is limited on both days. We recommend you register soon to secure your spot for one or both days of the SG2016Tour.
-<div class='center'><span style="font-size: larger;">**[Register Now](https://docs.google.com/forms/d/1mRO4uNXQd8jL1I9JNiQ4xd0fnrZKlQPQSORgJCpDeqg)**</span></div>
+## Friday Evening
+
+**We have a reservation at [Casanova](http://www.casanova-freiburg.de/) at 7PM.** The place is close to the train station ([google maps](http://tinyurl.com/h396lx3))
+
+
+
+
+## Registration
+Registration is free, but space is limited on both days. We recommend you register soon to secure your spot for one or both days of the SG2016Tour. Registration has been closed.
## Events
@@ -46,8 +61,9 @@ The [second day](/Events/Germany2016), October 21<sup>st</sup>, is a developers
## Location
-[Technische Fakultät; Albert-Ludwigs-Universität Freiburg; Georges-Köhler-Allee 101](http://www.uni-freiburg.de/universitaet-en/kontakt-und-wegweiser/lageplaene/engineering)
+[Technische Fakultät; Albert-Ludwigs-Universität Freiburg; Georges-Köhler-Allee 101](http://www.uni-freiburg.de/universitaet-en/kontakt-und-wegweiser/lageplaene/engineering) Building 101 (second floor)
+Take [Strassenbahn/Tramway # 4](http://tinyurl.com/ja7yqws) towards Technische Fakultät/Messe and get off at the last stop: Technische Fakultät ([time table](https://www.vag-freiburg.de/fileadmin/user_upload/documents/Linienplaene/Linie_04.pdf))
## Questions?
diff --git a/Events/Switzerland2016/index.md b/Events/Switzerland2016/index.md
index 0c1d43e..b2f8326 100644
--- a/Events/Switzerland2016/index.md
+++ b/Events/Switzerland2016/index.md
@@ -14,50 +14,33 @@ After the big success of the [first Swiss Galaxy Workshop](/Events/Switzerland20
This year, the workshop is aimed at Galaxy administrators and will collocate with the Oktober meetup of the [Galaxy-Admins discussion group](/Community/GalaxyAdmins). Similar to the regular Galaxy-Admins web-meetups, we intend to have a mixture of presentations about the use of the Galaxy framework and informations about the latest developments. We encourage presentations about your success stories using Galaxy as well as the problems you have encountered. Please indicate a preliminary title on the [registration page](https://docs.google.com/forms/d/1mRO4uNXQd8jL1I9JNiQ4xd0fnrZKlQPQSORgJCpDeqg).
-## Speakers and Topics
-
- [Dannon Baker](/DannonBaker)
- State of the Galaxy Project - priorities, plans, and community
-
- Andreas Tille
- Debian Med - Debian for medicine and life sciences
- Wolfgang Maier
- !CosmicNotes - Documenting your work in Galaxy
- Nikolay Vazov
- Customizing Galaxy for Large Institutions
- Devon Ryan
- deepTools and HiCExplorer
- Nicola Soranzo
- News from the [/IUC](/IUC) and the Galaxy tool ecosystem
- [Björn Grüning](/BjoernGruening)
- Fixing Bioinformatic Infrastructure
- [Hans-Rudolf Hotz](/HansrudolfHotz)
- Moving an old Galaxy server to new hardware
- Bérénice Batut
- [Galaxy Training Network](/Teach/GTN) - rebooted
-
-(These will be slotted into the schedule soon.)
-
-## Preliminary Schedule
+## Schedule
| Time | Speaker | Title | Slides |
| ---- | -------- | ------ | ------- |
| 9:15 - 9:30 | ARRIVAL |
-| 9:30 - 9:45 | [Hans-Rudolf Hotz](/HansrudolfHotz) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/BjoernGruening) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | |
-| 9:45 - 10:30 | a member from the Core Development Team | Status of the Galaxy Project | |
-| 10:30 - 11:00 | coffee Break |
-| 11:00 - 12:00 | individual presentations | | |
-| 12:00 - 13:30 | Lunch Break in nearby restaurants |
-| 13:30 - 15:00 | individual presentations | | |
-| 15:00 - 15:30 | coffee Break |
-| 15:30 - 17:00 | individual presentations | | |
-| 17:00 - 17:01 | [Hans-Rudolf Hotz](/HansrudolfHotz) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/BjoernGruening) ([University of Freiburg](http://www.uni-freiburg.de/)) | concluding remarks | |
-| 17:01 - 17:15 | ...going to the pub |
+| 9:30 - 9:45 | [Hans-Rudolf Hotz](/HansrudolfHotz) ([FMI](http://www.fmi.ch/)), [Björn Grüning](/BjoernGruening) ([University of Freiburg](http://www.uni-freiburg.de/)) | welcome | [slides](ATTACHMENT_URLSG2016T_intro.pdf) |
+| 9:45 - 10:30 | [Dannon Baker](/DannonBaker) | State of the Galaxy Project - priorities, plans, and community | |
+| 10:30 - 11:00 | Coffee Break |
+| 11:00 - 11:30 | [Nicola Soranzo](/NicolaSoranzo) | News from the [/IUC](/IUC) and the Galaxy tool ecosystem | [slides](https://docs.google.com/presentation/d/1F0AhDIueGUr9vptpZmZ1ZTCmsfXGymLDEquUtgJXPBc) |
+| 11:30 - 12:00 | Abdulrahman Azab | Deploying Galaxy in a secure environment to analyse sensitive data | [slides](ATTACHMENT_URLAbdulrahman_tsd-presentation.pptx) , docker provisioning [trick](https://github.com/ekorpela/cloud-vm-workshop/blob/master/materials/Docker/ProvisioningTrick.md ) |
+| 12:00 - 13:10 | Lunch Break in nearby restaurants |
+| 13:10 - 13:35 | Bérénice Batut | [Galaxy Training Network](/Teach/GTN) - rebooted | |
+| 13:35 - 14:10 | Roland Fehrenbacher | Debian Med - Debian for medicine and life sciences | |
+| 14:10 - 14:40 | Wolfgang Maier | !CosmicNotes - Documenting your work in Galaxy | |
+| 14:40 - 15:00 | Jochen Bick | Long way to solve short ncRNA data analysis problems – evaluation of small RNA-Seq datasets from non-model organisms in Galaxy | [slides](ATTACHMENT_URLsmall_RNAs_in_Galaxy_Jochen_Bick.pptx) |
+| 15:00 - 15:30 | Coffee Break |
+| 15:30 - 16:00 | Devon Ryan / Stephan Nothjunge | deepTools and HiCExplorer | |
+| 16:00 - 16:30 | Nikolay Vazov | Customizing Galaxy for Large Institutions | [slides](ATTACHMENT_URLGalaxy-Large-Institutions.pdf) |
+| 16:30 - 16:45 | Coffee Break |
+| 16:45 - 18:00 | lightning talks: Kristian Peters, Jelle Scholtalbers | | |
+| 18:00 - 18:01 | [Hans-Rudolf Hotz](/HansrudolfHotz), [Björn Grüning](/BjoernGruening) | concluding remarks ...going back to town | |
+| 19:00 - open end | ....we have a reservation at [Ganter Brauereiausschank](http://www.ganter-brauereiausschank.de) at 7PM |
## Location / Registration
-The workshop will be held at the Universität of Freiburg in Germany (see the [main page](/Events/SG2016) for details). Registration is free, and you can sign-up [here](https://docs.google.com/forms/d/1mRO4uNXQd8jL1I9JNiQ4xd0fnrZKlQPQSORgJCpDeqg).
+The workshop will be held at the Universität of Freiburg in Germany (see the [main page](/Events/SG2016) for details).
## Questions?
Contact [Hans-Rudolf Hotz](/HansrudolfHotz) or [Björn Grüning](/BjoernGruening)
diff --git a/Events/UUtahWorkshop/index.md b/Events/UUtahWorkshop/index.md
new file mode 100644
index 0000000..8245001
--- /dev/null
+++ b/Events/UUtahWorkshop/index.md
@@ -0,0 +1,103 @@
+----
+pagetitle: Introduction to Galaxy
+----
+<div class='center'>
+<a href='http://utah.edu/'><img src='/Images/Logos/UUtah.png' alt='University of Utah' width="150" /></a>
+
+
+
+**Instructor: [Dave Clements](/DaveClements)
+
+November 16, 2016<br />
+9:00-5:00<br /><br />
+BMI classroom, [421 Wakara Way](https://goo.gl/maps/ByLvhZ5bdXF2)<br />
+Suite 140, Research Park <br />
+[University of Utah](http://utah.edu/), Salt Lake City
+**
+</div>
+
+
+<div class='center'>
+This workshop is full.<br />
+<span style="font-size: larger;"> **[Get on the waiting list](https://docs.google.com/forms/d/e/1FAIpQLScidSa-MfpkOqzeaJbUqshhDoHTtzgeh82zxNOoh8SYNTkjvw/viewform)** </span>
+</div><br />
+
+Registration is free and open to any member, affiliate or guest of the University of Utah. Space is limited and available on a first-come, first served basis.
+
+## Audience
+Are you a life scientist who needs to do complex analysis on large datasets?
+
+Galaxy is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.
+
+Most of the workshop will be hands-on and teach participants how to integrate data, and perform simple and complex analysis within Galaxy. It will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy.
+
+No programming or Linux command line experience is required.
+
+## Agenda
+
+*The agenda below is tentative and should be considered a work in progress.*
+
+<table>
+ <tr class="th" >
+ <th> Time </th>
+ <th> Topic </th>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 9:00 </th>
+ <td> </strong>Welcome<strong><div class='indent'>Introductions and logistics</div> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 9:20 </th>
+ <td> </strong>Basic Analysis with Galaxy<strong><div class='indent'>Walk through a worked, hands-on example demonstrating basic analysis with Galaxy</div> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 10:45 </th>
+ <td style=" text-align: center;"> </strong>Break<strong> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 11:00 </th>
+ <td> </strong>Basic Analysis into Reusable Workflows<strong><div class='indent'>Genericize our analysis into something we can use again.</div> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 12:20 </th>
+ <td style=" text-align: center;"> </strong>Lunch<strong> (on your own) </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 1:20 </th>
+ <td> </strong>RNA-Seq Example Part I<strong><div class='indent'>Review 1) NGS data quality issues and some quality control options in Galaxy; and 2) Mapping and Splice Junction Calling</div> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 2:50 </th>
+ <td style=" text-align: center;"> </strong>Break<strong> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 3:05 </th>
+ <td> </strong>RNA-Seq Example Part II<strong><div class='indent'> Differential expression</div> </td>
+ </tr>
+ <tr>
+ <th style=" text-align: right;"> 5:00 </th>
+ <td style=" text-align: center;"> </strong>Done<strong> </td>
+ </tr>
+</table>
+
+
+
+<div class='right'><br />
+<a href='http://www.nih.gov/'><img src='/Images/Logos/NIHwithTagline.png' alt='National Institutes of Health (NIH)' width="220" /></a><br /><br />
+<div class='right'><a href='http://aws.amazon.com/'><img src='/Images/Logos/AWSLogo.png' alt='Amazon Web Services' width="120" /></a></div></div>
+
+## Support
+
+This workshop is generously supported by an [AWS in Education](http://aws.amazon.com/education/) research grant award, the [University of Utah](http://utah.edu/), and the [National Institutes of Health (NIH)](http://www.nih.gov/).
+
+## Slides
+
+* [Slides](ATTACHMENT_URLDocuments/Presentations/2016UUtahWorkshop.pdf)
+
+## Feedback
+
+* **[Please provide it!](https://docs.google.com/forms/d/1M5G8dAgIBpaojf1eSoPgyiklD0-pAlZHRK51YFR5KLg/edit)**
+
+## Questions?
+
+Contact [outreach AT galaxyproject DOT org](Galaxy Outreach) or [Karen Eilbeck](http://www.bioscience.utah.edu/faculty/molecular-biology-faculty/eilbeck/eilbeck.php).
diff --git a/Events/egdw2017/index.md b/Events/egdw2017/index.md
new file mode 100644
index 0000000..eff9498
--- /dev/null
+++ b/Events/egdw2017/index.md
@@ -0,0 +1,9 @@
+# European Galaxy Developer workshop 2017
+
+
+**Location:** Strasbourg, 7Hotels
+
+**Date:** 16 - 19 January 2017
+
+
+more details : [EGDW2017](https://www.france-bioinformatique.fr/en/evenements/EGDW2017)
diff --git a/Events/index.md b/Events/index.md
index d0b48d9..c42ee6c 100644
--- a/Events/index.md
+++ b/Events/index.md
@@ -22,11 +22,10 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
## Upcoming Events
<div class='center'>
-<a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=83'><img src='/Images/Logos/GenoToulLogo.png' alt='Metagenomic: amplicon analysis' height="60" /></a> &nbsp;
-<a href='https://www.facebook.com/events/1593583060947735/'><img src='/Images/Logos/CBioVikingsTrans.png' alt='Galaxy Workshop' height="80" /></a>
-<a href='http://www.france-bioinformatique.fr/en/evenements/galaxy4bioinformatics'><img src='/Images/Logos/IFBGalaxyWG.png' alt=' Galaxy4Bioinformatics' /></a>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width=120" /></a>
+<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width="120" /></a>
+<a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'><img src='/Images/Logos/PRABILogo.png' alt='Analyse de données RNA-seq sous l’environnement Galaxy' height="60" /></a>
+<a href='https://www.abdn.ac.uk/genomics/documents/201617_Workshops/Quality_Control_2016.pdf'><img src='/Images/Logos/UniversityOfAberdeen.png' alt='Quality Control of Next Generation Sequencing Reads' height="40" /></a>
+<a href='https://www.embl-abr.org.au/game2017/'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="120" /></a>
</div>
<table>
@@ -37,81 +36,6 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<th> Contact </th>
</tr>
<tr>
- <th> October 10-13 </th>
- <td> <em><a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=83'>Metagenomic: amplicon analysis</a></em> <div class='indent red'> Registration closes 4 October</div> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) INRA Auzeville, Auzeville, France </td>
- <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) Sarah Maman </td>
- </tr>
- <tr>
- <th> October 13 </th>
- <td> <em><a href='https://www.facebook.com/events/1593583060947735/'>Galaxy Workshop</a></em> <div class='indent red'>Workshop is full</div> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Copenhagen, Denmark </td>
- <td> <a href='http://jmgi.tk/'>Jose Maria (Txema) Gonzalez Izarzugaza</a> </td>
- </tr>
- <tr>
- <th> October 18-20 </th>
- <td> <em><a href='http://www.france-bioinformatique.fr/en/evenements/galaxy4bioinformatics'>Galaxy4Bioinformatics</a></em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Lyon, France </td>
- <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='http://www.france-bioinformatique.fr/en/node/17'>Contacts</a> </td>
- </tr>
- <tr>
- <th> October 20 </th>
- <td> <em>Genome Program Joint Workshop</em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Asia) <a href='http://kunsan.ac.kr'>Kunsan National University</a>, Gunsan, South Korea </td>
- <td> <a href='/anton'>Anton Nekrutenko</a> </td>
- </tr>
- <tr>
- <th> October 20-21 </th>
- <td> <em><a href='http://www.ebi.ac.uk/training/events/2016/bioexcel-workflow-training-computational-biomolecular-research?platform=hootsuite'>BioExcel: Workflow Training for Computational Biomolecular Research</a></em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Barcelona Supercomputing Center, Barcelona, Spain </td>
- <td> <a href='https://siastd.uab.es/pcde/fitxa_persona.jsf;jsessionid=2cdbb231e18e06bc59f766ae8951:4crB?id=161b3185c321992a'>Antonio Miguel Espinosa Morales</a> </td>
- </tr>
- <tr>
- <th> October 20 </th>
- <td> <em><a href='/Events/Switzerland2016'>(third Swiss) Galaxy Workshop</a></em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <strong><a href='/Events/SG2016'>2016 Swiss-German Galaxy Days</a></strong> in Freiburg, Germany </td>
- <td> <a href='/HansrudolfHotz'>Hans-Rudolf Hotz</a> and <a href='/BjoernGruening'>Bjoern Gruening</a> </td>
- </tr>
- <tr>
- <th> October 21 </th>
- <td> <em><a href='/Events/Germany2016'>(second German) Galaxy Developers Day</a></em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <strong><a href='/Events/SG2016'>2016 Swiss-German Galaxy Days</a></strong> in Freiburg, Germany </td>
- <td> <a href='/HansrudolfHotz'>Hans-Rudolf Hotz</a> and <a href='/BjoernGruening'>Bjoern Gruening</a> </td>
- </tr>
- <tr>
- <th> October 24 </th>
- <td> <em>Deployment of bioinformatics tools and services through Docker</em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='https://docs.google.com/document/d/1mxcQgPNI212YkTIJf9twGLX5OiTZBDXjLvPaOVVFQ80/edit#heading=h.83oyrjah164f'>ELIXIR Hackathon @ NETTAB 2016</a>, Rome, Italy </td>
- <td> <a href="mailto:paolo.romano@hsanmartino.it">Paolo Romano</a>, <a href="mailto:jison@cbs.dtu.dk">Jon Ison</a> </td>
- </tr>
- <tr>
- <th> October 25-27 </th>
- <td> <em><a href='http://www.igst.it/nettab/2016/programme/scientific-programme/'>The Galaxy tool lifecycle supporting reproducibility in scientific research</a></em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.igst.it/nettab/2016/'>NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics</a>, Rome, Italy </td>
- <td> <a href='/DannonBaker'>Dannon Baker</a>, <a href='/BjoernGruening'>Björn Grüning</a> </td>
- </tr>
- <tr>
- <td colspan=4 style=" background-color: #eef;"> </td>
- </tr>
- <tr>
- <th> November 2-3 </th>
- <td> <em><a href='https://github.com/bioconda/bioconda-recipes/issues/2277'>Bioconda Contribution Fest</a></em> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/World) <em>Online</em> </td>
- <td> <a href='/BjoernGruening'>Björn Grüning</a> </td>
- </tr>
- <tr>
- <th> November 7-8 </th>
- <td> <strong><a href='/Events/AdminTraining2016/BasicsSession'>Galaxy Admin Training: Introduction</a></strong> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) Salt Lake City, Utah, United States </td>
- <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/GalaxyTeam'>Galaxy Team</a> </td>
- </tr>
- <tr>
- <th> November 7-9 </th>
- <td> <em><a href='http://www.canceropole-idf.fr/formation-ngs-chipseq'>NGS & Cancer : Analyses ChIP-Seq</a></em><div class='indent red'>Workshop is full</div> </td>
- <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Paris, France </td>
- <td> <a href="mailto:communication@canceropole-idf.fr">Cancéropôle Île-de-France</a> </td>
- </tr>
- <tr>
<th> November 8-20 </th>
<td> <em><a href='https://meetings.cshl.edu/courses.aspx?course=c-seqtec&year=16'>Advanced Sequencing Technologies & Applications</a></em> <div class='indent'>Application deadline is July 15</div> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) <a href='https://cshl.edu/'>Cold Spring Harbor Laboratory</a>, New York, United States </td>
@@ -121,13 +45,37 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<th> November 9-11 </th>
<td> <strong><a href='/Events/AdminTraining2016/AdvancedSession'>Galaxy Admin Training: Advanced</a></strong> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) Salt Lake City, Utah, United States </td>
- <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/GalaxyTeam'>Galaxy Team</a> </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/Events/AdminTraining2016#instructors'>Instructors</a> </td>
+ </tr>
+ <tr>
+ <th> November 11 </th>
+ <td> <em><a href='https://www.eventbrite.com.au/e/introduction-to-the-gvl-and-galaxy-registration-28385990261'>Introduction to the GVL and Galaxy</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Australia) University of Melbourne, Melbourne, Victoria, Australia </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='https://www.vlsci.org.au/page/contacts'>VLSCI</a> </td>
</tr>
<tr>
<th> November 15-16 </th>
<td> <em><a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'>Analyse de données RNA-seq sous l’environnement Galaxy</a></em> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) PRABI, Lyon, France </td>
- <td> <a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'>Contact</a> </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'>Contact</a> </td>
+ </tr>
+ <tr>
+ <th> November 16 </th>
+ <td> <em><a href='https://www.abdn.ac.uk/genomics/documents/201617_Workshops/Quality_Control_2016.pdf'>Quality Control of Next Generation Sequencing Reads</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.abdn.ac.uk/genomics/bioinformatics/training/'>University of Aberdeen</a>, Scotland, United Kingdom </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:s.shaw@abdn.ac.uk">Sophie Shaw</a> </td>
+ </tr>
+ <tr>
+ <th> November 16 </th>
+ <td> <em><a href='http://bioexcel.eu/webinar-8-2016-11-16-workflows-galaxy-globus/'>Large-scale analytical workflows on the cloud using Galaxy and Globus</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/World) <em><a href='https://attendee.gotowebinar.com/register/5808939110698431491'>Online</a></em> </td>
+ <td> <a href='http://www.mcs.anl.gov/person/ravi-madduri'>Ravi Madduri</a> </td>
+ </tr>
+ <tr>
+ <th> November 16 </th>
+ <td> <em><a href='/Events/UUtahWorkshop'>Introduction to Galaxy Workshop</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) <a href='http://utah.edu/'>University of Utah</a>, Salt Lake City, Utah, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/DaveClements'>Dave Clements</a> </td>
</tr>
<tr>
<th> November&nbsp;20-25 </th>
@@ -136,25 +84,64 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:ecole-bioinfo@aviesan.fr">Email</a> </td>
</tr>
<tr>
+ <th> November 21 </th>
+ <td> <em><a href='https://galaxy.web.pasteur.fr/'>Pasteur_galaxy</a>: An open and sustainable Galaxy instance for NGS data analysis</em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/SouthAmerica) <a href='https://www.iscb.org/conference-program/iscb-latinamerica2016-agenda-glance'>ISCB-Latin America</a>, Buenos Aires, Argentina </td>
+ <td> Oussama Souiai </td>
+ </tr>
+ <tr>
<th> November 21-23 </th>
<td> <em><a href='https://urgi.versailles.inra.fr/content/view/full/3794'>Annotation of transposable elements</a></em> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) URGI, INRA Versailles, France </td>
<td> <a href='https://urgi.versailles.inra.fr/content/view/full/3794'>Contact</a> </td>
</tr>
<tr>
+ <th> November 28-30 </th>
+ <td> <em><a href='https://cnrsformation.cnrs.fr/stage-16148-Analyse-avancee-de-sequences.html?axe=97'>Analyse avancée de séquences</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Bordeaux, France </td>
+ <td> Macha Nikolski </td>
+ </tr>
+ <tr>
<th> November 28 - December 2 </th>
<td> <em><a href='http://workflow4metabolomics.org/training/w4mcourse2016'>Traitement des donnéesmétabolomiques sous Galaxy</a></em> <div class='indent red'>Les pré-inscriptions sont ouvertes jusqu'au 15 juillet 2016</div> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.sb-roscoff.fr/'>Station Biologique, Roscoff</a>, France </td>
<td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:contact@workflow4metabolomics.org">Contact</a> </td>
</tr>
<tr>
+ <th> November 29 </th>
+ <td> <em><a href='https://www.abdn.ac.uk/genomics/documents/201617_Workshops/Genome_Assembly_2016.pdf'>Genome Assembly and Annotation</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.abdn.ac.uk/genomics/bioinformatics/training/'>University of Aberdeen</a>, Scotland, United Kingdom </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:s.shaw@abdn.ac.uk">Sophie Shaw</a> </td>
+ </tr>
+ <tr>
+ <td colspan=4 style=" background-color: #eef;"> </td>
+ </tr>
+ <tr>
+ <th> December 15-16 </th>
+ <td> <em><a href='http://www.denbi.de/22-training-cat/training-courses/215-galaxy-rna-sequencing-data-analysis-workshop'>Galaxy RNA-sequencing data analysis workshop</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) RBC Freiburg, Germany </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:erxleben@informatik.uni-freiburg.de">Contact</a> </td>
+ </tr>
+ <tr>
<td colspan=4 style=" text-align: center; background-color: #eef;"> <span style="font-size: larger;"> <strong>2017</strong> </span> </td>
</tr>
<tr>
<th> January 14-18 </th>
- <td> <em>Galaxy Workshop</em> </td>
- <td> <a href='http://www.intlpag.org/'>Plant and Animal Genome XXV</a>, San Diego, California, United States </td>
- <td> <a href='/DaveClements'>Dave Clements</a> </td>
+ <td> <a href='/Events/PAG2017'>Galaxy @ Plant & Animal Genome XXIV (PAG 2017)</a> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) San Diego, California, United States </td>
+ <td> <a href='/Events/PAG2017'>Presenters</a> </td>
+ </tr>
+ <tr>
+ <th> January 16-19 </th>
+ <td> <strong><a href='https://www.france-bioinformatique.fr/en/evenements/EGDW2017'>European Galaxy Developer Workshop</a></strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Strasbourg, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:egdw2017.oc@groupes.france-bioinformatique.fr">Organisers</a> </td>
+ </tr>
+ <tr>
+ <th> January 30 </th>
+ <td> <em><a href='http://www.bioplatforms.com/rna-seq-using-galaxy-jan-2017/'>RNA-Seq Analysis Using Galaxy</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Australia) Australian National University, Canberra, ACT, Australia </td>
+ <td> <a href="mailto:kchamp@bioplatforms.com">Katherine Champ</a> </td>
</tr>
<tr>
<td colspan=4 style=" background-color: #eef;"> </td>
@@ -166,6 +153,12 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='https://www.embl-abr.org.au/organisers/'>Organisers</a> </td>
</tr>
<tr>
+ <th> February 13-17 </th>
+ <td> <em><a href='http://www.denbi.de/22-training-cat/training-courses/213-3rd-galaxy-high-throughput-sequencing-hts-data-analysis-workshop'>Galaxy Workshop on HTS data analysis for Scientists</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Freiburg, Germany </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:erxleben@informatik.uni-freiburg.de">Email</a> </td>
+ </tr>
+ <tr>
<td colspan=4 style=" background-color: #eef;"> </td>
</tr>
<tr>
@@ -247,9 +240,16 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<a href='https://github.com/galaxyproteomics/tools-galaxyp/issues/57#issuecomment-245934625'><img src='/Images/Logos/GalaxyPCondaHack.png' alt='Galaxy-P Conda hackathon' height="85" /></a>
<a href='http://www.jsbi.org/iibmp2016/program_bof/#B10'><img src='/Images/Logos/IIBMP2016Logo.png' alt='GalaxyによるNGSデータ解析 (Galaxy NGS Data Analysis BoF)' height="85" /></a> &nbsp;
<a href='https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3'><img src='/Images/GalaxyLogos/GTNLogo300.png' alt='Galaxy Training Contribution Fest' height="75" /></a> &nbsp;
+<a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=83'><img src='/Images/Logos/GenoToulLogo.png' alt='Metagenomic: amplicon analysis' height="60" /></a> &nbsp;
+<a href='https://www.facebook.com/events/1593583060947735/'><img src='/Images/Logos/CBioVikingsTrans.png' alt='Galaxy Workshop' height="80" /></a>
+<a href='http://www.france-bioinformatique.fr/en/evenements/galaxy4bioinformatics'><img src='/Images/Logos/IFBGalaxyWG.png' alt=' Galaxy4Bioinformatics' height="60" /></a>
+<a href='/Events/SG2016'><img src='/Images/Logos/SG2016T.V2_logo.png' alt='2016 Swiss German Galaxy Tour' height="80" /></a>
+<a href='http://www.igst.it/nettab/2016/'><img src='/Images/Logos/NETTAB.gif' alt='Galaxy @ NETTAB 2016' height="60" /></a>
+<a href='https://github.com/bioconda/bioconda-recipes/issues/2277'><img src='/Images/Logos/BiocondaO.png' alt='Bioconda Contribution Fest' height="80" /></a>
</div>
<br />
+
<table>
<tr class="th" >
<th> Date </th>
@@ -259,6 +259,142 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<th> Links </th>
</tr>
<tr>
+ <th> November 7-9 </th>
+ <td> <em><a href='http://www.canceropole-idf.fr/formation-ngs-chipseq'>NGS & Cancer : Analyses ChIP-Seq</a></em><div class='indent red'>Workshop is full</div> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Paris, France </td>
+ <td> <a href="mailto:communication@canceropole-idf.fr">Cancéropôle Île-de-France</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> November 7-9 </th>
+ <td> <em><a href='https://www.hd-hub.de/symposium'>Tool deployment and sustainability in bioinformatics – fixed!</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='https://www.hd-hub.de/symposium'>Bioinformatics for Human Health and Disease</a>, Heidelberg, Germany </td>
+ <td> Bérénice Batut </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> November 7-8 </th>
+ <td> <strong><a href='/Events/AdminTraining2016/BasicsSession'>Galaxy Admin Training: Introduction</a></strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) Salt Lake City, Utah, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/Events/AdminTraining2016#instructors'>Instructors</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> November 2-3 </th>
+ <td> <em><a href='https://github.com/bioconda/bioconda-recipes/issues/2277'>Bioconda Contribution Fest</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/World) <em>Online</em> </td>
+ <td> <a href='/BjoernGruening'>Björn Grüning</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 26 - November 3 </th>
+ <td> <em><a href='http://meetings.cshl.edu/courses.aspx?course=C-ECG&year=16'>Computational & Comparative Genomics</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) Cold Spring Harbor Laboratory, New York, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/JamesTaylor'>James Taylor</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <td colspan=5 style=" background-color: #eef;"> </td>
+ </tr>
+ <tr>
+ <th> October 26-29 </th>
+ <td> <em>Thousands of public epigenomic datasets can be exploited through the Galaxy-GenAP project and the GeEC tool</em> </td>
+ <td> <a href='https://meetings.cshl.edu/meetings.aspx?meet=DATA&year=16'>Biological Data Analysis</a>, Cold Spring Harbor Laboratory, New York, United States </td>
+ <td> Pierre-Etienne Jacques </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 26-29 </th>
+ <td> <em><a href='https://f1000research.com/posters/5-2567'>Planemo—A scientific workflow SDK</a></em> </td>
+ <td> <a href='https://meetings.cshl.edu/meetings.aspx?meet=DATA&year=16'>Biological Data Analysis</a>, Cold Spring Harbor Laboratory, New York, United States </td>
+ <td> <a href='/JohnChilton'>John Chilton</a> </td>
+ <td> <a href='https://f1000research.com/posters/5-2567'>Poster</a> </td>
+ </tr>
+ <tr>
+ <th> October 25-27 </th>
+ <td> <em>An Example of Galaxy – tranSMART Workflow Using NGS Data</em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) <a href='http://transmartfoundation.org/2016-annual-meeting/'>tranSMART Foundation 2016 Annual Meeting</a>, La Jolla, California, United States </td>
+ <td> Yulia Skovpen </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 25-27 </th>
+ <td> <em><a href='http://www.igst.it/nettab/2016/programme/scientific-programme/'>The Galaxy tool lifecycle supporting reproducibility in scientific research</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.igst.it/nettab/2016/'>NETTAB 2016 / EMBNet Joint Meeting on Reproducibility in Bioinformatics</a>, Rome, Italy </td>
+ <td> <a href='/DannonBaker'>Dannon Baker</a>, <a href='/BjoernGruening'>Björn Grüning</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 24 </th>
+ <td> <em>Deployment of bioinformatics tools and services through Docker</em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='https://docs.google.com/document/d/1mxcQgPNI212YkTIJf9twGLX5OiTZBDXjLvPaOVVFQ80/edit#heading=h.83oyrjah164f'>ELIXIR Hackathon @ NETTAB 2016</a>, Rome, Italy </td>
+ <td> <a href="mailto:paolo.romano@hsanmartino.it">Paolo Romano</a>, <a href="mailto:jison@cbs.dtu.dk">Jon Ison</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 20-21 </th>
+ <td> <em><a href='http://www.ebi.ac.uk/training/events/2016/bioexcel-workflow-training-computational-biomolecular-research?platform=hootsuite'>BioExcel: Workflow Training for Computational Biomolecular Research</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Barcelona Supercomputing Center, Barcelona, Spain </td>
+ <td> <a href='https://siastd.uab.es/pcde/fitxa_persona.jsf;jsessionid=2cdbb231e18e06bc59f766ae8951:4crB?id=161b3185c321992a'>Antonio Miguel Espinosa Morales</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 21 </th>
+ <td> <em><a href='/Events/Germany2016'>(second German) Galaxy Developers Day</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <strong><a href='/Events/SG2016'>2016 Swiss-German Galaxy Days</a></strong> in Freiburg, Germany </td>
+ <td> <a href='/HansrudolfHotz'>Hans-Rudolf Hotz</a> and <a href='/BjoernGruening'>Bjoern Gruening</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 20 </th>
+ <td> <em><a href='/Events/Switzerland2016'>(third Swiss) Galaxy Workshop</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <strong><a href='/Events/SG2016'>2016 Swiss-German Galaxy Days</a></strong> in Freiburg, Germany </td>
+ <td> <a href='/HansrudolfHotz'>Hans-Rudolf Hotz</a> and <a href='/BjoernGruening'>Bjoern Gruening</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 20 </th>
+ <td> <em>Genome Program Joint Workshop</em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Asia) <a href='http://kunsan.ac.kr'>Kunsan National University</a>, Gunsan, South Korea </td>
+ <td> <a href='/anton'>Anton Nekrutenko</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 18-20 </th>
+ <td> <em><a href='http://www.france-bioinformatique.fr/en/evenements/galaxy4bioinformatics'>Galaxy4Bioinformatics</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Lyon, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='http://www.france-bioinformatique.fr/en/node/17'>Contacts</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 18 </th>
+ <td> <em><a href='https://www.france-bioinformatique.fr/en/evenements/IFB-IBI?qt-view__ge_individuelle__block=1'>Utilisation de base du cloud IFB</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Gif-sur-Yvette, France </td>
+ <td> <a href="mailto:formation-cloud@france-bioinformatique.fr">Contact</a> </td>
+ <td> <a href='https://www.france-bioinformatique.fr/en/evenements/IFB-IBI?qt-view__ge_individuelle__block=1'>Materials</a> </td>
+ </tr>
+ <tr>
+ <th> October 18 </th>
+ <td> <em><a href='https://www.xsede.org/ecss-symposium#October 18, 2016'>Towards Large-scale Genomics, Transcriptomics, and Metagenomics for All</a></em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/World) <a href='https://www.xsede.org/ecss-symposium'>XSEDE Extended Collaborative Support Symposium</a>, <em>Online</em> </td>
+ <td> <a href='https://www.linkedin.com/in/philipblood'>Philip Blood</a> </td>
+ <td> <a href='https://www.xsede.org/documents/10157/1125659/Genomics_SymposiumTalk_2016.pdf/0da778e0-d60a-412c-b739-a3182020d4fa'>Slides</a>, <a href='https://www.youtube.com/watch?v=m1GXj7z3JYM'>Video</a> </td>
+ </tr>
+ <tr>
+ <th> October 10-13 </th>
+ <td> <em><a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=83'>Metagenomic: amplicon analysis</a></em> <div class='indent red'> Registration closes 4 October</div> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) INRA Auzeville, Auzeville, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) Sarah Maman </td>
+ <td> </td>
+ </tr>
+ <tr>
+ <th> October 13 </th>
+ <td> <em><a href='https://www.facebook.com/events/1593583060947735/'>Galaxy Workshop</a></em> <div class='indent red'>Workshop is full</div> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Copenhagen, Denmark </td>
+ <td> <a href='http://jmgi.tk/'>Jose Maria (Txema) Gonzalez Izarzugaza</a> </td>
+ <td> </td>
+ </tr>
+ <tr>
<th> October 10 </th>
<td> <em><a href='https://drive.google.com/file/d/0BwK61gB7NIcic1BnVmhxMFJEM3M/view'>Omics Data Services Platform: Supporting bacterial pathogen multi omics analysis</a></em> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/Australia) <a href='https://nectar.org.au/workshop-science-gateways/'>International Workshop on Science Gateways</a>, Melbourne, Australia </td>
@@ -873,7 +1009,7 @@ For events prior to this year, see the **[Events Archive](/Events/Archive)**.
<th> January 21 </th>
<td> <em><a href='http://www.qfab.org/event/workshop-rna-seq-analysis-using-galaxy-4/'>RNA-Seq analysis using Galaxy Workshop</a></em> </td>
<td> PLACEHOLDER_INCLUDE(/Events/Badges/Australia) <a href='http://www.qfab.org/'>QFAB</a>, Brisbane, Queensland, Australia </td>
- <td> <a href="mailto:training@qfab.org">Melinda Beawer</a> </td>
+ <td> <a href="mailto:training@qfab.org">Belinda Weaver</a> </td>
<td> </td>
</tr>
<tr>
diff --git a/FrontPage/BottomBox/index.md b/FrontPage/BottomBox/index.md
index a1c1886..a247312 100644
--- a/FrontPage/BottomBox/index.md
+++ b/FrontPage/BottomBox/index.md
@@ -5,29 +5,33 @@
<div class='bottomBoxNews'>
<div class='bottomBoxSectionHeader'>[Galaxy News](/News) <a href='http://feed43.com/galaxynews.xml'><img src='/Images/Icons/RSSIcon16x16.gif' /></a>
</div>
+[Wiki Migration is Underway](/News/WikiMigration)<br />
+[November 2016 News of the Galaxy!](/News/2016_11GalaxyUpdate)<br />
+[Galaxy Arabic Community](/News/GalaxyArabic)<br />
+[Galaxy on Jetstream update](/News/GalaxyOnJetstream1607)<br />
[October 2016 Galactic News](/News/2016_10GalaxyUpdate)<br />
[Galaxy Australia Community & GAMe 2017](/News/GalaxyAustralia)<br />
[GCC2018 Call for Host Proposals](/News/GCC2018CallForHost)<br />
-[September 2016 Galactic News](/News/2016_09GalaxyUpdate)<br />
-[July 2016 Galaxy Release (v 16.07)](/News/2016_07_GalaxyRelease)<br />
-[Galaxy Admin Training Nov 7-11](/News/GAT2016RegistrationOpen)<br />
-[August 2016 Galactic News](/News/2016_08GalaxyUpdate)<br />
[More ...](/News)<br />
<br />
----
<div class='bottomBoxSectionHeader'>[Upcoming Events](/Events)</div>
<div class='center'>
-<a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=83'><img src='/Images/Logos/GenoToulLogo.png' alt='Metagenomic: amplicon analysis' height="60" /></a> &nbsp;
-<a href='https://www.facebook.com/events/1593583060947735/'><img src='/Images/Logos/CBioVikingsTrans.png' alt='Galaxy Workshop' height="80" /></a>
-<a href='http://www.france-bioinformatique.fr/en/evenements/galaxy4bioinformatics'><img src='/Images/Logos/IFBGalaxyWG.png' alt=' Galaxy4Bioinformatics' /></a>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width=120" /></a></div>
+<a href='https://github.com/bioconda/bioconda-recipes/issues/2277'><img src='/Images/Logos/BiocondaO.png' alt='Bioconda Contribution Fest' height="80" /></a>
+<a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'><img src='/Images/Logos/PRABILogo.png' alt='Analyse de données RNA-seq sous l’environnement Galaxy' height="60" /></a>
+<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width="100" /></a>
+<a href='https://www.embl-abr.org.au/game2017/'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="100" /></a>
+</div>
</div>
<div class='bottomBoxHighlight'>
<div class='bottomBoxSectionHeader'>[Papers](/CiteULike)</div>
+[I'll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Data](https://www.research.manchester.ac.uk/portal/files/45989205/bagminid.pdf), Chard et al.
+
+[Flexible Container-Based Computing Platform on Cloud for Scientific Workflows](http://dx.doi.org/10.1109/icccri.2016.17), Liu et al.
+
[An Automated Tool Profiling Service for the Cloud](http://dx.doi.org/10.1109/ccgrid.2016.57), Chard et al.
[The Essential Components of a Successful Galaxy Service](http://dx.doi.org/10.1007/s10723-016-9379-6), !McGrath et al
@@ -38,10 +42,6 @@
[Streamlined analysis of duplex sequencing data with Du Novo](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1039-4), Stoler et al.
-[Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding)](http://dx.doi.org/10.1101/pdb.prot093187), Hung & Weng
-
-[Cloudflow - A framework for MapReduce pipeline development in Biomedical Research](https://figshare.com/articles/Cloudflow_A_Framework_for_MapReduce_Pipeline_Development_in_Biomedical_Research/1424739), Forer et al.
-
</div>
diff --git a/GalaxyTeam/index.md b/GalaxyTeam/index.md
index 76c11e2..d7d3ace 100644
--- a/GalaxyTeam/index.md
+++ b/GalaxyTeam/index.md
@@ -66,6 +66,11 @@ Carl Eberhard <br />
[Penn State](http://www.bx.psu.edu)
</div>
<div class='left center'>
+<a href='/VahidJalili'><img src='/Vahid.jpg' alt='Vahid Jalili' height="150" /></a><br />
+[Vahid Jalili](/VahidJalili)<br />
+[George Washington University](http://www.gwu.edu)
+</div>
+<div class='left center'>
<a href='/DelphineLariviere'><img src='/DelphineLariviere.jpg' alt='DelphineLariviere' height="150" /></a><br />
[Delphine Lariviere](/DelphineLariviere)<br />
[Penn State](http://www.bx.psu.edu)
diff --git a/GalaxyUpdates/2012_02/index.md b/GalaxyUpdates/2012_02/index.md
index 59e3edf..b906cd9 100644
--- a/GalaxyUpdates/2012_02/index.md
+++ b/GalaxyUpdates/2012_02/index.md
@@ -27,7 +27,7 @@ Plus [27 other papers](http://www.citeulike.org/group/16008/library) that use, r
## New Public Server: MGTAXA
-[MGTAXA, a free Galaxy server at JCVI for metagenomic taxonomy prediction](http://mgtaxa.jcvi.org/) was added to the list of [/Public Galaxy Servers](/Public Galaxy Servers) in January. Many thanks to JCVI and the MGTAXA team for making this publicly available.
+[MGTAXA, a free Galaxy server at JCVI for metagenomic taxonomy prediction](http://mgtaxa.jcvi.org/) was added to the list of [Public Galaxy Servers](/PublicGalaxyServers) in January. Many thanks to JCVI and the MGTAXA team for making this publicly available.
## Who's Hiring
diff --git a/GalaxyUpdates/2013_11/index.md b/GalaxyUpdates/2013_11/index.md
index cfd8237..62f5ce1 100644
--- a/GalaxyUpdates/2013_11/index.md
+++ b/GalaxyUpdates/2013_11/index.md
@@ -32,7 +32,7 @@ A [Visual Manual](http://intersci.ss.uci.edu/wiki/index.php/Visual_Manual) is av
## BioCiphers Lab Galaxy
-The [BioCiphers Lab Galaxy](http://avispa.biociphers.org/) provides a user friendly interface for analysis tools developed by the [BioCiphers Lab](http://biociphers.org/) at the University of Pennsylvania. This includes the AVISPA alternative splicing prediction and analysis tool. See Barash, *et al.,* "[AVISPA: a web tool for the prediction and analysis of alternative splicing](http://genomebiology.com/2013/14/10/R114)" *[Genome Biology](http://genomebiology.com/)* 2013, 14:R114. BCL Galaxy offers [email support](/Public Galaxy Servers#biociphers-lab-galaxy). It is open to anyone from an educational organization.
+The [BioCiphers Lab Galaxy](http://avispa.biociphers.org/) provides a user friendly interface for analysis tools developed by the [BioCiphers Lab](http://biociphers.org/) at the University of Pennsylvania. This includes the AVISPA alternative splicing prediction and analysis tool. See Barash, *et al.,* "[AVISPA: a web tool for the prediction and analysis of alternative splicing](http://genomebiology.com/2013/14/10/R114)" *[Genome Biology](http://genomebiology.com/)* 2013, 14:R114. BCL Galaxy offers [email support](/PublicGalaxyServers#biociphers-lab-galaxy). It is open to anyone from an educational organization.
<br />
# New Papers
diff --git a/GalaxyUpdates/2014_10/index.md b/GalaxyUpdates/2014_10/index.md
index 3e51a4c..5151843 100644
--- a/GalaxyUpdates/2014_10/index.md
+++ b/GalaxyUpdates/2014_10/index.md
@@ -49,7 +49,7 @@ Galaxy had a strong presence at [ECCB'14](/Events/ECCB2014). Galaxy was feature
<a href='http://www.qfab.org/events/upcoming/'><img src='/Images/Logos/QFABLogo.png' alt='QFAB Workshops' height="80" /></a>
<a href='http://wiki.data.dtls.nl/index.php/DTL_Programmers_Meeting'><img src='/Images/Logos/DTLLogo150.png' alt='iReport - A tool to create flexible, scalable Galaxy tool interface, presented at the DTL Programmers Meeting' height="90" /></a>
<a href='http://galaxy4bioinformatics.sb-roscoff.fr/'><img src='/Images/Logos/SB-RoscoffBig.JPG' alt='Des bonnes pratiques d'intégration d'outils sous Galaxy' height="60" /></a> &nbsp;
-[{{attachment:Images/Logos/GenoToulLogo.png|Galaxy Training Days|height="60"}}|Galaxy training days](http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=62) &nbsp;
+<a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=62'><img src='/Images/Logos/GenoToulLogo.png' alt='Galaxy Training Days' height="60" /></a> &nbsp;
</div>
<div class='right'><a href='http://bit.ly/gxycal'><img src='/Images/Icons/CalendarIcon.gif' /></a></div>
diff --git a/GalaxyUpdates/2014_11/index.md b/GalaxyUpdates/2014_11/index.md
index b38993f..b16d0fd 100644
--- a/GalaxyUpdates/2014_11/index.md
+++ b/GalaxyUpdates/2014_11/index.md
@@ -85,7 +85,7 @@ The *[Tools integration on Galaxy Workshop](http://go4bioinformatics.genouest.or
<div class='center'>
<a href='http://galaxy4bioinformatics.sb-roscoff.fr/'><img src='/Images/Logos/SB-RoscoffBig.JPG' alt='Des bonnes pratiques d'intégration d'outils sous Galaxy' height="60" /></a> &nbsp;
-[{{attachment:Images/Logos/GenoToulLogo.png|Galaxy Training Days|height="60"}}|Galaxy training days](http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=62) &nbsp;
+<a href='http://bioinfo.genotoul.fr/index.php?id=34&tx_seminars_pi1%5BshowUid%5D=62'><img src='/Images/Logos/GenoToulLogo.png' alt='Galaxy Training Days' height="60" /></a> &nbsp;
<a href='http://www.bioinformatica.crs4.it/next_generation_sequencing_course_with_galaxy_november_2014'><img src='/Images/Logos/CRS4Logo.jpg' alt='Analisi dati Next Generation Sequencing in Galaxy' width="130" /></a> &nbsp;
<a href='http://www.qfab.org/event/workshop-extended-rna-seq-analysis-1920-november-brisbane/'><img src='/Images/Logos/QFABLogo.png' alt='Workshop: Extended RNA-Seq analysis' height="80" /></a>
<a href='http://www.prabi.fr/spip.php?article215'><img src='/Images/Logos/PRABILogo.png' alt='RNA-Seq & ChIP-Seq analysis course using Galaxy' height="60" /></a>
diff --git a/GalaxyUpdates/2016_11/index.md b/GalaxyUpdates/2016_11/index.md
new file mode 100644
index 0000000..d66eabc
--- /dev/null
+++ b/GalaxyUpdates/2016_11/index.md
@@ -0,0 +1,613 @@
+----
+autotoc: true
+pagetitle: November 2016 Galaxy News
+----
+
+
+<div class='right'>
+<table>
+ <tr>
+ <td style=" border: none; width: 24em;"> </td>
+ </tr>
+</table>
+
+</div>
+
+<div class='right'><a href='/GalaxyUpdates'><img src='/Images/GalaxyLogos/GalaxyNews.png' alt='Galaxy News' width=150 /></a></div>
+
+Welcome to the November 2016 *[Galactic News](/GalaxyUpdates)*, a summary of what is going on in the Galaxy community.
+
+The big news this month is still a series of upcoming events:
+
+* **[Bioconda Contribution Fest](#bioconda-contribution-fest-november-2-3-online)**:
+ * November 2-3, [Online](https://github.com/bioconda/bioconda-recipes/issues/2277)
+* **[Galaxy Admin Training](#galaxy-admin-training-november-7-11-salt-lake-city-utah)**:
+ * November 7-11, Salt Lake City, Utah
+ * *On time registration ends October 16*
+* **[European Galaxy Developer Workshop](#european-galaxy-developer-workshop)**:
+ * January 16-19, Strasbourg, France
+* **[Galaxy Australasia Meeting (GAMe 2017)](#galaxy-australasia-meeting-game-2017-registration--abstract-submission-are-open)**:
+ * February 3-9, Melbourne, Victoria, Australia
+ * *Registration and abstract submission are now open.*
+
+If you have anything to include in the next News, please send it to [outreach AT galaxyproject DOT org](Galaxy Outreach).
+
+
+# Events
+
+There are a wealth of events coming up. Here are some highlights, and a report on one from last month too.
+
+## Galaxy Australasia Meeting (GAMe 2017)
+
+<div class='right'><a href='https://www.embl-abr.org.au/game2017/'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="120" /></a></div>
+
+[GAMe 2017](https://www.embl-abr.org.au/game2017/) will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia to share expertise across many levels.
+
+This meeting features three distinct events:
+
+* **[Researcher Training Day](https://www.embl-abr.org.au/game2017/training-day/)** on 3 February, aimed at biomedical researchers who need to analyse their biological data
+* The **[GAMe 2017 Conference](https://www.embl-abr.org.au/game2017/conference/)** starts 4 February and features two full days of keynotes, accepted and sponsor talks, poster and sponsor sessions, birds­-of-­a­-feather gatherings, a conference dinner and lots of opportunities for networking.
+* A **[four day workshop on Galaxy server administration](https://www.embl-abr.org.au/game2017/training-for-admin-workshop/)** runs 5-9 February.
+
+### Oral Presentation Abstracts Due 30 November
+
+Accepted talks will be presented during the 2-day conference, 4-5 February. Talks are 15-20 minutes long and the meeting is single track.
+
+**[Oral presentation abstract submission](https://www.embl-abr.org.au/game2017/submit-your-talkposter/) is open until 30 November 2016.** Abstracts are limited to 250 words or less.
+
+### Poster Submission and Early Registration
+
+[Poster abstract submission is open until we run out of poster space](https://www.embl-abr.org.au/game2017/submit-your-talkposter/). Abstracts are limited to 250 words or less. Poster abstracts are reviewed on a rolling basis and submitters will be notified of the decision within two weeks of the abstract’s submission date.
+
+**[Early registration is open until 31 December](https://www.embl-abr.org.au/game2017/registration/)**. Register now and save up to 43% off regular registration rates. There are also [scholarships available for eligible students and postdocs](https://www.embl-abr.org.au/game2017/registration/#scholarships). The scholarship application deadline is 18 November.
+
+
+## Bioconda Contribution Fest, November 2-3, Online
+
+<div class='left'><a href='http://blogs.biomedcentral.com/gigablog/2016/09/20/guest-posting-introducing-conda-for-galaxy/'><img src='/Images/Logos/BioCondaGalaxy.jpg' alt='BioConda and Galaxy' width="200" /></a></div>
+
+Our first [Bioconda Contribution Fest](https://github.com/bioconda/bioconda-recipes/issues/2277) will be on the 2-3 November! We will have an IRC channel (maybe gitter?) and a google hangout in place.
+
+We will start with a short presentation of all ideas and try to create small groups to tackle problems small groups.
+I guess it's a good idea if you fork bioconda-recipes and get your own travis setup up and running so we avoid the travis bottleneck.
+
+See [the event page](https://github.com/bioconda/bioconda-recipes/issues/2277) for ideas and more details.
+
+## European Galaxy Developer Workshop
+
+<div class='right'>
+<a href='https://www.france-bioinformatique.fr/en/evenements/EGDW2017'><img src='/Images/Logos/ElixirNoTextLogo.png' alt='' width="140" /></a><br />
+<a href='https://www.france-bioinformatique.fr/en/evenements/EGDW2017'><img src='/Images/Logos/IFBGalaxyWG.png' alt='' width="140" /></a>
+</div>
+
+**[Registration](https://www.france-bioinformatique.fr/en/evenements/EGDW2017?qt-view__ge_individuelle__block=2#qt-view__ge_individuelle__block)** is now open for the **[European Galaxy Developer Workshop](https://www.france-bioinformatique.fr/en/evenements/EGDW2017)** being held 16-19 January in Strasbourg, France.
+
+During this 4 day course, attendees will learn how to integrate high-quality tools and visualisations into Galaxy using best practice guidelines and finally how to deploy them. The last day will be spent to learn how to configure a production ready Galaxy server. Moreover, at the end of this course you will have a profound knowledge about Docker and Conda.
+
+Travel expenses and lodging need to be covered by each participant individually. *[ELIXIR-EXCELERATE](https://www.elixir-europe.org/documents/elixir-webinar-introduction-elixir-excelerate) and [IFB](https://www.france-bioinformatique.fr/) (French Node) are covering the meeting costs.*
+
+## Galaxy Admin Training, November 7-11, Salt Lake City, Utah
+
+<div class='left solid center'>
+<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width=170" /></a><br />
+[November 7-11](/Events/AdminTraining2016/Registration), 2016<br />University of Utah<br />Salt Lake City, Utah
+</div>
+
+**[There are still a few spaces left](/Events/AdminTraining2016).**
+
+[Galaxy Admin Training 2016](/Events/AdminTraining2016) is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before [Supercomputing 16 (SC16)](http://sc16.supercomputing.org/) meets in Salt Lake.
+
+**[Basics Session: November 7-8](/Events/AdminTraining2016/BasicsSession)**
+
+This two day [basics session](/Events/AdminTraining2016/BasicsSession) will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server.
+
+**[Advanced Session: November 9-11](/Events/AdminTraining2016/AdvancedSession)**
+
+The three day [advanced session](/Events/AdminTraining2016/AdvancedSession) will build on topics covered in the [basics section](/Events/AdminTraining2016/BasicsSession). This session extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The advanced workshop focuses on creating robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources.
+
+
+## Report: Galaxy training material: A Contribution Fest beyond any expectations
+
+On the 6 and 7th of October, the [Galaxy Training Network](/Teach/GTN) had its first [online Contribution Fest](https://github.com/bgruening/training-material) with an impressive amount of contributions and contributors! This was beyond any expectations!
+
+* 25 persons joined the Contribution Fest - a few of them had never contributed to an open source project on !GitHub. Institutions like ELIXIR, de.NBI and IFB had persons contributing to the this Contribution Fest.
+* During the two days, more than 44 commits went into the master branch. 24 pull request were opened and 15 of them were merged. 5 Issues were closed and 5 created. 16 previously opened issues were used to plan the further direction of this initiative.
+* Before the Fest, 9 topics were available with different materials (hands-on tutorials, slides, …). During the two days, 1 new topic and 2 new tutorials were proposed, 2 slide decks were created and 7 tutorials were updated to follow our guidelines.
+* More than 350 messages were exchanged over the Gitter channel during these few days. A few video calls were made to explain the goals and the guidelines. One main discussion point was the slide format which we defined - we will rethink this and propose a new one soon - this should go hand in hand with the new Galaxy wiki system.
+
+See [the full report](https://docs.google.com/document/d/1pThnwvQKvdN1C0ub1QWoXcWp71QinZb_msUKHLFxfFI/pub) for more.
+
+This Contribution Fest was fantastic and we learned a lot during these days. We would like to warmly thank all the participants. Great community effort!
+
+Bérénice and [Bjoern](/BjoernGruening)
+
+## Report: Swiss-German Galaxy Days
+
+<div class='right'>
+<a href='/Events/SG2016'><img src='/Images/Logos/SG2016T.V2_logo.png' alt='2016 Swiss German Galaxy Tour' height="120" /></a>
+</div>
+
+Well over 30 people from all over Europe (not just Germany and Switzerland) attended the "[Swiss German Galaxy Tour 2016](/Events/SG2016)" which took place over two days in Freiburg, Germany, mid October.
+
+On the first day several talks highlighted new developments coming from the wide Galaxy community, including updates wrt training and tool development. Participants had a chance to show how they use Galaxy and how they have implemented Galaxy locally. Many took the opportunity to discuss their challenges. And it was great to see how quickly solutions emerged from the group of participants.
+
+On the second, we tried a new hackathon format: A topic was presented with a short theoretical introduction. This was followed by 90 minutes of hacking and 15 minutes discussion. During the introduction a set of starting points was shown allowing the beginner to explore the topic and the advanced user to work on a real case. Three such mini hackathons were run covering: creating Conda packages, Galaxy tours, and creating Galaxy Docker flavors.
+
+We would like to thank for the financial support we got from [de.NBI](https://www.denbi.de/) [ELIXIR](https://www.elixir-europe.org/) and for all the help we got from the Galaxy team, especially for sending [Dannon](/DannonBaker) over to Europe. It was great to have him, and the event profited a lot from him.
+
+We are looking forward to the next Swiss German Galaxy Tour.
+
+[Björn](/BjoernGruening) and [Hans-Rudolf](/HansrudolfHotz)
+
+## All upcoming events
+
+There are [a plentitude of Galaxy related events coming up](/Events) in the next few months:
+
+<div class='center'>
+<a href='https://github.com/bioconda/bioconda-recipes/issues/2277'><img src='/Images/Logos/BiocondaO.png' alt='Bioconda Contribution Fest' height="80" /></a>
+<a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'><img src='/Images/Logos/PRABILogo.png' alt='Analyse de données RNA-seq sous l’environnement Galaxy' height="60" /></a>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width="120" /></a>
+<a href='https://www.embl-abr.org.au/game2017/'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="120" /></a>
+</div>
+
+<table>
+ <tr class="th" >
+ <th style=" width: 7em;"> Date </th>
+ <th> Topic/Event </th>
+ <th> Venue/Location </th>
+ <th> Contact </th>
+ </tr>
+ <tr>
+ <th> November 2-3 </th>
+ <td> </em><a href='https://github.com/bioconda/bioconda-recipes/issues/2277'>Bioconda Contribution Fest</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/World) </em>Online<em> </td>
+ <td> <a href='/BjoernGruening'>Björn Grüning</a> </td>
+ </tr>
+ <tr>
+ <th> November 7-8 </th>
+ <td> </strong><a href='/Events/AdminTraining2016/BasicsSession'>Galaxy Admin Training: Introduction</a><strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) Salt Lake City, Utah, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/Events/AdminTraining2016#instructors'>Instructors</a> </td>
+ </tr>
+ <tr>
+ <th> November 7-9 </th>
+ <td> </em><a href='http://www.canceropole-idf.fr/formation-ngs-chipseq'>NGS & Cancer : Analyses ChIP-Seq</a><em><div class='indent red'>Workshop is full</div> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Paris, France </td>
+ <td> <a href="mailto:communication@canceropole-idf.fr">Cancéropôle Île-de-France</a> </td>
+ </tr>
+ <tr>
+ <th> November 7-9 </th>
+ <td> </em><a href='https://www.hd-hub.de/symposium'>Tool deployment and sustainability in bioinformatics – fixed!</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='https://www.hd-hub.de/symposium'>Bioinformatics for Human Health and Disease</a>, Heidelberg, Germany </td>
+ <td> Bérénice Batut </td>
+ </tr>
+ <tr>
+ <th> November 8-20 </th>
+ <td> </em><a href='https://meetings.cshl.edu/courses.aspx?course=c-seqtec&year=16'>Advanced Sequencing Technologies & Applications</a><em> <div class='indent'>Application deadline is July 15</div> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) <a href='https://cshl.edu/'>Cold Spring Harbor Laboratory</a>, New York, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/JeremyGoecks'>Jeremy Goecks</a> </td>
+ </tr>
+ <tr>
+ <th> November 9-11 </th>
+ <td> </strong><a href='/Events/AdminTraining2016/AdvancedSession'>Galaxy Admin Training: Advanced</a><strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) Salt Lake City, Utah, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/Events/AdminTraining2016#instructors'>Instructors</a> </td>
+ </tr>
+ <tr>
+ <th> November 11 </th>
+ <td> </em><a href='https://www.eventbrite.com.au/e/introduction-to-the-gvl-and-galaxy-registration-28385990261'>Introduction to the GVL and Galaxy</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Australia) University of Melbourne, Melbourne, Victoria, Australia </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='https://www.vlsci.org.au/page/contacts'>VLSCI</a> </td>
+ </tr>
+ <tr>
+ <th> November 15-16 </th>
+ <td> </em><a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'>Analyse de données RNA-seq sous l’environnement Galaxy</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) PRABI, Lyon, France </td>
+ <td> <a href='http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-sous-l-environnement-GALAXY_a39.html'>Contact</a> </td>
+ </tr>
+ <tr>
+ <th> November 16 </th>
+ <td> </em><a href='https://www.abdn.ac.uk/genomics/documents/201617_Workshops/Quality_Control_2016.pdf'>Quality Control of Next Generation Sequencing Reads</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.abdn.ac.uk/genomics/bioinformatics/training/'>University of Aberdeen</a>, Scotland, United Kingdom </td>
+ <td> <a href="mailto:s.shaw@abdn.ac.uk">Sophie Shaw</a> </td>
+ </tr>
+ <tr>
+ <th> November 16 </th>
+ <td> </em><a href='/Events/UUtahWorkshop'>Introduction to Galaxy Workshop</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) <a href='http://utah.edu/'>University of Utah</a>, Salt Lake City, Utah, United States </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='/DaveClements'>Dave Clements</a> </td>
+ </tr>
+ <tr>
+ <th> November&nbsp;20-25 </th>
+ <td> </em><a href='http://www.france-bioinformatique.fr/evenements/EBA2016'>Ecole Bioinformatique AVIESAN</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.sb-roscoff.fr/'>Station Biologique, Roscoff</a>, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:ecole-bioinfo@aviesan.fr">Email</a> </td>
+ </tr>
+ <tr>
+ <th> November 21 </th>
+ <td> </em><a href='https://galaxy.web.pasteur.fr/'>Pasteur_galaxy</a>: An open and sustainable Galaxy instance for NGS data analysis<em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/SouthAmerica) <a href='https://www.iscb.org/conference-program/iscb-latinamerica2016-agenda-glance'>ISCB-Latin America</a>, Buenos Aires, Argentina </td>
+ <td> Oussama Souiai </td>
+ </tr>
+ <tr>
+ <th> November 21-23 </th>
+ <td> </em><a href='https://urgi.versailles.inra.fr/content/view/full/3794'>Annotation of transposable elements</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) URGI, INRA Versailles, France </td>
+ <td> <a href='https://urgi.versailles.inra.fr/content/view/full/3794'>Contact</a> </td>
+ </tr>
+ <tr>
+ <th> November 28 - December 2 </th>
+ <td> </em><a href='http://workflow4metabolomics.org/training/w4mcourse2016'>Traitement des donnéesmétabolomiques sous Galaxy</a><em> <div class='indent red'>Les pré-inscriptions sont ouvertes jusqu'au 15 juillet 2016</div> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.sb-roscoff.fr/'>Station Biologique, Roscoff</a>, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:contact@workflow4metabolomics.org">Contact</a> </td>
+ </tr>
+ <tr>
+ <th> November 29 </th>
+ <td> </em><a href='https://www.abdn.ac.uk/genomics/documents/201617_Workshops/Genome_Assembly_2016.pdf'>Genome Assembly and Annotation</a><em> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) <a href='http://www.abdn.ac.uk/genomics/bioinformatics/training/'>University of Aberdeen</a>, Scotland, United Kingdom </td>
+ <td> <a href="mailto:s.shaw@abdn.ac.uk">Sophie Shaw</a> </td>
+ </tr>
+ <tr>
+ <td colspan=4 style=" text-align: center; background-color: #eef;"> <span style="font-size: larger;"> </strong>2017<strong> </span> </td>
+ </tr>
+ <tr>
+ <th> January 14-18 </th>
+ <td> <a href='/Events/PAG2017'>Galaxy @ Plant & Animal Genome XXIV (PAG 2017)</a> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/NorthAmerica) San Diego, California, United States </td>
+ <td> <a href='/DaveClements'>Dave Clements</a> </td>
+ </tr>
+ <tr>
+ <th> January 16-19 </th>
+ <td> </strong><a href='https://www.france-bioinformatique.fr/en/evenements/EGDW2017'>European Galaxy Developer Workshop</a><strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Strasbourg, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:egdw2017.oc@groupes.france-bioinformatique.fr">Organisers</a> </td>
+ </tr>
+ <tr>
+ <td colspan=4 style=" background-color: #eef;"> </td>
+ </tr>
+ <tr>
+ <th> February 3-9 </th>
+ <td> </strong><a href='http://www.embl-abr.org.au/GAMe2017'>Galaxy Australasia Meeting (GAMe 2017)</a><strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Australia) University of Melbourne, Victoria, Australia </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href='https://www.embl-abr.org.au/organisers/'>Organisers</a> </td>
+ </tr>
+ <tr>
+ <td colspan=4 style=" background-color: #eef;"> </td>
+ </tr>
+ <tr>
+ <th> June 26-30 </th>
+ <td> </strong><a href='https://gcc2017.sciencesconf.org/'>2017 Galaxy Community Conference (GCC2017)</a><strong> </td>
+ <td> PLACEHOLDER_INCLUDE(/Events/Badges/Europe) Montpellier, France </td>
+ <td> PLACEHOLDER_INCLUDE(/Teach/GTN/Badge16) <a href="mailto:gcc2017_organization@groupes.france-bioinformatique.fr">Organisers</a> </td>
+ </tr>
+</table>
+
+
+<table>
+ <tr>
+ <td style=" border: none;"> <a href='/Teach/Trainers'><img src='/Images/Icons/GTN32.png' alt='Designates a training event offered by GTN Member' width="24" /></a> </td>
+ <td style=" border: none;"> <span style="font-size: smaller;"> <a href='/Teach/Trainers'>Designates a training event offered by GTN member(s)</a> </span> </td>
+ </tr>
+</table>
+
+
+See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on other events of interest to the community.
+
+----
+
+# New Publications
+
+**87 new publications** referencing, using, extending, and implementing Galaxy were added to the [Galaxy CiteULike Group](http://www.citeulike.org/group/16008/) in October.
+
+Some highlights from last month:
+
+* [Flexible Container-Based Computing Platform on Cloud for Scientific Workflows](http://dx.doi.org/10.1109/icccri.2016.17)
+ Kai Liu, Kento Aida, Shigetoshi Yokoyama, Yoshinobu Masatani, In 2016 International Conference on Cloud Computing Research and Innovations (ICCCRI) (May 2016), pp. 56-63, doi:10.1109/icccri.2016.17
+
+* [Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species](http://dx.doi.org/10.1186/s12864-016-3118-z)
+ Weizhong Li, R. Alexander Richter, Yunsup Jung, Qiyun Zhu, Robert W. Li, *BMC Genomics*, Vol. 17, No. 1. (27 September 2016), doi:10.1186/s12864-016-3118-z
+
+* [Software Provisioning Inside a Secure Environment as Docker Containers Using Stroll File-System](http://dx.doi.org/10.1109/ccgrid.2016.106)
+ Abdulrahman Azab, Diana Domanska, In 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) (May 2016), pp. 674-683, doi:10.1109/ccgrid.2016.106
+
+* [An Automated Tool Profiling Service for the Cloud](http://dx.doi.org/10.1109/ccgrid.2016.57)
+ Ryan Chard, Kyle Chard, Bryan Ng, et al., In 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) (May 2016), pp. 223-232, doi:10.1109/ccgrid.2016.57
+
+* [ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database](http://dx.doi.org/10.1093/bioinformatics/btw136)
+ Ying Yang, Xiaotao Jiang, Benli Chai, et al., *Bioinformatics*, Vol. 32, No. 15. (01 August 2016), pp. 2346-2351, doi:10.1093/bioinformatics/btw136
+
+* [APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data](http://dx.doi.org/10.1021/acs.jproteome.6b00660)
+ Brent M. Kuenzi, Adam L. Borne, Jiannong Li, et al., *J. Proteome Res.* (29 September 2016), doi:10.1021/acs.jproteome.6b00660
+
+## Tagged Publications
+
+The new papers were tagged with:
+
+<table>
+ <tr>
+ <th> # </th>
+ <th style=" width: 19%;"> Tag </th>
+ <td rowspan=5 style=" border: none;"> &nbsp;&nbsp; </td>
+ <th> # </th>
+ <th style=" width: 19%;"> Tag </th>
+ <td rowspan=5 style=" border: none;"> &nbsp;&nbsp; </td>
+ <th> # </th>
+ <th style=" width: 19%;"> Tag </th>
+ <td rowspan=5 style=" border: none;"> &nbsp;&nbsp; </td>
+ <th> # </th>
+ <th style=" width: 19%;"> Tag </th>
+ </tr>
+ <tr>
+ <td style=" text-align: right;"> 5 </td>
+ <td> <a href='http://bit.ly/gxyculcloud'>Cloud</a> </td>
+ <td style=" text-align: right;"> 3 </td>
+ <td> <a href='http://bit.ly/gxyculother'>Other</a> </td>
+ <td style=" text-align: right;"> 1 </td>
+ <td> <a href='http://bit.ly/gxyculshared'>Shared</a> </td>
+ <td style=" text-align: right;"> 7 </td>
+ <td> <a href='http://bit.ly/gxyculusemain'>UseMain</a> </td>
+ </tr>
+ <tr>
+ <td style=" text-align: right;"> - </td>
+ <td> <a href='http://bit.ly/gxyculhowto'>HowTo</a> </td>
+ <td style=" text-align: right;"> - </td>
+ <td> <a href='http://bit.ly/gxyculproject'>Project</a> </td>
+ <td style=" text-align: right;"> 6 </td>
+ <td> <a href='http://bit.ly/gxycultools'>Tools</a> </td>
+ <td style=" text-align: right;"> 22 </td>
+ <td> <a href='http://bit.ly/gxyculusepublic'>UsePublic</a> </td>
+ </tr>
+ <tr>
+ <td style=" text-align: right;"> 3 </td>
+ <td> <a href='http://bit.ly/gxyculisgalaxy'>IsGalaxy</a> </td>
+ <td style=" text-align: right;"> 14 </td>
+ <td> <a href='http://bit.ly/gxyculrefpublic'>RefPublic</a> </td>
+ <td style=" text-align: right;"> - </td>
+ <td> <a href='http://bit.ly/gxyculusecloud'>UseCloud</a> </td>
+ <td style=" text-align: right;"> - </td>
+ <td> <a href='http://bit.ly/gxyculviz'>Visualization</a> </td>
+ </tr>
+ <tr>
+ <td style=" text-align: right;"> 50 </td>
+ <td> <a href='http://bit.ly/gxyculmethods'>Methods</a> </td>
+ <td style=" text-align: right;"> 4 </td>
+ <td> <a href='http://bit.ly/gxyculrepro'>Reproducibility</a> </td>
+ <td style=" text-align: right;"> 8 </td>
+ <td> <a href='http://bit.ly/gxyculuselocal'>UseLocal</a> </td>
+ <td style=" text-align: right;"> 14 </td>
+ <td> <a href='http://bit.ly/gxyculworkbench'>Workbench</a> </td>
+ </tr>
+</table>
+
+
+----
+
+# Galaxy Arabic Community Launched
+
+<div class='left'>![Galaxy Arabic Speaking Community](/Community/Arabic/GalaxyArabic400.png)</div>
+
+<table>
+ <tr>
+ <td style=" text-align: right; border: none;"> أرشيف للقائمة البريدية جالاكسي بالعربية يحتوي على الاخبار والمناقشات والاعلانات الخاصة بمستخدمي جالاكسي من البلاد الناطقة بالعربية نرحب بانضمام أي شخص مهتم بالجلاكسي بلاتفورم<br />جالاكسي هي بلاتفورم لتحليل المعلومات الحيوية باستخدام أدوات برمجة أونلاين مجانا تتميز بأنها متاحة للجميع ونتائجها تتميز بالشفافية وبالقدرة على الحصول على نفس النتائج عند إجراء التحليل مرات عديدة.<br />السهولة : يمكن لأي شخص استخدام جالاكسي حتى لو لم تكن لديه خبرة كافية بتحليل المعلومات الحيوية<br />النتائج : تحصل على نفس النتائج مهما أجريت التجربة مرات عديدة وهذا يميز جالاكسي عن العديد من الأدوات الاخرى <br />الشفافية : يمكنك أن تشارك ما توصلت إليه مع زملائك والعالم كله ويمكنك النشر أيضا .<br />جالاكسي مفتوحة لكل المنظمات والسرفر الرئيسي يمكنك من إجراء تحليل على المعلومات الجينية وإيضا توجد مواد تعليمية للتدريب وأماكن العمل وخدمات النشر يمكنك استخدام جالاكسي أونلاين ويمكنك أيضا تنزيلها على الكمبيوتر الخاص بك واستخدامها </td>
+ </tr>
+</table>
+
+
+----
+
+We are pleased to announce the launch of the **[Galaxy Arabic community](/Community/Arabic).** Galaxy Arabic supports and promotes Galaxy activity for the Arabic speaking community and in Arabic speaking regions of the world.
+
+If you are interested in joining the community, please
+* Follow [@Galaxy_Arabic on Twitter](http://twitter.com/galaxy_arabic)
+* Join the [Galaxy Arabic mailing list](https://lists.galaxyproject.org/listinfo/galaxy-arabic). Regional Galaxy news will be posted here, and you can also ask fellow Arabic speakers support questions.
+* Join the [Galaxy Arabic Facebook group](http://bit.ly/2ek7fTh)
+
+We look forward to connecting and growing the Arabic speaking Galaxy community.
+
+Thanks,
+
+[abdelazeem_abdelhameed2015505@yahoo.com](Abdelazeem Abdelhameed) and [Dave Clements](/DaveClements)
+
+
+
+# Who's Hiring
+
+<div class='right'><br />![Please Help! Yes you!](/Images/GalaxyIsExpandingCloud.png)</div>
+
+The Galaxy is expanding! Please help it grow.
+
+* [Traitement de données métaomiques sur les écosystèmes microbiens](http://www.sfbi.fr/content/traitement-de-donn%C3%A9es-m%C3%A9taomiques-sur-les-%C3%A9cosyst%C3%A8mes-microbiens), Irstea, équipe BIOMIC, Antony, France
+* [Développement d’outil sous galaxy](http://www.sfbi.fr/content/d%C3%A9veloppement-d%E2%80%99outil-sous-galaxy-pour-la-reconstruction-phylog%C3%A9n%C3%A9tique-et-pour-l%E2%80%99analyse-st) pour la reconstruction phylogénétique et pour l’analyse statistique liée à la métagénomique, INRA GABI, Jouy en Josas France
+* [Development Scientist (Bioinformatics)](http://chk.tbe.taleo.net/chk05/ats/careers/requisition.jsp?org=NEB&cws=1&rid=272), New England Biolabs, Ipswich, Massachusetts, United States.
+* [Post Doctoral Research Associate](http://www.nature.com/naturejobs/science/jobs/594831-postdoctoral-scholar-position-in-plant-bioinformatics-and-cyberinfrastructure), Entomology and Plant Pathology, University of Tennessee, Knoxville.
+* [6 month position](https://twitter.com/bioinformAnt/status/773465361127710720) at [Public Health England](https://www.gov.uk/government/organisations/public-health-england) working [National Microbiology Laboratory](https://www.nml-lnm.gc.ca/index-eng.htm) in Canada to compare antimicrobial resistance isolates and software using [IRIDA](http://www.irida.ca/)/Galaxy
+* [Intégration d'outils pour la métagénomique phytovirale dans Galaxy](http://www.sfbi.fr/content/int%C3%A9gration-doutils-pour-la-m%C3%A9tag%C3%A9nomique-phytovirale-dans-galaxy-0), INRA, Bordeaux, France
+* [Post­doctoral Research Position](https://drive.google.com/file/d/0B5_H88SQ1C_7Z3dJY3FzU0hQMUU/view?pref=2&pli=1), Multi­omic Bioinformatics, University of Minnesota
+
+Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the [Galaxy News feed](/News) and include it in next month's [update](/GalaxyUpdates).
+
+<br />
+
+----
+
+
+# Public Galaxy Server News
+
+There are [over 80 publicly accessible Galaxy servers](/PublicGalaxyServers) and [five semi-public Galaxy services](/SemiPublicGalaxyServers). Here's what happened with them in October.
+
+## New Public Galaxy Servers
+
+### Insitut Curie
+
+<div class='right solid'><a href='https://galaxy-public.curie.fr/'><img src='/PublicGalaxyServers/InstitutCurieGalaxy.png' alt='Institut Curie' width="200" /></a></div>
+
+[Institut Curie Galaxy](https://galaxy-public.curie.fr/) is a general purpose genomic Galaxy server that contains tools for Ion Torrent data, many RNA-Seq tools, [ncPRO-seq](https://www.ncbi.nlm.nih.gov/pubmed/23044543), [RSAT](https://www.ncbi.nlm.nih.gov/pubmed/22156162), Nebula tools, copy number and LOH tools, and NGS diagnostic tools. It includes a [wealth of published histories](https://galaxy-public.curie.fr/history/list_published) and tutorials and screencasts, and [galaxy.contact@curie.fr](email support) are available.
+
+The server is sponsored by [Institut Curie](http://www.curie.fr/) and anyone can use it, once you have created a login.
+
+### Alveo
+
+<div class='left solid'><a href='http://galaxy.alveo.edu.au/'><img src='/PublicGalaxyServers/AlveoLogoWText.png' alt='Alveo' width="200" /></a></div>
+
+The [Alveo Galaxy server](http://galaxy.alveo.edu.au/) applies Galaxy to the Human Communication Science (HCS). "[Alveo](http://alveo.edu.au/about/) is a platform to support research in Human Communication. The Alveo repository holds large collections of speech, video and text data and provides an API for use by research tools. Our Galaxy server implements a number of research tools for working with speech and text data and we are exploring how best to adapt tools to this environment. Current tools allow data to be pulled from the Alveo repository and processed with various text and speech processing methods."
+
+[In-depth tutorials](http://alveo.edu.au/tutorials/), [extensive help pages](http://alveo.edu.au/help/) and an [Alveo support forum and FAQ](https://support.alveo.edu.au/support/home) are available.
+
+You'll need to create an account to use the server. Alveo is sponsored by many [organizations and universities](http://alveo.edu.au/about/#colophon) across Australia.
+
+### APOSTL
+
+<div class='right solid'><a href='http://apostl.moffitt.org/'><img src='/PublicGalaxyServers/APOSTLlogo300.png' alt='Automated Processing of SAINT Templated Layouts' width="200" /></a></div>
+
+The [APOSTL Galaxy Server](http://apostl.moffitt.org/) supports *Automated Processing of SAINT Templated Layouts (APOSTL).* It features a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. APOSTL utilizes Significance Analysis of INTeractome (SAINT), a popular command-line software for analyzing AP data. APOSTL can process AP results from !MaxQuant, Scaffold, !PeptideShaker, or any software that can export mzIdentML. Publication-quality visualizations are supported and include interactive bubble plots, protein-protein interaction networks through Cytoscape.js integration, and pathway enrichment/gene ontology plots.
+
+See [APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data](http://dx.doi.org/10.1021/acs.jproteome.6b00660), Brent M. Kuenzi, et al., *J. Proteome Res.,* DOI: 10.1021/acs.jproteome.6b00660 and
+[An Interactive Tool for Reproducible Analysis of Affinity Proteomics Data](http://sched.co/73yr) (presented by Paul A Stewart at GCC2016).
+
+A [Quick Start guide](http://apostl.moffitt.org/) is available. APOSTL support is provided by the [Haura](http://labpages2.moffitt.org/haura) and [Rix](https://moffitt.org/research-science/researchers/uwe-rix/) labs at the [Moffitt Cancer Center](https://moffitt.org/).
+
+### ARGs-OAP
+
+<div class='left solid'><a href='http://smile.hku.hk/SARGs'><img src='/PublicGalaxyServers/ARGs-OAP.png' alt='Structured ARG reference database Online Analysis Platform' width="200" /></a></div>
+
+The [ARGs-OAP Galaxy Server](http://smile.hku.hk/SARGs) performs fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. "SARG was curated to remove redundant sequences and optimized to facilitate query sequence identification by similarity. A database with a hierarchical structure (type-subtype-reference sequence) was then constructed to facilitate classification (assigning ARG-like sequence to type, subtype and reference sequence) of sequences identified through similarity search." The server integrates "ARDB and CARD, the two most commonly used databases into *SARG DB* and uses a hybrid functional gene annotation pipeline to do fast annotation and classification of ARG-like sequences from metagenomic data.
+
+See [ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database](http://dx.doi.org/10.1093/bioinformatics/btw136), Ying Yang et al., *Bioinformatics* (2016) 32 (15): 2346-2351. doi: 10.1093/bioinformatics/btw136. Source code is available on [GitHub](https://github.com/biofuture/Ublastx_stageone). ARGs-OAP has a [manual](https://github.com/biofuture/Ublastx_stageone) as well.
+
+The server is supported by the Environmental Biotechnology Laboratory, [Department of Civil Engineering](https://www.civil.hku.hk/h4v3_2_study_here.html), [The University of Hong Kong](http://www.hku.hk/); the School of Marine Sciences, [Sun Yat-Sen University](http://www.sysu.edu.cn/), Guangzhou, China, and [Department of Plant, Soil, and Microbial Sciences](http://www.psm.msu.edu/), [Michigan State University](http://www.msu.edu/)
+
+
+## Semi-Public Galaxy Services
+
+Jetstream was officially launched in September and was added to the [Semi-Public Galaxy Services list](/SemiPublicGalaxyServers):
+
+### US: Galaxy on Jetstream Cloud update
+
+<div class='right'>![](https://www.nsf.gov/news/mmg/media/images/jetstream_logo_f_fe60185c-962f-4c1f-99bf-e6ec82d54c21.jpg)</div>
+
+[Galaxy release 16.07](/News/2016_07_GalaxyRelease) is now available for free on the Jetstream cloud. This image contains the updated Galaxy application with a toolset that closely matches that of the public Galaxy server available at [usegalaxy.org](https://usegalaxy.org/) as well as a complete set of reference genomes available on that same server. Availability of the reference data was realized by enabling a connection to a (CVMFS-based) replica server that offers access to approximately 3TB of reference data (vs. ~50GB in the previous version of the image). An additional benefit of such integration is that the reference data is no longer stored on the machine image, reducing the size of that image to about 10GB, leaving more space for the analysis data. The base operating system is Ubuntu 14.04. The image was built using the cloud_setup flavor of the [GalaxyKickStart](https://github.com/ARTbio/GalaxyKickStart) Ansible playbook.
+
+# Galaxy Community Hubs
+
+<table>
+ <tr>
+ <td style=" text-align: center; border: none; width: 20%;"> <a href='/Teach'><img src='/Images/GalaxyLogos/GTNLogo300.png' alt='Galaxy Training Network' height="100" /></a> </td>
+ <td style=" text-align: center; border: none; width: 20%;"> <a href='/Community/Logs'><img src='/Images/Logos/LogBoardWText200.png' alt='Galaxy Community Log Board' height="100" /></a> </td>
+ <td style=" text-align: center; border: none; width: 20%;"> <a href='/Community/Deployments'><img src='/Images/Logos/GalaxyDeploymentCatalog200.png' alt='Galaxy Deployment Catalog' height="100" /></a> </td>
+ </tr>
+ <tr>
+ <td style=" text-align: center; vertical-align: top; border: none;"> </strong>Share your <a href='/Teach/Resources#add-a-training-resource'>training resources</a> and <a href='/Teach/Trainers#add-a-trainer'>experience</a> </em>now<em> <strong> </td>
+ <td style=" text-align: center; vertical-align: top; border: none;"> </strong><a href='/Community/Logs#add-a-log-page'>Share your experience</a> </em><a href='/Community/Logs#add-a-log-page'>now</a><em> <strong> </td>
+ <td style=" text-align: center; vertical-align: top; border: none;"> </strong><a href='/Community/Deployments#add-your-galaxy-deployment'>Describe your instance</a> </em><a href='/Community/Deployments#add-your-galaxy-deployment'>now</a><em> <strong> </td>
+ </tr>
+</table>
+
+<br />
+
+One new member organization joined the [Galaxy Training Network](/Teach/GTN) and 3 resources were added to the [Galaxy Training Resources directory](/Teach/Resources) in October:
+
+* [Peter Mac](/Teach/Trainers#peter-mac) in Melbourne, Australia Joined GTN
+* [Arabic language Intro to Galaxy slides](/Teach/Resource/GalaxyIntroArabic)
+* [ChIP-Seq avec Galaxy](/Teach/Resource/ChIP-SeqAvecGalaxy) (video in French)
+* [Analyse de données ExomeSeq avec Galaxy](/Teach/Resource/ExomeSeqAvecGalaxy) (video in French)
+* [Détection de variants structuraux](/Teach/Resource/DétectionDeVariantsStructuraux) (video in French)
+
+----
+
+# Releases
+
+<div class='right'><br /><a href='https://pypi.python.org/pypi/planemo/'><img src='/Images/GalaxyLogos/planemo-logo.png' alt='' width="200" /></a></div>
+
+## Planemo 0.34.1
+
+[Planemo](https://pypi.python.org/pypi/planemo) is a set of command-line utilities to assist in building tools for the Galaxy project. **Planemo saw two releases in October.** These included Conda fixes, new mulled features, and browser and pip related changes too.
+
+See [GitHub for details](https://github.com/galaxyproject/planemo/blob/0.34.1/HISTORY.rst#0341-2016-10-12).
+
+
+## galaxy-lib 16.10.10
+
+galaxy-lib is a subset of the Galaxy core code base designed to be used as a library. This subset has minimal dependencies and should be Python 3 compatible. It's available from [GitHub](https://github.com/galaxyproject/galaxy-lib) and [PyPi](https://pypi.python.org/pypi/galaxy-lib).
+
+The October releases (8 of them!) added mulled and Conda enhancements.
+
+
+## Earlier Releases
+
+Other packages that have been released in the prior 4 months.
+
+### Galaxy v16.07
+
+<div class='right'><a href='http://getgalaxy.org'><img src='/Images/Logos/GalaxyNewLogo_GalaxyProject_Trans.png' alt='GalaxyProject' width="200" /></a></div>
+
+The [Galaxy Committers team](https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organization.rst) is pleased to announce the **[July 2016 (v16.07) release of Galaxy](https://docs.galaxyproject.org/en/master/releases/16.07_announce.html)**.
+
+<span style="font-size: larger;"> Highlights </span>
+
+**Shift of Galaxy tool dependencies to Conda**
+
+Galaxy admins obtained the ability to install Galaxy tool’s dependencies using the Conda package manager. This is a Beta feature and we encourage interested deployers to opt-in by modifying configuration. Documentation that explains this switch and answers FAQ is [available](https://docs.galaxyproject.org/en/master/admin/conda_faq.html).
+
+**Dynamic tool destinations**
+
+Our friends from Canada National Microbiology Laboratory enhanced Galaxy with feature that allows dynamic mapping of tools to destinations based on finer grained admin-specified rules. Please see the [wiki](/Admin/Config/Jobs#dynamic-destination-mapping). Implemented in [PR #2579](https://github.com/galaxyproject/galaxy/pull/2579).
+
+**Galaxy chat**
+
+Admins can now plug in the included communication server to enable users of their instance to use real-time chat within the Galaxy interface. Please see the [documentation](https://docs.galaxyproject.org/en/master/admin/chat.html) to learn how to activate and use this feature. Implemented in [PR #2515](https://github.com/galaxyproject/galaxy/pull/2515).
+
+<span style="font-size: larger;"> [Github](https://github.com/galaxyproject/galaxy) </span>
+
+**New Galaxy repository**
+```
+$ git clone -b release_16.07 https://github.com/galaxyproject/galaxy.git
+```
+
+
+**Update of existing Galaxy repository**
+```
+$ git checkout release_16.07 && git pull --ff-only origin release_16.07
+```
+
+
+See [our wiki](/Develop/SourceCode) for additional details regarding the source code locations.
+
+<br />
+
+See the [full release notes](https://docs.galaxyproject.org/en/master/releases/16.07_announce.html) for more.
+
+#### Galaxy Docker Image 16.07
+
+And, thanks to [Björn Grüning](https://github.com/bgruening), there is also now [a Docker image for Galaxy 16.07](https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.07) as well.
+
+### CloudBridge 0.1.1
+
+[CloudBridge](https://github.com/gvlproject/cloudbridge) provides a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. The latest release adds support for advanced networking management and !OpenStack Keystone v3 support (required to use NSF Jetstream cloud).
+
+### BioBlend 0.8.0
+
+[BioBlend](http://bioblend.readthedocs.org/) is a Python library for interacting with CloudMan and Galaxy‘s API. !BioBlend makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy.
+
+See the [release notes](https://github.com/galaxyproject/bioblend/releases) for what's new in release 0.8.0.
+
+<div class='right'><br /><a href='https://pypi.python.org/pypi/pulsar-app/'><img src='/Images/GalaxyLogos/pulsar_transparent.png' alt='Pulsar' width="170" /></a></div>
+
+### Pulsar 0.7.1 - 0.7.2
+
+[Pulsar](https://pypi.python.org/pypi/pulsar-app/) updates were released in August. Pulsar is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transferred back to the Galaxy server - eliminating the need for a shared file system.
+
+
+### And the rest ...
+
+Other Galaxy packages that haven't had a release in the past four months can be [found on GitHub](https://github.com/galaxyproject).
+
+----
+
+<div class='right'><br /><a href='http://toolshed.g2.bx.psu.edu/'><img src='/Images/Logos/ToolShed.jpg' alt='Galaxy ToolShed' width=150 /></a></div>
+
+# ToolShed Contributions
+
+[Tool Shed contributions for October](/ToolShed/Contributions/2016_10).
+
+And, we are happy to announce that [Lance Parsons](https://github.com/lparsons) just joined the [/IUC](/IUC) to help the Galaxy community with improved and more user-friendly tools.
diff --git a/GetInvolved/index.md b/GetInvolved/index.md
index f592b11..131dd5c 100644
--- a/GetInvolved/index.md
+++ b/GetInvolved/index.md
@@ -36,7 +36,7 @@ Have an idea for a feature? Found a bug? You can submit reports on issues and
# Setup a Public Server
-If and when you [setup your own Galaxy instance](/Admin/GetGalaxy), you can make it available to researchers outside your organization. A number of groups [have done this](/Public Galaxy Servers), often making a different tool set from Main available. See [/Public Galaxy Servers](/Public Galaxy Servers).
+If and when you [setup your own Galaxy instance](/Admin/GetGalaxy), you can make it available to researchers outside your organization. A number of groups [have done this](/PublicGalaxyServers), often making a different tool set from Main available. See [Public Galaxy Servers](/PublicGalaxyServers).
# Share Your Deployment Experience
diff --git a/LargeDatasets/index.md b/LargeDatasets/index.md
index 8a73240..5692217 100644
--- a/LargeDatasets/index.md
+++ b/LargeDatasets/index.md
@@ -2,5 +2,3 @@
pagetitle: Large Datasets
----
-
-PLACEHOLDER_INCLUDE(/Under Construction)
diff --git a/Learn/CustomBuildForVis/index.md b/Learn/CustomBuildForVis/index.md
index 15aa86b..471bdb6 100644
--- a/Learn/CustomBuildForVis/index.md
+++ b/Learn/CustomBuildForVis/index.md
@@ -2,5 +2,3 @@
pagetitle: Custom Build for Visualization
----
-
-PLACEHOLDER_INCLUDE(/Under Construction)
diff --git a/Learn/DataSources/index.md b/Learn/DataSources/index.md
new file mode 100644
index 0000000..dcf05ff
--- /dev/null
+++ b/Learn/DataSources/index.md
@@ -0,0 +1,10 @@
+----
+autotoc: true
+pagetitle: Data Sources
+----
+
+
+PLACEHOLDER_INCLUDE(/Learn/LinkBox)
+<div class='left'></div>
+
+# Data sources in Galaxy
diff --git a/MailingListDetail/index.md b/MailingListDetail/index.md
index 9f186ac..a889d2d 100644
--- a/MailingListDetail/index.md
+++ b/MailingListDetail/index.md
@@ -8,6 +8,9 @@ Galaxy has several active [mailing lists](/MailingLists), each for a different p
<th> Archives (see <a href='/MailingLists#searching'>Searching</a>) </th>
</tr>
<tr>
+ <th style=" background-color: #eeeeee;"> General lists </th>
+ </tr>
+ <tr>
<th> <a href='http://announce.list.galaxyproject.org/'>galaxy-announce</a> </th>
<td> Announcements of interest to the Galaxy community. <em>Moderated and low volume.</em> </td>
<td> </td>
@@ -17,7 +20,22 @@ Galaxy has several active [mailing lists](/MailingLists), each for a different p
<th> <a href='http://dev.list.galaxyproject.org/'>galaxy-dev</a> </th>
<td> Local installation, configuration, and tool integration help, or to propose new features. <em><a href='/GalaxyProject/Statistics#mailing-lists'>High volume</a>.</em> </td>
<td> <a href="mailto:galaxy-dev AT lists DOT galaxyproject DOT org">galaxy-dev AT lists DOT galaxyproject DOT org</a> </td>
- <td> <a href='http://dev.list.galaxyproject.org/'>Nabble</a>, <a href='http://dir.gmane.org/gmane.science.biology.galaxy.devel'>GMane</a>, <a href='http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/info.html'>Mail-Archive.com</a>, <a href='http://osdir.com/ml/galaxy-development-source-control/'>OSDir</a>, <a href='https://lists.galaxyproject.org/pipermail/galaxy-dev/'>Mailman</a> </td>
+ <td> <a href='http://dev.list.galaxyproject.org/'>Nabble</a>, <a href='http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/info.html'>Mail-Archive.com</a>, <a href='http://osdir.com/ml/galaxy-development-source-control/'>OSDir</a>, <a href='https://lists.galaxyproject.org/pipermail/galaxy-dev/'>Mailman</a> </td>
+ </tr>
+ <tr>
+ <th style=" background-color: #eeeeee;"> <a href='/Community'>Regional, Domain, and Language based lists</a> </th>
+ </tr>
+ <tr>
+ <th> <a href='http://galaxy-arabic.2360877.n4.nabble.com/'>galaxy-arabic (العربية Galaxy)</a> </th>
+ <td> Regional news, announcements, discussion, and support within the <a href='/Community/Arabic'>Arabic speaking Galaxy Community</a>. Much of the content on this list is in Arabic. </td>
+ <td> <a href="mailto:galaxy-arabic AT lists DOT galaxyproject DOT org">galaxy-arabic AT lists DOT galaxyproject DOT org</a> </td>
+ <td> <a href='http://galaxy-arabic.2360877.n4.nabble.com/'>Nabble</a>, <a href='https://lists.galaxyproject.org/pipermail/galaxy-arabic/'>Mailman</a> </td>
+ </tr>
+ <tr>
+ <th> <a href='http://france.list.galaxyproject.org/'>galaxy-france</a> </th>
+ <td> Cette liste est destinée à l'information (et aux discussions) de la Communauté francaise Galaxy. (This list is for announcements to (and discussion within) the French Galaxy Community. Most list content is in French.) <em><a href='/GalaxyProject/Statistics#mailing-lists'>Faible volume / Low volume</a>.</em> </td>
+ <td> <a href="mailto:galaxy-france AT lists DOT galaxyproject DOT org">galaxy-france AT lists DOT galaxyproject DOT org</a> </td>
+ <td> <a href='http://france.list.galaxyproject.org/'>Nabble</a>, <a href='https://lists.galaxyproject.org/pipermail/galaxy-france/'>Mailman</a> </td>
</tr>
<tr>
<th> <a href='http://proteomics.list.galaxyproject.org/'>galaxy-proteomics</a> </th>
@@ -32,12 +50,6 @@ Galaxy has several active [mailing lists](/MailingLists), each for a different p
<td> <a href='http://galaxy-training-mailing-list-archive.35427.n7.nabble.com/'>Nabble</a>, <a href='https://lists.galaxyproject.org/pipermail/galaxy-training/'>Mailman</a> </td>
</tr>
<tr>
- <th> <a href='http://france.list.galaxyproject.org/'>galaxy-france</a> </th>
- <td> Cette liste est destinée à l'information (et aux discussions) de la Communauté francaise Galaxy. (This list is for announcements to (and discussion within) the French Galaxy Community. Most list content is in French.) <em><a href='/GalaxyProject/Statistics#mailing-lists'>Faible volume / Low volume</a>.</em> </td>
- <td> <a href="mailto:galaxy-france AT lists DOT galaxyproject DOT org">galaxy-france AT lists DOT galaxyproject DOT org</a> </td>
- <td> <a href='http://france.list.galaxyproject.org/'>Nabble</a>, <a href='https://lists.galaxyproject.org/pipermail/galaxy-france/'>Mailman</a> </td>
- </tr>
- <tr>
<th> <a href='https://groups.google.com/a/groups.galaxyproject.org/forum/#!forum/galaxy-uk'>galaxy-uk</a> </th>
<td> Mailing list for the <a href='http://galaxy-community.org.uk/'>Galaxy-UK community</a>. This is <em>not</em> a support list. </td>
<td> <a href="mailto:galaxy-uk AT groups DOT galaxyproject DOT org">galaxy-uk AT groups DOT galaxyproject DOT org</a> </td>
diff --git a/MailingLists/index.md b/MailingLists/index.md
index 3022cd8..781908d 100644
--- a/MailingLists/index.md
+++ b/MailingLists/index.md
@@ -97,6 +97,16 @@ To subscribe or unsubscribe from a list, click the link below and then follow th
<td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-dev#subscribers'>unsubscribe</a> </td>
</tr>
<tr>
+ <th> galaxy-arabic </th>
+ <td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-arabic'>subscribe</a> </td>
+ <td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-arabic#subscribers'>unsubscribe</a> </td>
+ </tr>
+ <tr>
+ <th> galaxy-france </th>
+ <td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-france'>subscribe</a> </td>
+ <td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-france#subscribers'>unsubscribe</a> </td>
+ </tr>
+ <tr>
<th> galaxy-proteomics </th>
<td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-proteomics'>subscribe</a> </td>
<td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-proteomics#subscribers'>unsubscribe</a> </td>
@@ -107,11 +117,6 @@ To subscribe or unsubscribe from a list, click the link below and then follow th
<td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-training'>unsubscribe</a> </td>
</tr>
<tr>
- <th> galaxy-france </th>
- <td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-france'>subscribe</a> </td>
- <td> <a href='https://lists.galaxyproject.org/listinfo/galaxy-france#subscribers'>unsubscribe</a> </td>
- </tr>
- <tr>
<th> galaxy-uk </th>
<td> <a href='https://groups.google.com/a/groups.galaxyproject.org/forum/#!forum/galaxy-uk'>subscribe</a> </td>
<td> <a href='https://groups.google.com/a/groups.galaxyproject.org/forum/#!forum/galaxy-uk'>unsubscribe</a> </td>
diff --git a/Main/index.md b/Main/index.md
index fe91e91..a2903b7 100644
--- a/Main/index.md
+++ b/Main/index.md
@@ -14,7 +14,7 @@ The Galaxy **Main** instance is available as a free public service at [UseGalaxy
Anyone can use the public servers, with or without an account, but Galaxy [user accounts](/Learn/User Accounts) are simple to create (email, password, user name and go!). With an account, data quotas are increased and full functionality across sessions opens up, such as naming, saving, sharing, and publishing Galaxy objects (Histories, Workflows, Datasets, Pages). Remember, Galaxy's **[Terms and Conditions](https://usegalaxy.org/static/terms.html)** specifically declare a "one-account per user" requirement.
-To understand if Main is the right Galaxy choice for your project, please see [Choices](/BigPicture/Choices) for a description of the different types of possible Galaxy instances. Galaxy is available to [install as a local instance](/Admin/GetGalaxy), to run [on the cloud](/CloudMan), to use at other [/Public Galaxy Servers](/Public Galaxy Servers), or preinstalled on your own Galaxy [appliance](http://www.bioteam.net/slipstream/galaxy-edition).
+To understand if Main is the right Galaxy choice for your project, please see [Choices](/BigPicture/Choices) for a description of the different types of possible Galaxy instances. Galaxy is available to [install as a local instance](/Admin/GetGalaxy), to run [on the cloud](/CloudMan), to use at other [Public Galaxy Servers](/PublicGalaxyServers), or preinstalled on your own Galaxy [appliance](http://www.bioteam.net/slipstream/galaxy-edition).
## Information about Main
diff --git a/Marten/index.md b/Marten/index.md
index 8f65093..3034f98 100644
--- a/Marten/index.md
+++ b/Marten/index.md
@@ -1,6 +1,9 @@
+<div class='right'>
+<br />
+<a href='/Marten'><img src='/GalaxyTeam/marten.jpg' alt='Marten Čech' /></a>
+</div>
-#language en
-# Martin Cech
+# Martin Čech
* Galaxy project member.
* Email: [marten AT SPAMFREETRALALALA bx.psu DOT edu](marten AT SPAMFREETRALALALA bx.psu DOT edu)
* Twitter: https://twitter.com/martenson
diff --git a/Microarrays/index.md b/Microarrays/index.md
index e7312c6..3e29f58 100644
--- a/Microarrays/index.md
+++ b/Microarrays/index.md
@@ -2,7 +2,7 @@ The [main Galaxy server](/Main) does not currently (2011/07) provide support for
## Public Galaxy Servers
-There are numerous other [/Public Galaxy Servers](/Public Galaxy Servers). These are known to provide some support for microarrays:
+There are numerous other [Public Galaxy Servers](/PublicGalaxyServers). These are known to provide some support for microarrays:
| Server | Purpose / Community | Other Comments | Restrictions | Sponsor |
| ------ | -------------------- | --------------- | ------------- | -------- |
diff --git a/News/2016_11GalaxyUpdate/index.md b/News/2016_11GalaxyUpdate/index.md
new file mode 100644
index 0000000..2938b24
--- /dev/null
+++ b/News/2016_11GalaxyUpdate/index.md
@@ -0,0 +1,31 @@
+<div class='newsItemHeader'>[November 2016 Galactic News](/News/2016_11GalaxyUpdate)</div>
+
+<div class='right'>
+<div class='right'><a href='/GalaxyUpdates/2016_11'><img src='/Images/GalaxyLogos/GalaxyNews.png' alt='Galaxy News' width=120 /></a></div><br />
+<a href='/GalaxyUpdates/2016_11#galaxy-australasia-meeting-game-2017'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="105" /></a>
+<a href='/GalaxyUpdates/2016_11#galaxy-admin-training-november-7-11-salt-lake-city-utah'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width="105" /></a><br />
+<a href='/GalaxyUpdates/2016_11#european-galaxy-developer-workshop'><img src='/Images/Logos/IFBGalaxyWG.png' alt='European Galaxy Developer Workshop' width="105" /></a>
+<a href='/GalaxyUpdates/2016_11#bioconda-contribution-fest-november-2-3-online'><img src='/Images/Logos/BioCondaGalaxy.jpg' alt='BioConda and Galaxy' width="105" /></a><br /><br />
+<div class='right'><a href='/GalaxyUpdates/2016_11#galaxy-arabic-community-launched'><img src='/Community/Arabic/GalaxyArabic400.png' alt='Galaxy Arabic Speaking Community' width="120" /></a></div>
+</div>
+
+The **[November Galactic News](/GalaxyUpdates/2016_11)** is out and **[upcoming events](/GalaxyUpdates/2016_11#events)** are again prominent:
+
+* **[Galaxy Australasia Meeting (GAMe 2017)](/GalaxyUpdates/2016_11#galaxy-australasia-meeting-game-2017)**: February 3-9, Melbourne, Victoria, Australia.
+ * **Talk abstracts are due 30 November**
+* **[Bioconda Contribution Fest](/GalaxyUpdates/2016_11#bioconda-contribution-fest-november-2-3-online)**: November 2-3, [Online](https://github.com/bioconda/bioconda-recipes/issues/2277)
+* **[European Galaxy Developer Workshop](/GalaxyUpdates/2016_11#european-galaxy-developer-workshop)**, 16-19 January, Strasbourg, France
+ * Registration is open and space is limited.
+* **[Galaxy Admin Training](/GalaxyUpdates/2016_11#galaxy-admin-training-november-7-11-salt-lake-city-utah)**: November 7-11, Salt Lake City, Utah.
+* Reports form the [Galaxy Training Material Contribution Fest](/GalaxyUpdates/2016_11#report-galaxy-training-material-a-contribution-fest-beyond-any-expectations) and [Swiss-German Galaxy Days](/GalaxyUpdates/2016_11#report-swiss-german-galaxy-days)
+* And of course, [other upcoming events](/GalaxyUpdates/2016_11#all-upcoming-events) too
+
+There is also the new [Arabic speaking Galaxy Community](/GalaxyUpdates/2016_11#galaxy-arabic-community-launched), [87 new publications](/GalaxyUpdates/2016_11#new-publications) (including six featured pubs), [seven open positions](/GalaxyUpdates/2016_11#whos-hiring), [four new public Galaxy servers](/GalaxyUpdates/2016_11#public-galaxy-server-news) and a [Jetstream update](/GalaxyUpdates/2016_11#semi-public-galaxy-services), [one new GTN member and four new training resources](/GalaxyUpdates/2016_11#galaxy-community-hubs), [new releases of galaxy-lib & Planemo](/GalaxyUpdates/2016_11#releases), and [new TooShed contributions](/GalaxyUpdates/2016_11#toolshed-contributions).
+
+We hope to see you in Melbourne, Strasbourg, Salt Lake, online, and around the world,
+
+[Dave Clements](/DaveClements) and the [Galaxy Team](/GalaxyTeam)
+
+<div class='newsItemFooter'>Posted to the [Galaxy News](/News) on PLACEHOLDER_DATE(2016-10-31T17:08:01Z)</div>
+
+CategoryNews
diff --git a/News/Archive/2016/index.md b/News/Archive/2016/index.md
index 716eb38..adc66ce 100644
--- a/News/Archive/2016/index.md
+++ b/News/Archive/2016/index.md
@@ -1,18 +1,28 @@
<div class='linkbox'>
**2016 News Archive**
----
-<div class='right'>apr</div>
+<div class='right'><span style="font-size: smaller;">Jul</span></div>
+[July 2016 Galactic News](/News/2016_07GalaxyUpdate)<br />
+----
+<div class='right'><span style="font-size: smaller;">Jun</span></div>
+[June 2016 Galactic News](/News/2016_06GalaxyUpdate)<br />
+----
+<div class='right'><span style="font-size: smaller;">May</span></div>
+[Galaxy CloudMan Release (v 16.05)](/News/1605_GalaxyCloudManRelease)<br />
+[April 2016 Galaxy Release (v 16.04)](/News/2016_04_GalaxyRelease)<br />
+----
+<div class='right'><span style="font-size: smaller;">Apr</span></div>
[May 2016 Galactic News](/News/2016_05GalaxyUpdate)<br />
[Conda Dependencies Codefest Report](/News/CondaDependencyCodefestReport)<br />
[Galaxy on Jetstream Cloud](/News/GalaxyOnJetstream)<br />
[Galactic News! April Edition](/News/2016_04GalaxyUpdate)<br />
----
-<div class='right'>mar</div>
+<div class='right'><span style="font-size: smaller;">Mar</span></div>
[Galaxy CloudMan Release (v 16.03)](/News/1603_GalaxyCloudManRelease)<br />
[Galaxy DevOps Workshop - Heidelberg](/News/DevOpsHeidelberg)<br />
[March 2016 Galactic News](/News/2016_03GalaxyUpdate)<br />
----
-<div class='right'>feb</div>
+<div class='right'><span style="font-size: smaller;">Feb</span></div>
[Jan 2016 Galaxy Release (v 16.01)](/News/2016_01_GalaxyRelease)<br />
[GCC2016 scholarships: Apply now!](/News/GCC2016Scholarships)<br />
[Bioinformaticist @ Johns Hopkins APL](/News/JHUAPLBioinformaticist)<br />
@@ -20,7 +30,7 @@
[Galaxy Goes Mobile](/News/GalaxyOnMobile)<br />
[Disease transcriptome postdoc, Oslo](/News/OsloDiseaseTranscriptPostDoc)<br />
----
-<div class='right'>jan</div>
+<div class='right'><span style="font-size: smaller;">Jan</span></div>
[January 2016 Galaxy News](/News/2016_01GalaxyUpdate)<br />
</div>
PLACEHOLDER_INCLUDE(/News/Archive/LinkBox)
diff --git a/News/GAT2016RegistrationOpen/index.md b/News/GAT2016RegistrationOpen/index.md
index 7a0607f..c57ce4b 100644
--- a/News/GAT2016RegistrationOpen/index.md
+++ b/News/GAT2016RegistrationOpen/index.md
@@ -1,7 +1,7 @@
<div class='newsItemHeader'>[Galaxy Admin Training, Nov 7-11](/News/GAT2016RegistrationOpen)</div>
<div class='right solid center'>
-<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width=200" /></a><br />
+<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width="200" /></a><br />
November 7-11, 2016<br />University of Utah<br />Salt Lake City, Utah<br />United States<br /><br /> [Registration is open](/Events/AdminTraining2016/Registration)
</div>
diff --git a/News/GalaxyArabic/index.md b/News/GalaxyArabic/index.md
new file mode 100644
index 0000000..6901834
--- /dev/null
+++ b/News/GalaxyArabic/index.md
@@ -0,0 +1,30 @@
+<div class='newsItemHeader'>[Galaxy Arabic Community](/News/GalaxyArabic)</div>
+
+<div class='left'>![Galaxy Arabic Speaking Community](/Community/Arabic/GalaxyArabic400.png)</div>
+
+<table>
+ <tr>
+ <td style=" text-align: right; border: none;"> أرشيف للقائمة البريدية جالاكسي بالعربية يحتوي على الاخبار والمناقشات والاعلانات الخاصة بمستخدمي جالاكسي من البلاد الناطقة بالعربية نرحب بانضمام أي شخص مهتم بالجلاكسي بلاتفورم<br />جالاكسي هي بلاتفورم لتحليل المعلومات الحيوية باستخدام أدوات برمجة أونلاين مجانا تتميز بأنها متاحة للجميع ونتائجها تتميز بالشفافية وبالقدرة على الحصول على نفس النتائج عند إجراء التحليل مرات عديدة.<br />السهولة : يمكن لأي شخص استخدام جالاكسي حتى لو لم تكن لديه خبرة كافية بتحليل المعلومات الحيوية<br />النتائج : تحصل على نفس النتائج مهما أجريت التجربة مرات عديدة وهذا يميز جالاكسي عن العديد من الأدوات الاخرى <br />الشفافية : يمكنك أن تشارك ما توصلت إليه مع زملائك والعالم كله ويمكنك النشر أيضا .<br />جالاكسي مفتوحة لكل المنظمات والسرفر الرئيسي يمكنك من إجراء تحليل على المعلومات الجينية وإيضا توجد مواد تعليمية للتدريب وأماكن العمل وخدمات النشر يمكنك استخدام جالاكسي أونلاين ويمكنك أيضا تنزيلها على الكمبيوتر الخاص بك واستخدامها </td>
+ </tr>
+</table>
+
+
+----
+
+We are pleased to announce the launch of the **[Galaxy Arabic community](/Community/Arabic).** Galaxy Arabic supports and promotes Galaxy activity for the Arabic speaking community and in Arabic speaking regions of the world.
+
+If you are interested in joining the community, please
+* Follow [@Galaxy_Arabic on Twitter](http://twitter.com/galaxy_arabic)
+* Join the [Galaxy Arabic mailing list](https://lists.galaxyproject.org/listinfo/galaxy-arabic). Regional Galaxy news will be posted here, and you can also ask fellow Arabic speakers support questions.
+* Join the [Galaxy Arabic Facebook group](http://bit.ly/2ek7fTh)
+
+We look forward to connecting and growing the Arabic speaking Galaxy community.
+
+Thanks,
+
+[abdelazeem_abdelhameed2015505@yahoo.com](Abdelazeem Abdelhameed) and [Dave Clements](/DaveClements)
+
+
+<div class='newsItemFooter'>Posted to the [Galaxy News](/News) on PLACEHOLDER_DATE(2016-10-27T15:48:38Z)</div>
+
+CategoryNews
diff --git a/News/GalaxyOnJetstream/index.md b/News/GalaxyOnJetstream/index.md
index 14eae6c..4dcb69a 100644
--- a/News/GalaxyOnJetstream/index.md
+++ b/News/GalaxyOnJetstream/index.md
@@ -10,7 +10,7 @@ You must be a US-based academic to access Jetstream cloud. Access is free but it
### How do I launch my own Galaxy server?
After you have your XSEDE account and an active allocation:
1. Visit https://use.jetstream-cloud.org/
-2. Browse the available images and choose "Galaxy 16.01 Standalone"
+2. Browse the available images and choose "Galaxy Standalone"
3. Follow the prompts on the screen to launch an instance
4. In less than 5 minutes, you should have your own, fully configured Galaxy server
diff --git a/News/GalaxyOnJetstream1607/index.md b/News/GalaxyOnJetstream1607/index.md
new file mode 100644
index 0000000..1f17af0
--- /dev/null
+++ b/News/GalaxyOnJetstream1607/index.md
@@ -0,0 +1,9 @@
+<div class='newsItemHeader'>[Galaxy on Jetstream Cloud update](/News/GalaxyOnJetstream1607)</div>
+
+<div class='right'>![](https://www.nsf.gov/news/mmg/media/images/jetstream_logo_f_fe60185c-962f-4c1f-99bf-e6ec82d54c21.jpg)</div>
+
+[Galaxy release 16.07](/News/2016_07_GalaxyRelease) is now available for free on the Jetstream cloud. This image contains the updated Galaxy application with a toolset that closely matches that of the public Galaxy server available at [usegalaxy.org](https://usegalaxy.org/) as well as a complete set of reference genomes available on that same server. Availability of the reference data was realized by enabling a connection to a (CVMFS-based) replica server that offers access to approximately 3TB of reference data (vs. ~50GB in the previous version of the image). An additional benefit of such integration is that the reference data is no longer stored on the machine image, reducing the size of that image to about 10GB, leaving more space for the analysis data. The base operating system is Ubuntu 14.04. The image was built using the cloud_setup flavor of the [GalaxyKickStart](https://github.com/ARTbio/GalaxyKickStart) Ansible playbook.
+
+<div class='newsItemFooter'>Posted to the [Galaxy News](/News) on PLACEHOLDER_DATE(2016-10-17T16:11:14Z)</div>
+
+CategoryNews
diff --git a/News/WikiMigration/index.md b/News/WikiMigration/index.md
new file mode 100644
index 0000000..df597d8
--- /dev/null
+++ b/News/WikiMigration/index.md
@@ -0,0 +1,23 @@
+<div class='newsItemHeader'>[Wiki Migration is Underway](/News/WikiMigration)</div>
+
+<div class='right'>
+<table>
+ <tr>
+ <td style=" width: 19em;"> <span style="font-size: smaller;"> </em>The wiki migration is part of a general overhaul of Galaxy documentation that started with the creation of <a href='https://docs.galaxyproject.org/'>docs.galaxyproject.org</a>. We also plan to move most admin documentation inside of Galaxy releases, and to support community maintainable training materials.<em> </span> </td>
+ </tr>
+</table>
+
+</div>
+
+We are migrating the [Galaxy wiki](/FrontPage) from MoinMoin to a [GitHub](http://github.com) based solution using [GitHub Flavored Markdown](https://help.github.com/articles/basic-writing-and-formatting-syntax/) for content, and the [Metalsmith static site generator](http://www.metalsmith.io/) to render the actual site. The move to !GitHub will allow us to take full advantage of !GitHub's collaboration features and will move the documentation to a source format (Markdown) that more people are familiar with. Using Metalsmith to generate the site will give us much more flexibility in how we present semi-structured content such as the [events calendar](/Events), the [public Galaxy servers list](/PublicGalaxyServers), and the GTN [trainer](/Teach/Trainers) and [training resources](/Teach/Resources) directories.
+
+You'll be able to update the documentation entirely on !GitHub. If you are inclined to go deeper you can clone the repository, make changes, and build and serve the entire site locally.
+
+The migration has started. This wiki has been frozen. We will bring up a beta version of the new site at a different URL within a few days. We then expect a flurry of activity while the team *and the community* make improvements to the new site before it goes official on November 21.
+
+We'll include guides on how to use the new setup, and what you'll need to know if you decide to dive into Metalsmith.
+
+
+<div class='newsItemFooter'>Posted to the [Galaxy News](/News) on PLACEHOLDER_DATE(2016-11-10T21:27:16Z)</div>
+
+CategoryNews
diff --git a/News/index.md b/News/index.md
index f2ffd50..7b80564 100644
--- a/News/index.md
+++ b/News/index.md
@@ -3,6 +3,10 @@
<div class='linkbox'>
**[News Items](/News)**
----
+[Wiki Migration is Underway](/News/WikiMigration)<br />
+[November 2016 News of the Galaxy!](/News/2016_11GalaxyUpdate)<br />
+[Galaxy Arabic Community](/News/GalaxyArabic)<br />
+[Galaxy on Jetstream update](/News/GalaxyOnJetstream1607)<br />
[October 2016 Galactic News](/News/2016_10GalaxyUpdate)<br />
[Galaxy Australia Community & GAMe 2017](/News/GalaxyAustralia)<br />
[GCC2018 Call for Host Proposals](/News/GCC2018CallForHost)<br />
@@ -11,10 +15,6 @@
[Galaxy Admin Training Nov 7-11](/News/GAT2016RegistrationOpen)<br />
[August 2016 Galactic News](/News/2016_08GalaxyUpdate)<br />
[Multi-omics Postdoc Opening](/News/MultiOmicsPostDocMinnesota)<br />
-[July 2016 Galactic News](/News/2016_07GalaxyUpdate)<br />
-[June 2016 Galactic News](/News/2016_06GalaxyUpdate)<br />
-[Galaxy CloudMan Release (v 16.05)](/News/1605_GalaxyCloudManRelease)<br />
-[April 2016 Galaxy Release (v 16.04)](/News/2016_04_GalaxyRelease)<br />
----
[News Feed](http://feed43.com/galaxynews.xml) <a href='http://feed43.com/galaxynews.xml'><img src='/Images/Icons/RSSIcon16x16.gif' alt='Galaxy News RSS Feed' height="12" /></a><br />
[News Archive](/News/Archive)
diff --git a/PublicGalaxyServers/index.md b/PublicGalaxyServers/index.md
index 7b0a37d..487c790 100644
--- a/PublicGalaxyServers/index.md
+++ b/PublicGalaxyServers/index.md
@@ -54,7 +54,7 @@ These servers implement a broad range of tools and and aren't specific to any pa
## Biomina
-<div class='right solid'><a href='http://biominavm-galaxy.biomina.be/galaxy/'><img src='/Biomina300.png' alt='Biomina Galaxy' /></a></div>
+<div class='right solid'><a href='http://biominavm-galaxy.biomina.be/galaxy/'><img src='/PublicGalaxyServers/Biomina300.png' alt='Biomina Galaxy' /></a></div>
* *Link:*
* [Biomina Galaxy](http://biominavm-galaxy.biomina.be/galaxy/)
@@ -344,6 +344,23 @@ These servers implement a broad range of tools and and aren't specific to any pa
Domain servers specialize in either a particular branch of the tree of life or in particular types of analysis. However, within their specializations, domain servers offer a wide variety of tools.
+## Alveo: Human Communication Science Virtual Laboratory
+
+<div class='right solid'><a href='http://galaxy.alveo.edu.au/'><img src='/PublicGalaxyServers/AlveoLogoWText.png' alt='Alveo' width="300" /></a></div>
+
+* *Links:*
+ * [Alveo Galaxy server](http://galaxy.alveo.edu.au/)
+* *Domain/Purpose:*
+ * Human Communication Science (HCS).
+* *Comments:*
+ * "[Alveo](http://alveo.edu.au/about/) is a platform to support research in Human Communication. The Alveo repository holds large collections of speech, video and text data and provides an API for use by research tools. Our Galaxy server implements a number of research tools for working with speech and text data and we are exploring how best to adapt tools to this environment. Current tools allow data to be pulled from the Alveo repository and processed with various text and speech processing methods.
+* *User Support:*
+ * [In-depth tutorials](http://alveo.edu.au/tutorials/), [extensive help pages](http://alveo.edu.au/help/) and an [Alveo support forum and FAQ](https://support.alveo.edu.au/support/home) are available.
+* *Quotas:*
+ * A login is required and everybody can create a login.
+* *Sponsor(s):*
+ * Many [organizations and universities](http://alveo.edu.au/about/#colophon) across Australia.
+
## ballaxy
<div class='right solid'><a href='https://ballaxy.bioinf.uni-sb.de'><img src='/BallaxySlide.png' alt='ballaxy' /></a></div>
@@ -780,9 +797,30 @@ Domain servers specialize in either a particular branch of the tree of life or i
* *Sponsor(s):*
* Developed under the broad initiative of [OSDD (Open Source Drug Discovery)](http://www.osdd.net/) of [CSIR (Council of Scientific and Industrial Research, Govt. of India)](http://www.csir.res.in/home.asp). The site is being hosted from [IICT](http://www.iictindia.org/), Hyderabad, India.
+## PhenoMeNal
+
+<div class='right solid'><a href='http://public.phenomenal-h2020.eu/'><img src='/PublicGalaxyServers/PhenoMeNal.png' alt='PhenoMeNal' /></a></div>
+
+* *Link:*
+ * [PhenoMeNal](http://public.phenomenal-h2020.eu/) server
+* *Domain/Purpose:*
+ * Large scale computing for medical informatics
+* *Comments:*
+ * "The [PhenoMeNal Galaxy installation](http://public.phenomenal-h2020.eu/) allows users to access all of the [PhenoMeNal](http://phenomenal-h2020.eu/home/) containerised tools through a workflow environment, on an scalable infrastructure that can be deployed to public and private cloud installations.<br /><br />
+
+ This !PhenoMeNal H2020 Galaxy instance, and all of its tools, run as containers on top of [Kubernetes](http://kubernetes.io/), an open source container orchestrator system backed by Google. If you wish to [deploy the PhenoMeNal Galaxy installation](https://github.com/phnmnl/docker-galaxy-k8s-runtime/tree/develop) on top of your own [Kubernetes](http://kubernetes.io/) instance, you can find instructions at our [wiki](http://phenomenal-h2020.eu/home/wiki/#galaxy-with-k8s).
+
+* *User Support:*
+ * [Submit a ticket](http://phenomenal-h2020.eu/home/help/)
+* *Quotas:*
+* *Sponsor(s):*
+ * The [PhenoMeNal consortium](http://phenomenal-h2020.eu/home/) is driven by 14 European research groups with strong experience in the development of tools and methods for large data acquisition, integration and analysis for metabolic phenotypes, genome and cross-omics data.
+ * !PhenoMeNal is funded by European Commission's Horizon2020 programme, grant agreement number 654241.
+The Galaxy Project is supported in part by NHGRI, NSF, The Huck Institutes of the Life
+
## PopGenIE / PlantGenIE
-<div class='right solid'><a href='http://galaxy.popgenie.org:8080/'><img src='/PopGemIE.png' alt='PopGenIE' /></a></div>
+<div class='right solid'><a href='http://galaxy.popgenie.org:8080/'><img src='/PublicGalaxyServers/PopGemIE.png' alt='PopGenIE' /></a></div>
* *Link:*
* [PlantGenIE](http://galaxy.plantgenie.org:8080/)
@@ -1085,7 +1123,7 @@ The distinction between [domain servers](#domain-servers) and tool publishing se
## ARGs-OAP
-<div class='right solid'><a href='http://smile.hku.hk/SARGs'><img src='/PublicGalaxyServers/SARGs.png' alt='Structured ARG reference database Online Analysis Platform' width="300" /></a></div>
+<div class='right solid'><a href='http://smile.hku.hk/SARGs'><img src='/PublicGalaxyServers/ARGs-OAP.png' alt='Structured ARG reference database Online Analysis Platform' height="200" /></a></div>
* *Link:*
* [ARGs-OAP Galaxy Server](http://smile.hku.hk/SARGs)
@@ -1096,9 +1134,9 @@ The distinction between [domain servers](#domain-servers) and tool publishing se
* See [ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database](http://dx.doi.org/10.1093/bioinformatics/btw136), Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje, and Tong Zhang. *Bioinformatics* (2016) 32 (15): 2346-2351. doi: 10.1093/bioinformatics/btw136
* Source code is available on [GitHub](https://github.com/biofuture/Ublastx_stageone).
* *User Support:*
- *
+ * Please refer to the [manual page for ARGs-OAP](https://github.com/biofuture/Ublastx_stageone)
* *Quotas:*
- *
+ * Supports anonymous access and creation of user logins.
* *Sponsor(s):*
* Environmental Biotechnology Laboratory, [Department of Civil Engineering](https://www.civil.hku.hk/h4v3_2_study_here.html), [The University of Hong Kong](http://www.hku.hk/)
* School of Marine Sciences, [Sun Yat-Sen University](http://www.sysu.edu.cn/), Guangzhou, China
@@ -1162,6 +1200,24 @@ The distinction between [domain servers](#domain-servers) and tool publishing se
* This instance of Galaxy is managed by the [BISTRO platform](http://bioinfo-bistro.fr/bioinfo-bistro/).
+## BitLAB
+
+<div class='right solid'><a href='http://pistacho.ac.uma.es/galaxy/'><img src='/PublicGalaxyServers/Bitlab.png' alt='BitLAB Galaxy' width="300" /></a></div>
+
+* *Link:*
+ * [BitLAB Galaxy](http://pistacho.ac.uma.es/galaxy/)
+* *Domain/Purpose:*
+ * Detailed analysis of metagenomes.
+* *Comments:*
+ * From [Computational workflow for the fine-grained analysis of metagenomic samples](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3063-x) by Esteban Pérez-Wohlfeil, Jose A. Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun and Oswaldo Trelles, *BMC Genomics* 2016 17(Suppl 8):802 DOI: 10.1186/s12864-016-3063-x
+ " ... provides new tools and datafile specifications that facilitate the identification of differences in abundance of reads assigned to taxa (mapping), enables the detection of reads of low-abundance bacteria (producing evidence of their presence), provides new concepts for filtering spurious matches, etc. Innovative visualization ideas for improved display of metagenomic diversity are also proposed to better understand how reads are mapped to taxa."
+* *User Support:*
+ * There is an [extensive tutorial](http://www.bitlab-es.com/gecko/documents/GalaxyGuidedExercise.pdf) on how to use the server.
+* *Quotas:*
+ * Must create a login to use it.
+* *Sponsor(s):*
+ * [Bioinformatics and Information Technologies Laboratory (BitLAB)](http://www.bitlab-es.com/bitlab/), [Department of Computer Architecture](http://www.ac.uma.es/), [University of Málaga](http://www.uma.es/)
+
## Chemical Annotation Retrieval Toolkit (CART)
<div class='right solid'><a href='http://cart.embl.de/'><img src='/PublicGalaxyServers/CART.png' alt='Chemical Annotation Retrieval Toolkit (CART) Galaxy' width="300" /></a></div>
@@ -1698,28 +1754,6 @@ The distinction between [domain servers](#domain-servers) and tool publishing se
* *Sponsor(s):*
* [Laboratory of Systems and Synthetic Biology](http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Agrotechnology-and-Food-Sciences/Laboratory-of-Systems-and-Synthetic-Biology.htm), [Wageningen University](http://www.wageningenur.nl/)
-## ARG-OAP
-
-<div class='right solid'><a href='http://smile.hku.hk/SARGs'><img src='/PublicGalaxyServers/SARGs.png' alt='Structured ARG reference database Online Analysis Platform' width="300" /></a></div>
-
-* *Link:*
- * [ARG-OAP Galaxy Server](http://smile.hku.hk/SARGs)
-* *Domain/Purpose:*
- * Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data.
-* *Comments:*
- * Integrated "ARDB and CARD, the two most commonly used databases. SARG was curated to remove redundant sequences and optimized to facilitate query sequence identification by similarity. A database with a hierarchical structure (type-subtype-reference sequence) was then constructed to facilitate classification (assigning ARG-like sequence to type, subtype and reference sequence) of sequences identified through similarity search." The server utilizes the SARG DB and a hybrid functional gene annotation pipeline to do fast annotation and classification of ARG-like sequences from metagenomic data.
- * See [ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database](http://dx.doi.org/10.1093/bioinformatics/btw136), Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje,* and Tong Zhang. *Bioinformatics* (2016) 32 (15): 2346-2351.
-doi: 10.1093/bioinformatics/btw136
-* Source code is available on [GitHub](https://github.com/biofuture/Ublastx_stageone).
-* *User Support:*
- *
-* *Quotas:*
- *
-* *Sponsor(s):*
- * Environmental Biotechnology Laboratory, [Department of Civil Engineering](https://www.civil.hku.hk/h4v3_2_study_here.html), [The University of Hong Kong](http://www.hku.hk/)
- * School of Marine Sciences, [Sun Yat-Sen University](http://www.sysu.edu.cn/), Guangzhou, China
- * [Department of Plant, Soil, and Microbial Sciences](http://www.psm.msu.edu/), [Michigan State University](http://www.msu.edu/)
-
## SIFTED
<div class='right solid'><a href='http://thebrain.bwh.harvard.edu/sifted.html'><img src='/PublicGalaxyServers/SIFTEDLandingPage.png' alt='SIFTED' /></a></div>
diff --git a/SetUpREnvironment/index.md b/SetUpREnvironment/index.md
index 1b6d00b..e49200e 100644
--- a/SetUpREnvironment/index.md
+++ b/SetUpREnvironment/index.md
@@ -34,7 +34,7 @@ The Galaxy computational analysis framework facilitates exposing R (and other) c
As developers quickly discover, each new Galaxy tool requires some hand coding of what is essentially predictable boilerplate. It is possible to create relatively simple new tools using a specialised Galaxy tool to generate all the biolerplate required to wrap scripts - the Tool Factory. Generated tools are in the form of a Tool Shed repository tarball and include the XML defining the recipe to install the script as a tool. The more recent Tool Factory 2 allows arbitrary parameters to be included in the generated tool, multiple input files and also enables the script to be reproducibly executed by a specific toolshed packaged version of the appropriate interpreter (eg package_r_3_1_2) if desired.
-This page concerns processes developers will face toward the end of the tool development process, when the working script is being converted into a self-installing tool shed repository, including using "setup_r_environment" to install a long list of package and dependency tarball URLs in a tool_dependencies.xml file, to make your work available to any Galaxy user. If that sounds interesting, read on. For an example of the horrors you may face, see [#tdxml](#tdxml)
+This page concerns processes developers will face toward the end of the tool development process, when the working script is being converted into a self-installing tool shed repository, including using "setup_r_environment" to install a long list of package and dependency tarball URLs in a tool_dependencies.xml file, to make your work available to any Galaxy user. If that sounds interesting, read on. For an example of the horrors you may face, see [TDXML](#tdxml)
## tool_dependencies.xml
diff --git a/SideBar/index.md b/SideBar/index.md
index 9f5b7fd..b25e378 100644
--- a/SideBar/index.md
+++ b/SideBar/index.md
@@ -1,10 +1,12 @@
#acl VettedEditorGroup:read,write,revert All:read
<div class='center'>
+**[Wiki Migration is Underway](/News/WikiMigration)**<br /> <span style="font-size: smaller;"> (Updates are frozen) </span>
+<br /><br />
+----
+<a href='https://www.embl-abr.org.au/game2017/'><img src='/Images/Logos/GAMeLogo200.png' alt='Galaxy Australasia Meeting 2017' width="120" /></a>
<br />
-<a href='/Events/AdminTraining2016'><img src='/Images/Logos/AdminTraining2016-500.png' alt='Galaxy Project Admin Training' width=140" /></a><br />
-[November 7-11](/Events/AdminTraining2016)<br />
-**[Register by Oct 16](/Events/AdminTraining2016)**
+**[Galaxy Australasia Meeting 3-9 Feb Melbourne](https://www.embl-abr.org.au/game2017/)**
</div>
# Use Galaxy
diff --git a/Support/AboutGalaxy/index.md b/Support/AboutGalaxy/index.md
index 849a4ec..5b3e6eb 100644
--- a/Support/AboutGalaxy/index.md
+++ b/Support/AboutGalaxy/index.md
@@ -14,7 +14,7 @@ Back to [/Support](/Support)
There are many [Choices](/BigPicture/Choices) when you want to learn more **[about using Galaxy](/Support/AboutGalaxy)**!
-In addition to using the [public Galaxy server](http://usegalaxy.org), you can also install your [own instance of Galaxy](/Admin/GetGalaxy), or create an [instance of Galaxy on the cloud using CloudMan](/CloudMan) and explore all [/Cloud](/Cloud) resources. Another option is to use one of the ever-increasing number of [/Public Galaxy Servers](/Public Galaxy Servers) hosted by other organizations. And if you or your lab is looking to run their own local instance that is "ready-to-go", learn more about the [Slipstream Appliance: Galaxy Edition](http://www.bioteam.net/slipstream/galaxy-edition).
+In addition to using the [public Galaxy server](http://usegalaxy.org), you can also install your [own instance of Galaxy](/Admin/GetGalaxy), or create an [instance of Galaxy on the cloud using CloudMan](/CloudMan) and explore all [/Cloud](/Cloud) resources. Another option is to use one of the ever-increasing number of [Public Galaxy Servers](/PublicGalaxyServers) hosted by other organizations. And if you or your lab is looking to run their own local instance that is "ready-to-go", learn more about the [Slipstream Appliance: Galaxy Edition](http://www.bioteam.net/slipstream/galaxy-edition).
The GALAXY Framework at the highest level is a set of reusable software components. Learn more about [Galaxy's Architecture](/Admin/Internals/Implementation Info).
diff --git a/Teach/Resource/GalaxyIntroArabic/index.md b/Teach/Resource/GalaxyIntroArabic/index.md
new file mode 100644
index 0000000..ed098ee
--- /dev/null
+++ b/Teach/Resource/GalaxyIntroArabic/index.md
@@ -0,0 +1,27 @@
+----
+pagetitle: [Introduction to Galaxy Project Slides, in Arabic](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.pptx)
+----
+<div class='center'>
+<a href='http://linkToResourceOrOrg'><img src='/Community/Arabic/GalaxyArabic400.png' alt='Introduction to Galaxy Project Slides, in Arabic' width="200" /></a>
+</div>
+
+
+
+<div class='deploymentbox'>
+ Resource:: **[Introduction to Galaxy Project Slides, in Arabic](/Teach/Resource/GalaxyIntroArabic)**
+ Types:: Slides
+ Domains:: **Galaxy Project**
+ Owners:: [abdelazeem_abdelhameed2015505@yahoo.com](Abdelazeem Abdelhameed)
+ Formats:: [Slides](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.pptx)
+ Date:: 2016/10
+</div>
+
+A [set of slides](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.pptx) introducing the Galaxy Project, in Arabic.
+
+## Links
+
+* [Slides in PowerPoint](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.pptx), [PDF](ATTACHMENT_URLDocuments/Presentations/GalaxyProjectIntroArabic.PDF)
+* [Arabic Speaking Galaxy Community](/Community/Arabic)
+
+
+CategoryTrainingResource
diff --git a/Teach/Trainers/index.md b/Teach/Trainers/index.md
index c8030a2..8dc5905 100644
--- a/Teach/Trainers/index.md
+++ b/Teach/Trainers/index.md
@@ -8,7 +8,7 @@ PLACEHOLDER_INCLUDE(/Teach/Header)
PLACEHOLDER_INCLUDE(/Teach/LinkBox)
-<div class='left'> <a href='http://bit.ly/gxytrnmap'><img src='/Teach/GalaxyTrainingMapThumb.png' alt='Galaxy Training Network: Trainer Locations Map' width="220" /></a> <div class='center'> [Find trainers near you in the](http://bit.ly/gxytrnmap)<br />[Galaxy Training Network](http://bit.ly/gxytrnmap)</div></div>
+<div class='left'> <a href='http://bit.ly/gxytrnmap'><img src='/Teach/GalaxyTrainingMapThumb.png' alt='Galaxy Training Network: Trainer Locations Map' width="180" /></a> <div class='center'> [Find trainers near you](http://bit.ly/gxytrnmap)</div></div>
The *Galaxy Trainer Directory* is a service of the [Galaxy Training Network](/Teach/GTN) which aims to make it easy to share and find [Galaxy training resources](/Teach/Resources). This directory lists individuals and groups that do Galaxy training. The contacts listed here are willing to present Galaxy at meetings and workshops. The directory includes particular areas of expertise and how far the instructors are willing to travel.
@@ -57,7 +57,7 @@ Trainers are potentially willing to travel globally to present Galaxy Training.
* [Contact](http://www.up.ac.za/en/centre-for-bioinformatics-and-computational-biology/article/29861/contact-us)
* [The Centre for Bioinformatics and Computational Biology, University of Pretoria](http://www.up.ac.za/centre-for-bioinformatics-and-computational-biology)
-### The FMI Bioinformatics and Functional Genomics Core Facilities
+### The FMI Bioinformatics Core Facilities
<div class='right'><a href='http://www.fmi.ch'><img src='/Images/Logos/FMILogo.jpg' alt='The FMI Bioinformatics and Functional Genomics Core Facilities' width="180" /></a></div>
@@ -74,7 +74,6 @@ Trainers are potentially willing to travel globally to present Galaxy Training.
* *Links & Contact*
* [FMI Bioinfomatics platform](http://www.fmi.ch/bioinformatics)
- * [FMI Functional Genomics platform](http://www.fmi.ch/functional.genomics)
* Email contact: [hrh AT fmi DOT ch](Hans-Rudolf Hotz)
### Freiburger Galaxy Project
@@ -264,7 +263,6 @@ Trainers are potentially willing to travel globally to present Galaxy Training.
* *Links & Contact*
* [QFAB Bioinformatics website](http://qfab.org)
- * [Bio page for Mark Crowe](http://www.qfab.org/mark-crowe/), QFAB's Training Manager and Galaxy specialist
* E-mail contact [training AT qfab DOT org](training AT qfab DOT org)
### Stingray@Galaxy
@@ -607,6 +605,25 @@ These trainers don't travel, but their workshops are open to researchers outside
* E-mail contact [training AT earlham DOT ac DOT uk](training AT earlham DOT ac DOT uk)
+### Peter Mac
+
+<div class='right'><a href='https://www.petermac.org/'><img src='/Images/Logos/PeterMac.png' alt='Peter MacCallum Cancer Center' width="200" /></a></div>
+
+* *Description:*
+ * [Peter Mac](https://www.petermac.org/) is one of the world’s leading cancer research, education and treatment centres globally and is Australia’s only public hospital solely dedicated to caring for people affected by cancer. We have over 2,500 staff, including more than 580 laboratory and clinical researchers, all focused on providing better treatments, better care and potential cures for cancer.
+
+* *Domains:*
+ * General usage, cancer genomics
+
+* *Reach*
+ * Training is held at [Peter Mac](https://www.petermac.org/) in Melbourne, Australia, and are open to all researchers and students.
+
+* *Links & Contact*
+ * [Peter Mac](https://www.petermac.org/)
+ * E-mail contact [Maria DOT Doyle AT petermac DOT org](Maria Doyle)
+
+
+
### Texas A&M University/Center for Phage Technology
<div class='right'><a href='https://cpt.tamu.edu/'><img src='/Images/Logos/TAMULogo.png' alt='Texas A&M University/Center for Phage Technology' width="150" /></a></div>
@@ -660,6 +677,27 @@ These trainers don't travel, but their workshops are open to researchers outside
* Contact us [bioinformatics DOT core AT ucdavis DOT edu](via email)
+### University of Aberdeen Centre for Genome Enabled Biology and Medicine
+
+<div class='right'><a href='http://www.abdn.ac.uk/genomics/'><img src='/Images/Logos/UniversityOfAberdeen.png' alt='University of Aberdeen Centre for Genome Enabled Biology and Medicine' width="200" /></a></div>
+
+* *Description:*
+ * The [Centre for Genome Enabled Biology and Medicine](http://www.abdn.ac.uk/genomics/) organises and runs workshops in order to help aid researchers in analysis of next generation sequencing data. We offer workshops covering both Galaxy and command line approaches to make computational analysis accessible to all.
+
+* *Domains:*
+ * Next Generation Sequencing specific workshops including:
+ * Quality Control of NGS data
+ * Genome Assembly and Annotation
+ * RNA Sequencing and Differential Expression
+ * Alignment, Visualisation and Variant Calling
+ * ChIP Sequencing
+* *Reach*
+ * All [CGEBM workshops](http://www.abdn.ac.uk/genomics/bioinformatics/training/) are run at the [University of Aberdeen](http://www.abdn.ac.uk/), Scotland, UK. Our team members do travel and help run external workshops internationally depending on the circumstances.
+* *Links & Contact*
+ * [Information on the CGEBM](http://www.abdn.ac.uk/genomics/)
+ * [Upcoming workshop listings](http://www.abdn.ac.uk/genomics/bioinformatics/training/)
+ * For workshop enquiries contact [s.shaw AT abdn DOT ac DOT uk](Sophie Shaw) and for general enquiries contact [e.collie-dugui dAT abdn DOT ac DOT uk](Elaina Collie-Duguid).
+
### University of Cambridge Bioinformatics Training Facility
<div class='right'><a href='http://www.bio.cam.ac.uk/facilities/research/training/bioinformatics'><img src='/Images/Logos/UniCambridgeLogoWide.png' alt='University of Cambridge Bioinformatics Training Facility' width="200" /></a></div>
diff --git a/ToolShed/Contributions/2016_10/index.md b/ToolShed/Contributions/2016_10/index.md
new file mode 100644
index 0000000..fc5c4d5
--- /dev/null
+++ b/ToolShed/Contributions/2016_10/index.md
@@ -0,0 +1,50 @@
+----
+autotoc: true
+----
+<div class='right'></div>
+
+<div class='right'><a href='http://toolshed.g2.bx.psu.edu/'><img src='/Images/Logos/ToolShed.jpg' alt='Galaxy ToolShed' width=200 /></a></div>
+
+Tools contributed to the Galaxy Project Tool Shed in [October 2016](/GalaxyUpdates/2016_11).
+
+### New Tools
+
+#### unrestricted
+
+* *From [nicolas](https://toolshed.g2.bx.psu.edu/view/nicolas):*
+ * [oghma](https://toolshed.g2.bx.psu.edu/view/nicolas/oghma): tools for the genomic selection project
+
+* *From [mingchen0919](https://toolshed.g2.bx.psu.edu/view/mingchen0919):*
+ * [package_r_limma_3_30_0](https://toolshed.g2.bx.psu.edu/view/mingchen0919/package_r_limma_3_30_0): Data analysis, linear models and differential expression for microarray data
+ * [package_bioconductor_edger_3_16_1](https://toolshed.g2.bx.psu.edu/view/mingchen0919/package_bioconductor_edger_3_16_1): Differential expression analysis of RNASeq data
+ * [package_r_locfit_1_5_9_1](https://toolshed.g2.bx.psu.edu/view/mingchen0919/package_r_locfit_1_5_9_1): Local regression, likelihood and density estimation
+
+* *From [charles-bernard](https://toolshed.g2.bx.psu.edu/view/charles-bernard):*
+ * [alfa](https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa): Compute and display distribution of reads by genomic categories ALFA provides a global overview of features distribution composing New Generation Sequencing dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.
+
+* [data_manager_build_alfa_indexes](https://toolshed.g2.bx.psu.edu/view/charles-bernard/data_manager_build_alfa_indexes): build ALFA indexes from automatically downloaded gtf annotation file
+1. The tool asks the admin to enter a 'species_name' and automatically download the last release of the corresponding gtf annotation file on Ensembl.
+2. The tool calls ALFA to generate the alfa indexes from this gtf file.
+3. Resulting indexes are stored in the child directory 'alfa_indexes' of the dir <galaxy_data_manager_data_path> defined in config/galaxy.ini
+4. Finally, the tool adds the new entry to the table 'alfa_indexes.loc'. This .loc file is where the data table 'alfa_indexes' points, as defined in config/shed_tool_data_table.conf.xml
+5. At the end of the process, when a user will use alfa (https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa), the built-in indexes corresponding to the 'species_name' will be available
+
+* *From [rachel-929292](https://toolshed.g2.bx.psu.edu/view/rachel-929292):*
+ * [extract_fragment_counts_for_chromosomes](https://toolshed.g2.bx.psu.edu/view/rachel-929292/extract_fragment_counts_for_chromosomes): extracts fragment counts for chromosomes Extracts Fragment Counts for Chromosomes
+
+* *From [nedias](https://toolshed.g2.bx.psu.edu/view/nedias):*
+ * [blast_tool](https://toolshed.g2.bx.psu.edu/view/nedias/blast_tool): BLAST API caller for orf tool BLAST API caller for orf tool
+ * [orf_tools](https://toolshed.g2.bx.psu.edu/view/nedias/orf_tools): Tools for searching open reading frame from mRNA sequence Tools for searching open reading frame from mRNA sequence
+
+* *From [chrisd](https://toolshed.g2.bx.psu.edu/view/chrisd):*
+ * [resistome_analyzer](https://toolshed.g2.bx.psu.edu/view/chrisd/resistome_analyzer): A simple tool for analyzing the resistome of metagenomic sequence data
+ * [rarefaction_analyzer](https://toolshed.g2.bx.psu.edu/view/chrisd/rarefaction_analyzer): A simple tool for creating rarefaction curves for metagenomic sequence data
+
+* *From [nml](https://toolshed.g2.bx.psu.edu/view/nml):*
+ * [stringmlst](https://toolshed.g2.bx.psu.edu/view/nml/stringmlst): Rapid and accurate identification of the sequence type (ST)
+
+* *From [davidvanzessen](https://toolshed.g2.bx.psu.edu/view/davidvanzessen):*
+ * [shm_csr](https://toolshed.g2.bx.psu.edu/view/davidvanzessen/shm_csr): Somatic hypermutation and class switch recombination pipeline Performs a summary/analysis of an IMGT HighV-QUEST (https://www.imgt.org/HighV-QUEST/) ZIP file for Somatic hypermutation and class switch recombination.
+
+* *From [galaxyp](https://toolshed.g2.bx.psu.edu/view/galaxyp):*
+ * [sixgill](https://toolshed.g2.bx.psu.edu/view/galaxyp/sixgill): Build Six-frame Genome-Inferred Search Database for LC-MS/MS Sixgill (Six-frame Genome-Inferred Libraries for LC-MS/MS) is a tool for using shotgun metagenomics sequencing reads to construct databases of metapeptides: short protein fragments for database search of LC-MS/MS metaproteomics data.
diff --git a/VahidJalili/index.md b/VahidJalili/index.md
new file mode 100644
index 0000000..39dccd4
--- /dev/null
+++ b/VahidJalili/index.md
@@ -0,0 +1,21 @@
+----
+pagetitle: Vahid Jalili
+----
+
+
+<div class='right'>![](/GalaxyTeam/Vahid.jpg)</div>
+Vahid is a post-doctoral researcher at George Washington University, where he works on extending Galaxy in the areas of databases, information retrieval, visual analytics, and cancer informatics. In 2016 he was awarded his Ph.D. degree on Information Technology at the [Politecnico di Milano](http://www.polimi.it/), with a dissertation entitled "[Efficient data structures for cross-samples inferences on genomic data](https://www.politesi.polimi.it/handle/10589/120263)" focused on tertiary analysis of Next Generation Sequencing (NGS) data, discussing systematic solutions for analytical and computational challenges of NGS data. His research interest spans topics in computational biology, cognitive science, and artificial intelligence; such as information retrieval and data mining in Genomics, cognitive inhibition and visual perception, and application of artificial intelligence to games.
+
+
+## Details
+
+<table>
+ <tr>
+ <th> E-mail </th>
+ <td> <a href="mailto:jalili DOT vahid AT gmail DOT com">jalili DOT vahid AT gmail DOT com</a> </td>
+ </tr>
+</table>
+
+
+----
+CategoryHomepage
diff --git a/VettedEditorGroup/index.md b/VettedEditorGroup/index.md
index 7654335..0346a8b 100644
--- a/VettedEditorGroup/index.md
+++ b/VettedEditorGroup/index.md
@@ -1,1205 +1,21 @@
#acl All:read
List of wiki logins that have been vetted and no longer need to answer [TextChas](/HelpOnSpam) to edit pages. If you want to get on this list, please send your wiki login to [outreach@galaxyproject.org](Galaxy Outreach).
-#### A-Ah
-
-* [/Razan Abbass](/Razan Abbass)
-* [Mohamed Abdelraheem](/mohammed2003w)
-* [Lucie Abrouk](/lucieabrouk)
-* [Cesar Acevedo](/CesarAcevedo)
-* [Aneesha Acharya](/Aneesha Acharya)
-* [Ed Acker](/edacker)
-* [Neto Adhemar](/azneto)
* [Enis Afgan](/EnisAfgan)
-* [Dan Alford](/Dan Alford)
-* [Ali Alqahtani](/Ali Alqahtani)
-* [Jens Allmer](/jallmer)
-* [Diego Alonso](/Diego Alonso)
-* [Renato Alves](/RenatoAlves)
-* [Ambrose Andongabo](/ambrose)
-* [Paul-Michael Agapow](/PaulAgapow)
-* [Lawrence Aggerbeck](/Aggerbeck)
-* [Vartika Agrawal](/VartikaAgrawal)
-* [Zaki Ahmad](/ZakiAhmad)
-* [Kreshnik Ahmeti](/Kreshnik Ahmeti)
-
-#### Ai-Az
-
-* [Lakshmi Akileswaran](/lakshmi akileswaran)
-* [Mike Allevato](/mikeallevato)
-* [Cristina Alonso](/CristinaAlonso)
-* [Jose Alquicira](/JoseAlquicira)
-* [Mercedes Ames](/MercedesAmes)
-* [Erika Andrade](/erikaandrade)
-* [Florent Angly](/FlorentAngly)
-* [Midas Anijs](/MidasAnijs)
-* [Katri Anttonen](/KatriAnttonen)
-* [Maryam Anwar](/MaryamAnwar)
-* [Brian Arand](/brainArid)
-* [Veronica Araoz](/VeronicaAraoz)
-* [Valerie Arboleda](/valerie.arboleda@gmail.com)
-* [Muhammad Arif](/Muhammad Arif)
-* [Amin Arnaout](/aminarnaout)
-* [Kelvin Asemota](/kelvinasemota)
-* [Ashutosh Ashutosh](/Ashutosh Ashutosh)
-* [Abdulrahman Azab](/azab)
-
-#### Ba-Bd
-
* [Dannon Baker](/DannonBaker)
-* [Aladje Balde](/Aladje Balde)
-* [Lucie Baillon](/LucieBaillon)
-* [Atreyi Banerjee](/AtreyiBanerjee)
-* [Asma Bankapur](/Asma Bankapur)
-* [Davis Banks](/davisbanks)
-* [Kushagra Bansal](/KushagraBansal)
-* [Matteo Barcella](/Matteo Barcella)
-* [Guillaume Barreau](/Guillaume Barreau)
-* [/Angela Barrett](/Angela Barrett)
-* [Craig Barrett](/CraigBarrett)
-* [Jiri Barta](/fredy)
-* [David Bass](/DavidBass)
-* [Paola Batta](/PaolaBatta)
-* [Jonathan Bd](/JonathanBD)
-
-#### Be-Bi
-* [Glen Beane](/GlenBeane)
-* [Emily Beck](/EmilyBeck)
-* [Tomasz Bednarz](/tomaszbednarz)
-* [Ivan Bedzhov](/Bedzhov)
-* [Bradley Belfiore](/BradleyBelfiore)
-* [Kristin Bell](/KristinBell)
-* [Simon Belluzzo](/SimonBelluzzo)
-* [Maximiliano Bendek](/maxbendek)
-* [Derek Benson](/DerekBenson)
-* [Peter Bergholz](/PeterBergholz)
-* [Casey Bergman](/CaseyBergman)
-* [Alessandro Bertero](/AlessandroBertero)
-* [Jean Fr Berthelot](/JeanFrédéricBerthelot)
-* [Pierre Bertin](/PierreBertin)
-* [Nicole Bertram](/NicoleBertram)
-* [Anshu Bhardwaj](/Anshu Bhardwaj)
-* [Diti Chatterjee Bhowmick](/diticb)
-* [David Bibby](/DavidBibby)
-* [Subinoy Biswas](/Subinoy Biswas)
-
-##### Bj-Bq
-* [Josh Black](/JoshBlack)
-* [Ann Black-Ziegelbein](/Ann Black-Ziegelbein)
* [Dan Blankenberg](/Dan)
-* [Paul Boddie](/PaulBoddie)
-* [Jessica Boehler](/JessicaBoehler)
-* [Sidney Bolden](/SidneyBolden)
-* [Diego Bonatto](/DiegoBonatto)
-* [Humberto Boncristiani](/Humberto Boncristiani)
-* [Tim Booth](/TimBooth)
-* [Rohan Borkar](/rohan)
-* [Carlos Borroto](/CarlosBorroto)
-* [Alex Bossers](/Alex Bossers)
* [Dave Bouvier](/DaveBouvier)
-* [Paul Bowyer](/paulbowyer)
-
-##### Br-Bz
-* [Remi Branco](/RemiBranco)
-* [David Brandt](/David Brandt)
-* [Bal Brankovics](/Balázs Brankovics)
-* [Adam Brenner](/AdamBrenner)
-* [Christian Brenninkmeijer](/ChristianBrenninkmeijer)
-* [Chris Bridson](/ChrisBridson)
-* [Chris Broberg](/ChrisBroberg)
-* [Jeff Brockman](/Jeff Brockman)
-* [Stu Brown](/StuBrown)
-* [Anushka Brownley](/anushkanet)
-* [David Bujold](/DavidBujold)
-* [Shaheen Bundhoo](/ShaheenBundhoo)
-* [Philip Burnham](/PhilipBurnham)
-* [Jessica Burr](/JessicaBurr)
-* [Ben Busby](/BenBusby)
-* [Stephen Bush](/StephenBush)
-
-#### C-Cg
-
-* [Davide Cacchiarelli](/davidecacchiarelli)
-* [Hugh Cahill](/HughCahill)
-* [Melissa Caimano](/MelissaCaimano)
-* [Matthew Caley](/matthewcaley)
-* [/Christopher Callaway](/Christopher Callaway)
-* [Patrick Callegari](/PatrickCallegari)
-* [Gray Camp](/Gray Camp)
-* [Corey Campbell](/CoreyCampbell)
-* [Greg Campbell](/GregCampbell)
-* [Miguel Reina Campos](/MiguelReinaCampos)
-* [Javier Canton](/JavierCanton)
-* [Huifen Cao](/hfcao)
-* [Leandro Lunardini Cardoso](/Leandro Lunardini Cardoso)
-* [Paula Carlson](/Paula Carlson)
-* [Pierre Carrier](/Pierre Carrier)
-* [Jennifer Carter](/JenniferCarter)
-* [Giancarlo Castellano](/GiancarloCastellano)
-* [Elena Castellanos](/ElenaCastellanos)
-* [Vincent Castric](/VincentCASTRIC)
-* [Manuel Castro](/ManuelCastro)
-* [Alessia Catozzi](/AlessiaCatozzi)
-* [Armand Cavé-Radet](/Armand Cavé-Radet)
* [Martin Čech](/Marten)
-
-##### Cha-Che
-
-* [Marc Chakiachvili](/MarcChakiachvili)
-* [Matt Chambers](/Matt Chambers)
-* [Andrew Chapman](/Andrew Chapman)
-* [Brad Chapman](/BradChapman)
-* [Mathieu Charles](/MathieuCharles)
-* [Kumardeep Chaudhary](/kumardeep)
-* [Saumyadripta Chaudhuri](/Saumyadripta Chaudhuri)
-* [Lianfu Chen](/Lianfu Chen)
-* [Liang Chen](/Liang Chen)
-* [Mark Chen](/markchen)
-* [Shuwen Chen](/ShuwenChen)
-* [Wen Chen](/wenchen)
-* [Wuyan Chen](/wuyanchen)
-* [Zhao Chen](/zhao chen)
-* [Iouri Chepelev](/IouriChepelev)
-* [Andrew Cchess](/andrew.chess@mssm.edu)
-* [Kyle Chessman](/Kyle Chessman)
-* [Sergei Chetyrkin](/SergeiChetyrkin)
-* [Tom Cheung](/Tom Cheung)
-
-##### Chf-Cn
-
-* [Milan Chheda](/MilanChheda)
-* [Rayan Chikhi](/rayan)
-* [Alistair Chilcott](/Alistair Chilcott)
* [John Chilton](/JohnChilton)
-* [Ginam Cho](/GinamCho)
-* [Nikhil Chopra](/chopranik)
-* [Ratan Chopra](/RATAN CHOPRA)
-* [Saket Choudhary](/Saket Choudhary)
-* [Baharul Choudhury](/Baharul)
-* [Kapeel Chougule](/kapeel)
-* [Nivedita Chowdhury](/NiveditaChowdhury)
-* [Shimul Chowdhury](/ShimulChowdhury)
-* [Cynthia Clark](/CynthiaClark)
* [Dave Clements](/DaveClements)
-* [Olivier Claude](/OlivierClaude)
-
-##### Co
-
-* [Tina Cochran](/TinaCochran)
-* [Peter Cock](/peterjc)
-* [Ilsa Coleman](/IlsaColeman)
-* [Michael Collins](/MCollins)
-* [Serafin Colmenares](/Serafin Colmenares)
-* [Arturo Contreras](/ArturoContreras)
-* [Tanya Copley](/TanyaCopley)
-* [Ira Cooke](/iracooke)
-* [Steven Coon](/StevenCoon)
-* [Daniel Cooper](/DanielCooper)
-* [Kerry Cooper](/KerryCooper)
-* [Frederik Coppens](/Frederik Coppens)
-* [Maddalena Coppo](/MaddalenaCoppo)
* [Nate Coraor](/nate)
-* [Elihu Cortes](/ElihuCortes)
-* [Frederico Costa](/FredericoCosta)
-* [Eleanor Cottam](/EleanorCottam)
-
-##### Cp-Cz
-
-* [Dustin Cram](/DustinCram)
-* [Emily Crane](/Emily Crane)
-* [Jeroen Crappe](/JeroenCrappe)
-* [Daniel Crespo](/dan)
-* [Mark Crowe](/MarkCrowe)
-* [Michael Crusoe](/mcrusoe)
-* [Gianmauro Cuccuru](/GianmauroCuccuru)
-* [Jun Cui](/JunCui)
-
-#### D-Dd
-
-* [Nathan D](/Nathan)
-* [David Dai](/David Dai)
-* [Richard Daines](/Richard Daines)
-* [Ryan Dalton](/ryandalton)
-* [Yanir Damti](/yanir)
-* [Linh Dang](/LinhDang)
-* [Jonatan Darr](/jonatandarr)
-* [Benjamin Datko](/bdatko)
-* [Romina Daurizo](/Romina)
-* [Marco Davila](/MarcoDavila)
-* [Mary Davis](/MaryDavis)
-* [Wade Davis](/WadeDavis)
-
-#### De
-
-* [Pieter De Bleser](/Pieter De Bleser)
-* [Thon Deboer](/ThonDeboer)
-* [Thon de Boer](/Thondeboer)
-* [Freek de Bruijn](/FreekDeBruijn)
-* [Regis Debruyne](/RegisDebruyne)
-* [Nanine de Groot](/NaninedeGroot)
-* [Gabe De Leon](/Gabe De Leon)
-* [Michael Demeure](/MichaelDemeure)
-* [Gulfem Demir](/GulfemDemir)
-* [Kam Tai Dermawan](/Kam Tai Dermawan)
-* [Vivien Deshaies](/VivienDeshaies)
-* [Matt De Smet](/matthdsm)
-* [Marie de Tayrac](/DE TAYRAC)
-* [Peter DeWitt](/PeterDeWitt)
-
-##### Di-Dr
-
-* [Bianca Diaz](/BiancaDiaz)
-* [Rachel Dickinson](/racheldickinson)
-* [Cody Diehl](/CodyDiehl)
-* [Riccardo Di Guida](/RiccardoDiGuida)
-* [Samuel Dodd](/SamuelDodd)
-* [Michael Donaldson](/MichaelDonaldson)
-* [Frank Donovan](/FrankDonovan)
-* [Charles Dorward](/CharlesDorward)
-* [Alex Douglas](/Alex D)
-* [Scott Doyle](/ScottDoyle)
-* [Anne Drolet](/AnneDrolet)
-* [Jan Drouaud](/JanDrouaud)
-
-##### Ds-Dz
-
-* [Steve D'Sa](/SteveD)
-* [Isabel Duarte](/Isabel Duarte)
-* [CRA Duff-Farrier](/celiaduff)
-* [Rachel Duffie](/RachelDuffie)
-* [Tomas Duffy](/Tomas Duffy)
-* [Karel van Duijvenboden](/KarelvanDuijvenboden)
-* [/Luke Dunning](/Luke Dunning)
-* [Yen Duong](/yhduong)
-* [Sekhar Duraisamy](/Sekhar Duraisamy)
-* [Bas Dutilh](/dutilh)
-* [Mick Dye](/Mick Dye)
-* [Matt Dyer](/MattDyer)
-
-#### E
-
-* [Carl Eberhard](/CarlEberhard)
-* [James Eddy](/JamesEddy)
-* [Michel Edwar](/MichelEdwar)
-* [Greg Edwards](/GregEdwards)
-* [John Edwards](/JohnEdwards)
-* [Johannes Eichner](/JohannesEichner)
-* [Abdel Elkahloun](/Elkahloun abdel)
-* [Pekka Ellonen](/PekkaEllonen)
-* [Salah Fatouh Abou Elwafa](/Salah Fatouh Abou-Elwafa)
-* [Eric Enns](/EricEnns)
-* [John Eppley](/John Eppley)
-* [Elizabeth Epps](/ElizabethEpps)
-* [Burcu Ermetal](/BurcuErmetal)
-* [Raniel Esguerra](/RanielEsguerra)
-* [Graham Etherington](/GrahamEtherington)
-* [Jason Evans](/JasonEvans)
-
-#### F
-
-* [Annum Faisal](/Annum)
-* [Luka Fajs](/LukaFajs)
-* [Hossein Fallahi](/hosseinfallahi)
-* [Itay Fayerverker](/ItayFayerverker)
-* [Alexander Favorov](/favorov)
-* [Giancarlo Feliciello](/Giancarlo Feliciello)
-* [Maria Fergusson](/MariaFergusson)
-* [Shawn Ferguson](/ShawnFerguson)
-* [Mark Fernandes](/MarkFernandes)
-* [Andrew Fields](/AndrewFields)
-* [Chris Fields](/cjfields)
-* [Harry Fischl](/HarryFischl)
-* [Giuseppe Fiume](/GiuseppeFiume)
-* [Ellis Fok](/ellisfok)
-* [Brian Foley](/BrianFoleyLANL)
-* [David Foltz](/DavidFoltz)
-* [Christian Fougner](/ChristianFougner)
-* [Gary Fox](/garylfox)
-* [Warren Francis](/WarrenFrancis)
-* [Gus Frangou](/GusFrangou)
-* [Michael Freiberg](/MichaelFreiberg)
-* [Kenlee Friesen](/KenleeFriesen)
-* [Tanja Froehlich](/Tanja Froehlich)
-
-#### G-Ge
-
-* [Pranavathiyani G](/Pranavathiyani G)
-* [Sierra Gabriel](/SierraGabriel)
-* [Michele Gabriele](/MicheleGabriele)
-* [Sean Gallaher](/SeanGallaher)
-* [Prasad Gandham](/prasadgandham)
-* [Khanjan Gandhi](/KhanjanGandhi)
-* [Carrie Ganote](/CarrieGanote)
-* [Alexander Garcia-Zea](/alexander)
-* [Rodrigo Garcia](/RodrigoGarcia)
-* [Aaron Gardner](/Aaron)
-* [Carmen Garrido](/CarmenGarrido)
-* [GCC2016 Editor](/GCC2016Editor)
-* [Tom Geissmann](/Tom Geissmann)
-* [Diego Gelsinger](/DiegoGelsinger)
-* [Mathieu Genete](/MathieuGENETE)
-* [Glenn S. Gerhard](/Glenn S. Gerhard)
-* [Sylvie Gervier](/sylvieGervier)
-
-#### Gf-Gn
-
-* [Hamid Ghaedi](/HamidGhaedi)
-* [Almas Gheyas](/AlmasGheyas)
-* [Tania Ghosh](/taniaghosh)
-* [Abbie Gillen](/AbbieGillen)
-* [Patrick Gillevet](/pmgillevet)
-* [Aman Gill](/amango1029)
-* [Genna Gliner](/GennaGliner)
-* [Christophe Ginevra](/ChristopheGinevra)
-* [Simon Gladman](/SimonGladman)
-* [Jonathan Glass](/JonathanGlass)
-
-##### Go-Go
-
* [Jeremy Goecks](/JeremyGoecks)
-* [Preethi Golconda](/PreethiGolconda)
-* [Ted Goldstein](/TedGoldstein)
-* [Ryan Golhar](/RyanGolhar)
-* [Carlos Goller](/CarlosGoller)
-* [Kseniya Golovnina](/KseniyaGolovnina)
-* [Eugene Goltsman](/EugeneGoltsman)
-* [Ann Gomez](/AnnGomez)
-* [Jose Gomez-Arroyo](/Jose Gomez-Arroyo)
-* [Adrian Gonzalez](/adrian gonzalez)
-* [Getzabet Gonzalez](/Getzabet Gonzalez)
-* [George Gooden](/GeorgeGooden)
-* [Nuwan Goonasekera](/Nuwan Goonasekera)
-* [Daniel Gordillo](/Daniel Gordillo)
-* [Paul Gordon](/PaulGordon)
-* [Samridhi Goswami](/SamridhiGoswami)
-* [Y Gou](/YG)
-
-#### Gp-Gz
-
-* [Melissa Graham](/MelissaGraham)
-* [Vladimir Gritsenko](/VladimirGritsenko)
-* [Maya Groner](/MayaGroner)
-* [Christian Schulze Gronover](/ChristianSchulzeGronover)
-* [Bjoern Gruening](/BjoernGruening)
-* [Stefanie Grunwald](/Stefanie Grunwald)
-* [Dongqing Gu](/holly)
-* [Isabel Guerreiro](/isabelguerreiro)
* [Sam Guerler](/guerler)
-* [Mehmet Gültas](/mehmetgültas)
-* [Bing Guo](/BingGuo)
-* [Ankit Gupta](/Ankit Gupta)
-* [Sukrit Gupta](/Sukrit)
-* [Montserrat Gustems](/montsegustems)
-* [Lionel Guy](/LionelGuy)
-
-#### H-Hh
-
-* [Yuhui H](/eyecat)
-* [Eric Haag](/EricHaag)
-* [Christophe Habib](/christopheH)
-* [Waseem Haider](/WaseemHaider)
-* [Vahid Hajihoseini](/vdhoseini)
-* [/Rashi Halder](/Rashi Halder)
-* [Khaled Hazzouri](/Khaled Hazzouri)
-* [Bing He](/Bing He)
-* [Ding He](/dinghe)
-* [Renjie He](/MDACC)
-* [Zhengshan He](/sanvva)
-* [David Hearn](/DavidHearn)
-* [Abdel Heddar](/AbdelHEDDAR)
-* [Leo Heijnen](/LeoHeijnen)
-* [Hanna Helgeland](/HannaHelgeland)
-* [Bart Hellemans](/Bart Hellemans)
-* [Curtis Hendrickson](/CurtisHendrickson)
-* [Curtis Hendrickson](/curtish@uab.edu)
-* [Diego Herrera](/Diego Herrera)
-* [Daisy Hessenberger](/DaisyHessenberger)
-* [Naomi Heuer](/NaomiHeuer)
* [Mo Heydarian](/MoHeydarian)
-
-#### Hi-Ht
-
-* [Alison Hill](/AlisonHill)
-* [Richard Hill](/Richard Hill)
-* [Andrew Hillhouse](/AndrewHillhouse)
-* [Saskia Hiltemann](/SaskiaHiltemann)
-* [Dan Holle](/DanHolle)
-* [Myles Hollenbach](/MylesHollenbach)
-* [William Holtz](/WilliamHoltz)
-* [Youri Hoogstrate](/yhoogstrate)
-* [Aniruddho Chokroborty Hoque](/aniruddhochokrobortyhoque)
-* [Adam Horn](/AdamHorn)
-* [Ron Horst](/RonHorst_UQ)
-* [Hans-Rudolf Hotz](/HansrudolfHotz)
-* [Torsten Houwaart](/TorstenHouwaart)
-
-#### Hu-Hz
-
-* [Nicholas Hu](/Nicholas Hu)
-* [Zhenhua Hu](/Zhenhua Hu)
-* [Lei Huang](/Lei Huang)
-* [Lijia Huang](/LijiaHuang)
-* [Yen-Hua Huang](/Yen-Hua Huang)
-* [Megan Hudgell](/MeganHudgell)
-* [/Laura Hug](/Laura Hug)
-* [Asgar Hussain](/asgarhussain)
-* [Stephan Hutter](/StephanHutter)
-* [Michelle Hwang](/Michelle Hwang)
-
-#### I
-
-* [Rebeca Ibarra](/RebecaIbarra)
-* [Hubert Klein Ikkink](/Hubert Klein Ikkink)
-* [M. A. Iquebal](/asif)
-
-#### J-Jn
-
* [Jennifer Jackson](/JenniferJackson)
-* [/Joachim Jacob](/Joachim Jacob)
-* [Joachim Jacob](/JoachimJacob)
-* [/Rohit Jadhav](/Rohit Jadhav)
-* [Benjamin Jahnes](/bmiben)
-* [Vahid Jalili](/VahidJalili)
-* [Michael James](/Michael JAMES)
-* [Maika Jangal](/MaikaJangal)
-* [Ranveer Jayani](/RanveerJayani)
-* [Kiran Jaycee](/Kiran Jaycee)
-* [Brendan Jeffrey](/BrendanJeffrey)
-* [XiaoRao Jiang](/biofutureJIANG)
-* [Mingda Jin](/MingdaJin)
-* [Seung Gi Jin](/Seung-Gi Jin)
-
-#### Jo-Jz
-
-* [Simon Jochems](/SimonJochems)
-* [Ed Johnson](/EdJohnson)
-* [JJ Johnson](/jjohnson)
-* [Nathan Johnson](/Nathan Johnson)
-* [Sean Johnson](/SeanJohnson)
-* [David Jones](/DavidJones)
-* [Robert Jones](/Robert Jones)
-* [Tyler Jones](/TylerJones)
-* [Francois Jordier](/francois jordier)
-* [Nikhil Joshi](/NikhilJoshi)
-* [Jaimy Joy](/JaimyJoy)
-* [Segun Jung](/SegunJung)
-* [Sean Jungbluth](/SeanJungbluth)
-
-#### K-Kg
-
-* [Neethukrishna K](/nkausthu)
-* [Priyanka Kachroo](/PriyankaKachroo)
-* [Tim Kahlke](/TimKahlke)
-* [Hossein Valipour Kahrood](/HosseinValipourKahrood)
-* [Larisa Kamga](/LarisaKamga)
-* [Iyad Kandalaft](/IyadKandalaft)
-* [Junsu Kang](/junsu_kang)
-* [Kyuho Kang](/KyuhoKang)
-* [Qing Kang](/Qing Kang)
-* [Jan Kanis](/JanKanis)
-* [Amrit Karki](/Amrit Karki)
-* [Oleksiy Karpenko](/OleksiyKarpenko)
-* [Ravi Karra](/RaviKarra)
-* [Hatakeyama Katsunori](/Hatakeyama Katsunori)
-* [Alaattin Kaya](/Alaattin Kaya)
-* [John Kearsing](/kearsing)
-* [Ken Keiler](/KenKeiler)
-* [Caroline Keroack](/CarolineKeroack)
-* [Grainne Kerr](/grainnekerr)
-* [Jessica Keys](/JessicaKeys)
-
-#### Kh-Ki
-
-* [Vadim Khaychuk](/Vadim Khaychuk)
-* [Radhika Khetani](/RadhikaKhetani)
-* [Hamid Khoja](/hamidkhoja)
-* [Kyusik Kim](/kyusikkim)
-* [Min-Sik Kim](/MinsikKim)
-* [Sanghyun Kim](/SanghyunKim)
-* [Heather Kinkead](/heatherkinkead)
-* [Noah Kinstlinger](/NoahKinstlinger)
-* [Ilya Kirov](/Ilya)
-* [Edward Kirton](/EdwardKirton)
-
-##### Kj-Kq
-
-* [Kevin Klatt](/KevinKlatt)
-* [Karin Klauke](/KarinKlauke)
-* [Kjetil Klepper](/KjetilKlepper)
-* [David Klinzing](/DavidKlinzing)
-* [Jared Knoblauch](/JaredKnoblauch)
-* [Kamila Knapik](/KamilaKnapik)
-* [Guus Koch](/guuskoch)
-* [Felix Kokocinski](/felix kokocinski)
-* [Joseph Koral](/JosephKoral)
-* [Katharine Korunes](/KatharineKorunes)
-* [Madhuri Kota](/MadhuriK)
-* [Evgueni Kountikov](/kount002)
-* [Yousef Kowsar](/YousefKowsar)
-* [Krzysztof Kozak](/KrzysztofKozak)
-
-#### Kr-Kz
-
-* [Jason Kralj](/JasonKralj)
-* [Krish Krishnan](/Krish Krishnan)
-* [Alper Kucukural](/AlperKucukural)
-* [Joanna Kuehn](/JoannaKuehn)
-* [Aneesh Kumar](/Aneesh)
-* [Arun Kumar](/arund-123)
-* [G. Prashanth Kumar](/G Prashanth kumar)
-* [Gaurav Kumar](/GauravKumar)
-* [Raina Kumar](/RainaKumar)
-* [Sanjay Kumar](/SanjayKumar)
-* [Dale Kunde](/DaleKunde)
-* [Sharbadeb Kundu](/SharbadebKundu)
-* [Cheng-Ju Kuo](/noturtle)
-* [Vlad Kustanovich](/VladKustanovich)
-* [Ryan Kuster](/RyanKuster)
-* [Jenny Kuo](/jennykuo)
-* [ Vladimir Yurjevich Kuryshev](/vkuryshev)
-* [Jaana Kuuskeri](/JaanaKuuskeri)
-
-#### L-Ld
-
-* [Paul Labhart](/PaulLabhart)
-* [Arnaud Lagarde](/arnaudlagarde)
-* [Kevin Lahmers](/KevinLahmers)
-* [Yec'han Laizet](/ylaizet)
-* [Ellen Lambrecht](/EllenLambrecht)
-* [John Lane](/John Lane)
-* [Yuekun Lang](/yuekun)
-* [Brad Langhorst](/BradLanghorst)
-* [John Lapage](/JohnLapage)
-* [Jason Laramie](/JasonLaramie)
-* [Delphine Lariviere](/DelphineLariviere)
-* [Yaniv Lerenthal](/yanivlerenthal)
-* [Amanda Larracuente](/AmandaLarracuente)
-* [Charles Lawrie](/claw)
-* [Heather Lawson](/HeatherLawson)
-* [Lucinda Lawson](/Lucinda.Lawson)
-* [Fides Lay](/fideslay)
-* [Dejan Lazarevic](/dejan lazarevic)
* [Ross Lazarus](/fubar)
-
-##### Le-Lh
-
-* [Anh Le](/AnhLe)
-* [Zach LeBlanc](/zach)
-* [Yvan Le Bras](/YvanLeBras)
-* [Hyungro Lee](/HyungroLee)
-* [Jae Hyung Lee](/JaeHyungLee)
-* [Jacqueline Lee](/JacquelineLee)
-* [Jeehun Lee](/JeehunLee)
-* [/Keunsub Lee](/Keunsub Lee)
-* [Kwanghyuk Lee](/KwanghyukLee)
-* [Nate Lee](/NateLee)
-* [Seungwoo Lee](/SeungwooLee)
-* [Đức LêHoàng](/lehoangduc)
-* [Mary Beth Leigh](/MaryBethLeigh)
-* [Alex Lenail](/AlexLenail)
-* [Sarah Lenhert](/Sarah)
-* [Andreas Lennartsson](/andreaslennartsson)
-* [Kathleen Lennon](/Kathleen Lennon)
-* [Janet Leung](/JanetLeung)
-* [Brandt Levitt](/BrandtLevitt)
-* [Susanna Lewis](/SusannaLewis)
-
-##### Li-Lim
-
-* [Brittney Li](/BrittneyLi)
-* [Jay Li](/jay li)
-* [Kanwei Li](/KanweiLi)
-* [Miaozhu Li](/selaginella)
-* [Siyang Li](/SiyangLi)
-* [Yan-Hui Li](/yanhuili)
-* [Yongsheng Li](/lyshaerbin)
-* [Yudong Li](/adong)
-* [Yongle Li](/yongle.li)
-* [Chun Liang](/ChunLiang)
-* [Yupu Liang](/yupuliang)
-* [Zhange Liangtao](/ZhangeLiangtao)
-* [Noha Lim](/limnoha)
-* [Robyn Lim](/RobynLim)
-* [Yasmin Lima](/Yasmin Lima)
-
-##### Lin-Liz
-
-* [Biaoyang Lin](/blin98021)
-* [/Dave Lin](/Dave Lin)
-* [Yao Cheng Lin](/YaoChengLin)
-* [Scott Lindner](/ScottLindner)
-* [Lauren Lindsey](/LaurenLindsey)
-* [Scott Linford](/Scott Linford)
-* [Elwood Linney](/ElwoodLinney)
-* [Tomislav Lipic](/TomislavLipic)
-* [Karlos Lisboa](/Karloslisboa)
-* [Bryce Little](/BryceLittle)
-* [Natasha Little](/nlittle)
-* [Thomas Little](/ThomasLittle)
-* [David Liu](/davidliu)
-* [Feng Liu](/Feng Liu)
-* [Yuting Liu](/yuting)
-* [Veranja Liyanapathirana](/Veranja Liyanapathirana)
-
-##### Lj-Lz
-
-* [Jesus Llanderal](/Jesus Llanderal)
-* [Cecilia Lopez](/MCeciliaLopez)
-* [Joseph Loturco](/josephloturco)
-* [Feng Lou](/fenglou)
-* [Wei-Zhao Lu](/wzlu)
-* [Yih-Kuang Lu](/ylu32@asu.edu)
-* [Yih Kuang Lu](/Yih-Kuang Lu)
-* [Yuping Lu](/yupinglu)
-* [Brian Luerman](/BrianLuerman)
-* [Caroline Lund](/CarolineLund)
-* [Jun Luo](/JUNLUO)
-* [Teresa Luperchio](/Teresa Luperchio)
-* [Patrick Lynch](/PatrickLynch)
-* [Heather Lynn](/Heather Lynn)
-
-#### M-Man
-
-* [Jian Ma](/jianma)
-* [Weiwei Ma](/Weiwei Ma)
-* [Philip Mabon](/PhilipMabon)
-* [Glener Diniz Macedo](/Glener Diniz Macedo)
-* [Srinivas Maddhi](/SrinivasMaddhi)
-* [Ravi Madduri](/RaviMadduri)
-* [Chidambareswaren Mahadevan](/chidambareswaren mahadevan)
-* [Aekkapol Mahavihakanont](/AekkapolMahavihakanont)
-* [Ketan Maheshwari](/ketancmaheshwari)
-* [John Major](/john.major)
-* [Jessica Makofske](/JessicaMakofske)
-* [Shivani Malik](/shivani malik)
-* [Ken Mandl](/KenMandl)
-* [Ion Mandoiu](/IonMandoiu)
-* [Evelyne Mann](/Evelyne Mann)
-* [Whitney Mann ](/Whitney Mann)
-* [Mosè Manni](/mosemanni)
-* [Rolando Mantilla](/RolandoMantilla)
-
-#### Mao-Mc
-
-* [Seraya Maouche](/Seraya Maouche)
-* [Remi Marenco](/RemiMarenco)
-* [Michael Marotta](/MichaelMarotta)
-* [Jose Martinez](/JoseMartinez)
-* [Fernanda Maruri](/FernandaMaruri)
-* [Shawn Massoni](/ShawnMassoni)
-* [Takashi Matsumoto](/TakashiMatsumoto)
-* [Chris Mattocks](/mattockscx)
-* [Evangelina Lopez Maturana](/Evangelina)
-* [Laurent Mauvieux](/laurentmauvieux)
-* [Anyi Mazo](/Anyi Mazo)
-* [Andrew McArthur](/AndrewMcArthur)
-* [Honour McCann](/HonourMcCann)
-* [Jan McDowell](/JanMcDowell)
-* [Martin McGavin](/MartinMcGavin)
-* [Nick Mcglincy](/nickMcglincy)
-* [Steve McMahon](/SteveMcMahon)
-* [Scott McManus](/ScottMcManus)
-* [Malcolm McRoberts](/MalcolmMcRoberts)
-* [Emily McTish](/EmilyMcTish)
-
-##### Md-Mn
-
-* [Oliver Mead](/Olivermead89)
-* [Sudeep Mehrotra](/SudeepMehrotra)
-* [Leon Mei](/LeonMei)
-* [Lisa Meihls](/lisameihls)
-* [Roberta Menafra](/Roberta_Menafra)
-* [Daniel Mendez](/Daniel Mendez)
-* [Mirian Mendoza](/mirianmendoza)
-* [Clemens Messerschmidt](/ClemensMesserschmidt)
-* [Jordan Metzgar](/JordanMetzgar)
-* [Gabriel McKinsey](/Gabriel McKinsey)
-* [Marco Miele](/marco)
-* [Max Mikheev](/Max Mikheev)
-* [Aaron Miller](/Aaron Miller)
-* [Emily Miller](/EmilyMiller)
-* [Ross Milne](/RossMilne)
-* [Fayyaz Minhas](/FayyazMinhas)
-* [Anderson Mioranza](/Anderson Mioranza)
-* [Raies Mir](/Raies Mir)
-* [Dianne Mitchell](/DianneMitchell)
-* [Suman Mitra](/suman mitra)
-* [Akira Mitsui](/AkiraMitsui)
-
-##### Mo-Mz
-
-* [Marghoob Mohiyuddin](/Marghoob Mohiyuddin)
-* [Matthias Monfort](/MatthiasM)
-* [Vincent Montoya](/VincentMontoya)
-* [SeongRyeol Moon](/moon)
-* [Raymond Moore](/Raymond Moore)
-* [Blai Morales](/BlaiMorales)
-* [Pablo Moreno](/PabloMoreno)
-* [Melissa Morine](/MelissaMorine)
-* [Maria Morris](/MariaMorris)
-* [Marco Morselli](/MarcoMorselli)
-* [Oleksandr Moskalenko](/OleksandrMoskalenko)
-* [Kambiz Mousavi](/Kambiz Mousavi)
-* [Eileen Muhs](/EileenMuhs)
-* [Robert Mukiibi](/Robert Mukiibi)
-* [Sanjit Mukherjee](/SanjitMukherjee)
-* [Subhas Mukherjee](/Subhas Mukherjee)
-* [McKay Mullen](/McKay Mullen)
-* [Ann Mullin](/AnnMullin)
-* [Koichi Murata](/KoichiMurata)
-* [Bri Murphy](/BriMurphy)
-* [Charles Murphy](/Charles Murphy)
-* [Gabe Musso](/GabeMusso)
-* [Munyaradzi Musvosvi](/MunyaradziMusvosvi)
-
-#### N
-
-* [Krystyna Nadachowska-Brzyska](/Krystyna Nadachowska-Brzyska)
-* [Jin-Wu Nam](/jinwunam)
-* [Sara Napoli](/SaraNapoli)
-* [Yayoi Natsume](/Yayoi Natsume)
-* [Vincent Navratil](/navratil)
-* [Anuraj Nayarisseri](/Anuraj)
-* [Alex Neagu](/AlexNeagu)
* [Anton Nekrutenko](/anton)
-* [James Nelson](/JamesNelson)
-* [Nathan Nelson-Maney](/NathanNelsonManey)
-* [Ulrich Neuss](/UlrichNeuss)
-* [Helene Neyret-Kahn](/Helene Neyret-Kahn)
-* [Taylor Nicholas](/Taylor Nicholas)
-* [Minghua Nie](/minghuanie)
-* [Malwina Niemczyk](/MalwinaNiemczyk)
-* [Taina Nieminen](/Taina Nieminen)
-* [Farshad Niri](/Farshad Niri)
-* [James Nishiura](/JamesNishiura)
-* [Julie Nocq](/JulieNocq)
-* [Shelly Nolin](/Shelly Nolin)
-* [Shelly Nolin](/ShellyNolin)
-* [Elphège-Pierre Nora](/enora)
-
-#### O
-
-* [Olabisi Ojo](/bisiojo)
-* [Sara Oppenheim](/SaraOppenheim)
-* [Anthony Oro](/anthonyoro)
-* [Marc Oshiro](/Marc Oshiro)
-
-
-#### Pa
-
-* [Annalise Paaby](/AnnalisePaaby)
-* [ES Paegle](/ES Paegle)
-* [Scott Page](/ScottPage)
-* [Rish Pai](/RishPai)
-* [Mariano Palena](/MarianoPalena)
-* [Peter Palenchar](/PeterPalenchar)
-* [C Parameswaran](/Parameswaran)
-* [Christian Parisod](/ChristianParisod)
-* [Anson Parker](/AnsonParker)
-* [Valeria Parreira](/Valeria Parreira)
-* [Jean Parry](/JeanParry)
-* [Shikha Parsai](/ShikhaParsai)
-* [Lance Parsons](/LanceParsons)
-* [Marianna Pasquariello](/MariannaPasquariello)
-* [Ferran Pastor](/Ferran)
-* [Barak Pat](/barakpat)
-* [Chinar Patil](/ChinarPatil)
-* [Bill Pavan](/BillPavan)
-* [Paolo Pavan](/PaoloPavan)
-* [Shantanu Pavgi](/ShantanuPavgi)
-* [Kevin Pawlik](/KevinPawlik)
-* [Rosalia Paz](/Rosalia Paz)
-
-##### Pb-Pi
-
-* [Stéphane PEILLET](/StéphanePEILLET)
-* [Richard Pelikan](/richardpelikan)
-* [Matt Pelletier](/MattPelletier)
-* [Xiaoxiao Peng](/pxxjuve)
-* [Mark Pepin](/Mark Pepin)
-* [Serrano Pereira](/swp)
-* [Cristian Perez](/CristianPerez)
-* [Christel Petersen](/ChristelPetersen)
-* [Jessica Petersen](/JessicaPetersen)
-* [Giuseppe Petrosino](/GiuseppePetrosino)
-* [Christopher Phiel](/ChristopherPhiel)
-* [Matthieu Pichaud](/MatthieuPichaud)
-* [Ruth Pidsley](/RuthPidsley)
-* [Robert Ping](/RobertPing)
-
-##### Pj-Pz
-
-* [/Beatrice Plougastel](/Beatrice Plougastel)
-* [Michael Plunkett](/MichaelPlunkett)
-* [Lexy Plumer](/LexyPlumer)
-* [A. A. Pochtovyy](/A_Pochtovyy)
-* [Harry Podschwit](/HarryPodschwit)
-* [Renita Polk](/RENITA POLK)
-* [Dmitrii Polev](/Dmitrii Polev)
-* [/Trinadh Potina](/Trinadh Potina)
-* [/Bindu Poudel](/Bindu Poudel)
-* [Alexandre Prokoudine](/AlexandreProkoudine)
-* [Caroline Puente](/CarolinePuente)
-* [Antonio Puertas-Gallardo](/antonio.pg)
-* [Jane Pulman](/JanePulman)
-* [Amaury Pupo](/AmauryPupo)
-
-#### Q
-
-* [Danjuma Quarless](/danjumaquarless)
-* [Roel Quintens](/Roel Quintens)
-
-#### R-Rh
-
-* [Tori R](/ToriR)
-* [Henry Raab](/HenryRaab)
-* [Xue-Qin RAN](/xqran)
-* [Utkarsh Raghuvanshi](/utkarsh raghuvanshi)
-* [Raghu Rajasekaran](/Raghu Rajasekaran)
-* [Saumita Rajeevan](/SaumitaRajeevan)
-* [Anto Rajkumar](/antoprajkumar)
-* [M V Ramanujam](/M V RAMANUJAM)
-* [Thiru Ramaraj](/Thiru Ramaraj)
-* [Thomas Randall](/Thomas Randall)
-* [Carlo Randise-Hinchliff](/carlohinchliff)
-* [/Noa Rappaport](/Noa Rappaport)
-* [Eric Rasche](/EricRasche)
-* [Sebastian Raveendar](/Sebastian Raveendar)
-* [Adarsh Reddy](/AdarshReddy)
-* [Chethan Reddy](/ChethanReddy)
-* [Puli Chandramouli Reddy](/pulichandramoulireddy)
-* [Amy Reed](/AmyReed)
-* [Wu Rentian](/wurentian)
-* [Justyna Resztak](/Justyna Resztak)
-* [Tony Reynolds](/TonyReynolds)
-* [Tim Rhoads](/TimRhoads)
-
-##### Ri-Rz
-
-* [Karlos Ribeiro](/karlosribeiro)
-* [Jonathan Richards](/JonathanRichards)
-* [Vera Rinaldi](/VeraRinaldi)
-* [Yazmin Rivera](/YazminRivera)
-* [Eli Roberson](/eli)
-* [Britt Robinette](/BrittRobinette)
-* [Steven Rodriguez](/Steven)
-* [Clare Rollie](/ClareRollie)
-* [Bruce Rosa](/BruceRosa)
-* [Toon Rosseel](/ToonRosseel)
-* [Simona Rossi](/SimonaRossi)
-* [Kevin Rosso](/Kevin Rosso)
-* [Pascal Rousse](/PascalRousse)
-* [Julian Rozenberg](/JulianRozenberg)
-* [Jeremy Rualo Sr](/JeremyRualoSr)
-* [Luca Rubino](/LucaRubino)
-* [Vasilisa Rudneva](/VasilisaRudneva)
-* [Amit Rupani](/Amit Rupani)
-* [Julia Russell](/Julia Russell)
-* [Candice Ryan](/CandiceRyan)
-* [Devon Ryan](/DevonRyan)
-* [Kalle Rytkonen](/KalleRytkonen)
-
-#### S-Sb
-
-* [Frank Sainsbury](/FrankSainsbury)
-* [Rehan Saleem](/linx786)
-* [Ahmad Salehi](/Ahmad Salehi)
-* [Elias Salfati](/Eliyas)
-* [Dhanushki Samaranayake](/Dhanushki Samaranayake)
-* [Duleep Kumar Samuel](/dksamuel@gmail.com)
-* [Jessika Samuels](/Jessika Samuels)
-* [Sukhinder Sandhu](/Sukhinder Sandhu)
-* [Rosiane Santos](/Rosiane)
-* [Santosh](/santosh)
-* [Kavyashree Santoshkumar](/Kavyashree)
-* [Sean Sapcariu](/SeanSapcariu)
-* [Sarika](/sarika)
-* [Viswanathan Satheesh](/Viswanathan Satheesh)
-* [Andrea Sbardellati](/sbardell)
-
-##### Sc
-
-* [Sebastian Schaaf](/SebastianSchaaf)
-* [Du Toit Schabort](/Du Toit Schabort)
-* [Claudia Scheckel](/ClaudiaScheckel)
-* [Herb Schellhorn](/HerbSchellhorn)
-* [Andreas Scherer](/AndreasScherer)
-* [Armin Schmitt](/Quiddity)
-* [Sebastian Schoenherr](/SebastianSchoenherr)
-* [Jelle Scholtalbers](/Jelle)
-* [Matthew Scholz](/matthewscholz)
-* [Peter Schotland](/PeterSchotland)
-* [Christian Schudoma](/ChristianSchudoma)
-* [Sebastian Schultheiss](/SebastianSchultheiss)
-* [Michael Schultze](/Michael Schultze)
-* [Katharine Schulz](/KatharineSchulz)
-* [Rachel Schwallier](/RachelSchwallier)
-* [Laura Scifo](/Laura Scifo)
-
-##### Sd-Se
-
-* [Anna Seekatz](/Anna)
-* [Rebecca Seipelt-Thiemann](/RebeccaSeipeltThiemann)
-* [Nick Semenkovich](/NickSemenkovich)
-* [Arun Sethuraman](/arunsethuraman)
-* [Surya Setiyaputra](/SuryaSetiyaputra)
-* [Fernando Seixas](/FernandoSeixas)
-* [Rahil Sethi](/Rahil Sethi)
-
-##### Sf-Sh
-
-* [Nilay Shah](/Nilay Shah)
-* [Zeeshan Ali Shah](/zeeshanalishah)
-* [Esmaeil Shahsavari](/esmaeilshahsavari)
-* [Mike Shamblott](/mikeshamblott)
-* [Boyoung Shin](/Boyoung Shin)
-* [Matt Shirley](/MattShirley)
-* [Ido Shlomovich](/idoshlomovich)
-* [Dylan Short](/DylanShort)
-* [Brikha Shrestha](/Brikha Shrestha)
-* [Megan Shortridge](/MeganShortridge)
-* [Louise Shuey](/LouiseShuey)
-
-##### Si
-
-* [Thomas Sibley](/trs)
-* [Nikos Sidiropoulos](/NikosSidiropoulos)
-* [Marojahan Mula Timbul Sigiro](/marojahan)
-* [Kenneth Sikora](/KennethSikora)
-* [Christophe Simian](/Christophe SIMIAN)
-* [Rachel Simister](/rachelsimister)
-* [Christopher Simmons](/ChristopherSimmons)
-* [Seth Sims](/Seth Sims)
-* [Arpit Singh](/Arpit Singh)
-* [Ashish Kumar Singh](/ashish kumar singh)
-* [Manu Singh](/Manu Singh)
-* [Narinderbir Singh](/Narinderbir Singh)
-* [Prashant K Singh](/Prashant K Singh)
-* [Sanjay Singh](/sanjaysingh)
-* [Sugandha Singh](/Sugandha Singh)
-* [Ryan Sisk](/RyanSisk)
-* [Mio Sison](/MioSison)
-
-##### Sj-Ss
-
-* [Nikolai Slavov](/NikolaiSlavov)
-* [Cameron Smith](/CameronSmith)
-* [Eric Smith](/EricSmith)
-* [Robin Smith](/RobinSmith)
-* [Zach Smith](/ZachSmith)
-* [Redmond Smyth](/RedmondSmyth)
-* [Daniel Sobral](/DanielSobral)
-* [Ramakrishna Sompallae](/Ramakrishna)
-* [Nicola Soranzo](/NicolaSoranzo)
-* [Daan Speth](/DaanSpeth)
-* [Ola Spjuth](/OlaSpjuth)
-* [/Kim Spradling](/Kim Spradling)
-* [Sridhar Srinivasan](/sridharsrinivasan)
-* [Pisitsak Sriwimol](/PisitsakSriwimol)
-* [Reuben Ssali](/Reuben SSALI)
-
-##### St
-
-* [Helen Stagg](/HelenStagg)
-* [Ian Stansfield](/IanStansfield)
-* [Kelly Steele](/KellySteele)
-* [Franck Stefani](/FranckStefani)
-* [James Stegen](/JamesStegen)
-* [Jaroslav Steinhaisl](/JaroslavSteinhaisl)
-* [Suzan Stelloo](/Suzan)
-* [Jared Steranka](/JaredSteranka)
-* [Nick Stoler](/nickstoler)
-* [William Strauss](/Cyclotouriste)
-* [Magdalena Strzelecka](/MagdalenaStrzelecka)
-
-##### Su-Sz
-
-* [Mack Su](/Mack Su)
-* [Subu Subramanian](/subu)
-* [Chihiro Suga](/Chihiro Suga)
-* [Gauthaman Sukumar](/Gauthaman Sukumar)
-* [/Dan Sullivan](/Dan Sullivan)
-* [Hanfei Sun](/hanfeisun)
-* [Melanie Sun](/MelanieSun)
-* [Yanan Sun](/YananSun)
-* [Peter Sung](/PeterSung)
-* [Naeem Hasan Syed](/Naeem Hasan Syed)
-* [Ilya Sytchev](/IlyaSytchev)
-* [Robert Syme](/RobertSyme)
-* [Scott Szakonyi](/ScottSzakonyi)
-* [Jamie Sziklay](/jamies28)
-
-#### T-Th
-
-* [Raymond Tam](/rawtam)
-* [Fei Tan](/Fei Tan)
-* [Yen An Tang](/Yen-An Tang)
-* [Watip Tangjitttipokin](/watip)
-* [Bensellak Taoufik](/bensellaktaoufik)
-* [David Tarazona](/David Tarazona)
-* [Manuel Tavares](/Manuel Tavares)
-* [Jack Taylor](/JackTaylor)
* [James Taylor](/JamesTaylor)
-* [Steve Taylor](/Steve Taylor)
-* [Sven Templer](/setempler)
-* [Maximilian Teutsch](/Maximilian Teutsch)
-* [William Thistle](/williamthistle)
-* [Daniel Thomas](/DanielThomas)
-* [Deepthi Thomas](/DeepthiThomas)
-* [Paul Thomas](/PaulThomas)
-* [Andrew Thompson](/AndrewThompson)
-
-#### Ti-Tz
-
-* [Xue Tian](/xue tian)
-* [Timothy Tickle](/TimothyTickle)
-* [Emma Timmins-Schiffman](/emmatimminsschiffman)
-* [Libert Brice Tonfack](/LB Tonfack)
-* [Tomithy Too](/TomithyToo)
-* [Eric Tremblay](/Eric Tremblay)
-* [Keriann Tremblay](/KeriannTremblay)
-* [David Trudgian](/DavidTrudgian)
-* [Nitesh Turaga](/nturaga)
* [Nitesh Turaga](/NiteshTuraga)
-* [Nik Tuzov](/NikTuzov)
-* [Oleksii Tymchenko](/OleksiiTymchenko)
-
-#### U
-
-* [/Anthony Underwood](/Anthony Underwood)
-* [Alibek Utyubayev](/AlibekUtyubayev)
-
-#### Va
-
-* [Daniel Valbuena](/dvalbuena)
-* [Venkatagopinath Vaija](/venkatagopinath)
-* [Somaye Vaissi](/Somaye)
-* [Leonardo Valdivia](/LeonardoValdivia)
-* [Moez Valliani](/MoezValliani)
-* [Steven Van Belleghem](/Steven Van Belleghem)
-* [Bram Van Bergh](/Bram Van den Bergh)
-* [Marius Van den Beek](/MariusVandenbeek)
-* [Jackie Van der Schoor](/JackieVanderSchoor)
-* [Peter Van Heusden](/PeterVanHeusden)
-* [Edwin van Zon](/Edwinvanzon)
-* [Gabriel Vargas](/GabrielVargas)
-* [Naresh Vasani](/nareshvasani)
-* [Elena Vataga](/ElenaVataga)
-* [Erin Vaughn](/ErinVaughn)
-
-##### Vb-Vz
-
-* [Olaf Vela](/César Olaf Pérez Vela)
-* [Dmitry Velmeshev](/Dmitry Velmeshev)
-* [Anand Venkataraman](/AnandVenkataraman)
-* [Daphne Verdelet](/DaphneVerdelet)
-* [Soetkin Versteyhe](/SoetkinVersteyhe)
-* [Martin Vickers](/mjv08)
-* [Sanja Vickovic](/SanjaVickovic)
-* [James Vincent](/JamesVincent)
-* [Kelly Vincent](/kpvincent@bx.psu.edu)
-* [Juan Vivar](/JuanVivar)
-* [Greg von Kuster](/greg_vonkuster)
-* [Rutger Vos](/RutgerVos)
-* [Alexander Vowinkel](/AlexanderVowinkel)
-
-#### W-Wd
-
-* [Carola Wagner](/CarolaWagner)
-* [Sean Walkowiak](/SeanWalkowiak)
-* [Veryl Walstrom](/Veryl Walstrom)
-* [Jun Wan](/JunWan)
-* [Baohua Wang](/BaohuaWang)
-* [Dongxue Wang](/DongxueWang)
-* [Gang Wang](/wanggang)
-* [Hong Wang](/HongWang)
-* [Jianghui Wang](/JianghuiWang)
-* [Lingyu Wang](/LingyuWang)
-* [Lu Wang](/luwang)
-* [Paul Wang](/Paul Wang)
-* [Weiqi Wang](/weiqi)
-* [Xue Wang](/xuewang)
-* [Yin-Chu Wang](/YCWang)
-* [Yuliang Wang](/Yuliang Wang)
-* [Zheng Wang](/ZhengWang)
-* [Susanne Warrenfeltz](/SusanneWarrenfeltz)
-* [Peter Wasson](/Peter Wasson)
-* [Charles Waters](/CharlesWaters8)
-
-##### We-Wh
-
-* [Eric Weatherford](/Eric Weatherford)
-* [Shaun Webb](/ShaunWebb)
-* [Chris Wedeles](/Chriswedeles)
-* [Pei-Chi Wei](/PeiChiWei)
-* [Zhi Wei](/bnfo620)
-* [Rory Welsh](/RoryWelsh)
-* [Jered Wendte](/Jered Wendte)
-* [Adam Wespiser](/AdamWespiser)
-* [Gordon Wells](/GordonWells)
-* [Adam Wespiser](/AdamWespiser)
-* [Diana West](/DianaWest)
-* [Terry Weymouth](/TerryWeymouth)
-* [Frank White](/Frank White)
-* [Malcolm White](/MalcolmWhite)
-
-##### Wi-Wz
-
-* [Giovanni Widmer](/GiovanniWidmer)
-* [Edwin Wiest](/EdwinWiest)
-* [Julia Wilflingseder](/JuliaWilflingseder)
-* [April Williams](/AprilWilliams)
-* [Scooter Willis](/Scooter Willis)
-* [Janna Willoughby](/JannaWilloughby)
-* [Jane Wilson](/JaneWilson)
-* [Leora Witkowski](/Leora)
-* [Steven Woll](/StevenWoll)
-* [Mike Wosczyna](/wosczyna@stanford.edu)
-* [Daniel Wright](/DanielWright)
-* [Glenn Wozniak](/GlennW)
-
-#### X
-
-* [Wei Xiong](/wei.xiong)
-* [Hong Xu](/Hong Xu)
-* [Zidian Xie](/zidianxie)
-
-#### Y
-
-* [Ryota Yamanaka](/RyotaYamanaka)
-* [Qi Yang](/qi yang)
-* [Sa Yang](/SaYang)
-* [Xi Yang](/XiYang)
-* [Yong Yang](/yongyang)
-* [Ming Yanzhang](/mingyanzhang)
-* [Galip Yardimci](/GalipYardimci)
-* [Dean Yimlamai](/DeanYimlamai)
-* [Kathleen Yin](/KathleenYin)
-* [Kevin Ying](/KevinYing)
-* [Wang Yongqing](/Wang Yongqing)
-* [Ned Young](/NedYoung)
-* [Sewall Young](/SewallYoung)
-* [Kim Youngki](/Kim Youngki)
-* [Julie Yu](/JulieYu)
-* [Sebata Yu](/SebataYu)
-* [Tun Ping Yu](/Tun-Ping Yu)
-* [Jiaxing Yue](/JiaxingYue)
-* [Lilly Yuen](/LillyYuen)
-
-#### Z
-
-* [Konstantinos Zagganas](/KonstantinosZagganas)
-* [David Zappulla](/DavidZappulla)
-* [Lydia Zeglin](/LydiaZeglin)
-* [Chaomei Zhang](/czhang)
-* [Clark Zhang](/clarkxzhang)
-* [Jianhua Zhang](/jianhuazhang)
-* [Qiu X Zhang](/qiuxue198598)
-* [Sen Zhang](/zhan3621)
-* [Zhiyu Zhao](/ZhiyuZhao)
-* [Yueli Zheng](/YueliZheng)
-* [Ariel Zhou](/arielzhou)
-* [Jamie Zhou](/jamiezhou@mednet.ucla.edu)
-* [Bethany Zumwalde](/BethanyZumwalde)
CategoryGroup
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