slarson/OpenWorm-Office-12-5-12

## OpenWorm-Office-12-5-12
[09:27] <juan_idolo> Yolo!
[09:27] <@OpenWorm> haha
[09:29] <@OpenWorm> How are we doing ?
[09:35] <juan_idolo> all good ;)
[09:35] <@OpenWorm> To kick off our conversation, I wanted to show you guys the progress we made in release 3: https://docs.google.com/document/d/1cg1YnKI92tN9HZeXachTfpRlKP10OuJhXlRBabeTnuI/edit#
[09:35] <@OpenWorm> We are still working to add links to this document before mailing it out, but the accomplishments are there.
[09:36] <@OpenWorm> if folks have questions about this stuff it would be interesting to hear as I can clarify them now
[09:36] == Jeff2 [~Adium@cpc1-cmbg14-2-0-cust156.5-4.cable.virginmedia.com] has joined #openworm-office
[09:36] <@OpenWorm> Hi Jeff
[09:36] <Jeff2> Hello
[09:37] <@OpenWorm> Just before you arrived I linked to a list of project accomplishments in the last 6 months here: http://g.ua/Mtm9
[09:38] <@OpenWorm> And am looking for any questions / comments / feedback on this
[09:39] == tarelli [56a48cec@gateway/web/freenode/ip.86.164.140.236] has joined #openworm-office
[09:39] <@OpenWorm> hi tarelli
[09:39] <tarelli> yo
[09:39] <tarelli> what up
[09:40] <@OpenWorm> Reviewing the release 3 accomplishments doc here: http://g.ua/Mtm9
[09:40] <@OpenWorm> So far its a pretty quiet room though ... :)
[09:42] <@OpenWorm> Any questions, any one?
[09:43] <Jeff2> I have a question, though likely not related to the project accomplishments list (so far).
[09:43] <@OpenWorm> that's fine
[09:43] <@OpenWorm> ask away
[09:46] <Jeff2> The Nemaload project, by David Dalrymple, recently updated its website with more information.
[09:46] <Jeff2> I understand David is a collaborator of the OpenWorm project. How does the Nemaload project relate to OpenWorm?
[09:48] <@OpenWorm> We both want to see the c. elegans reverse engineered as a means of understanding nervous systems.  We've met a few times and he contributes on the mailing list.  We have a different approach right now, but I think they are complimentary and could be unified down the road.  We don't have any specific plans to do so yet
[09:49] <@OpenWorm> Both projects have a lot of up front development work that we are doing now
[09:49] <@OpenWorm> Us mainly in software and integrating data that already exists
[09:50] <@OpenWorm> Him in building an ambitious experimental set up to collect a never-before-gathered dataset
[09:51] <@OpenWorm> Good question :)
[09:51] == srd| [~srd@cpc5-sgyl34-2-0-cust276.sgyl.cable.virginmedia.com] has joined #openworm-office
[09:51] <Jeff2> Thank you very much!
[09:51] <@OpenWorm> No problem
[09:52] <@OpenWorm> Hi srd
[09:52] <srd|> hey there
[09:52] <srd|> how much did I miss?
[09:52] <srd|> the whole of it?
[09:52] <@OpenWorm> Answered one question so far and posted a doc from our accomplishments last release for comment: http://g.ua/Mtm9
[09:52] <srd|> ah
[09:52] <@OpenWorm> Open to any additional questions folks may have on any topic
[09:53] <tarelli> hi srd
[09:53] <srd|> evenin' tarelli
[09:54] <@OpenWorm> In the last two weeks we started a high volume discussion list and separated it from the main mailing list
[09:55] <@OpenWorm> We responded to an interesting question on Quora: http://www.quora.com/Mind/Is-the-C-elegans-nematode-suitable-for-a-Kurzweilian-Singularity-mind-transfer
[09:55] <@OpenWorm> Paul King is more pessimistic than we are, but is a solid thinker in the space too
[09:56] <srd|> that's not readable, I'm afraid
[09:57] <@OpenWorm> Which?
[09:57] <srd|> everything past paul king's answer
[09:58] <@OpenWorm> haha
[09:58] <@OpenWorm> uh oh
[09:58] <@OpenWorm> why?
[09:58] <@OpenWorm> too long?
[09:58] <srd|> it wants me to be signed in to facebook, twitter, or quora
[09:58] <@OpenWorm> oh bother
[09:58] <@OpenWorm> only the top answer is public huh
[09:59] <@OpenWorm> interesting
[09:59] <srd|> (which is the main reason stackexchange is preferable)
[09:59] <@OpenWorm> yeah gotcha.  Is there a stackexchange that asks these kinds of questions though?
[10:02] <srd|> http://philosophy.stackexchange.com/ ? http://biology.stackexchange.com/ ?
[10:03] <@OpenWorm> Interesting: http://biology.stackexchange.com/search?q=elegans
[10:03] <@OpenWorm> Starts to get there
[10:04] <@OpenWorm> Is there any interest in an OpenWorm meetup in London?
[10:04] <@OpenWorm> I'm starting to notice an increased number of UK folks are interested
[10:04] <Jeff2> +1
[10:05] <srd|> possibly; what would happen there?
[10:05] <@OpenWorm> First thing would just be a chance to meet the other folks working on the project
[10:05] <@OpenWorm> There are 3 regular contributors between london and cambridge
[10:06] <@OpenWorm> And London is a good city because others pass through from time to time
[10:07] <@OpenWorm> Second thing would just be an additional opportunity to find out what others are up to
[10:10] <@OpenWorm> Alright well sounds like there's some interest -- may be something to target for the spring
[10:10] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has joined #openworm-office
[10:11] <@OpenWorm> Hi Andy
[10:11] <AndyL> Hi Open Worm
[10:11] <AndyL> How are office hours going?
[10:11] <@OpenWorm> Good!
[10:12] <@OpenWorm> Do you have any questions?
[10:12] <AndyL> Not specifically. I'm a C. elegans reseracher, and I'm excited about your project. I saw your tweet and thought I would say hi.
[10:13] <@OpenWorm> Srd -- can you read this link: http://qr.ae/1nrQ5 ?
[10:13] <@OpenWorm> Awesome :)
[10:13] <@OpenWorm> What do you work on in c. elegans?
[10:14] == kanzure [~kanzure@131.252.130.248] has joined #openworm-office
[10:14] <kanzure> hello
[10:14] <AndyL> Well I am using optical neurophysiology techniques, including optogenetics, calcium imaging and voltage imaging to how simple neural networks generate behavior.
[10:14] <AndyL> Actually you guys tweeted about a paper I was involved in last week.
[10:14] <@OpenWorm> Hi kanzure!
[10:15] <kanzure> OpenWorm: who are you?
[10:15] <@OpenWorm> Awesome, which paper?
[10:15] <kanzure> i recognize a few of your usernames, like slarson and juan_idolo
[10:15] <kanzure> but OpenWorm is an enigma
[10:15] <AndyL> The paper was by Quan Wen on  how proprioceptive coupling drives locomotory behavior
[10:15] <@OpenWorm> Today its slarson behind the OpenWorm account
[10:15] <AndyL> Just came out in Neuron. My contribution was mainly on the optogenetics.
[10:15] <@OpenWorm> and the slarson account is serving the role of observer for the log
[10:16] <kanzure> okay then
[10:16] <@OpenWorm> OH that paper!
[10:16] <@OpenWorm> That paper has a special place in my heart right now
[10:16] <@OpenWorm> Thanks for stopping by!
[10:16] <@OpenWorm> its exciting work
[10:16] <AndyL> I'm glad you like it!
[10:16] <AndyL> So do you guys all ever meet up somewhere physically?
[10:16] <kanzure> i would be highly interested in acquiring dumps of papers that you guys are reading
[10:16] <kanzure> here's what i read: http://diyhpl.us/~bryan/papers2/neuro/
[10:17] <@OpenWorm> We are particularly interested because we think our simulator will be in a position to generate some additional hypotheses for you because we are getting close to merging our mechanical model of cells that can "bend" with electrical models of cells
[10:18] == archels [~foo@sascha.esrac.ele.tue.nl] has joined #openworm-office
[10:18] <AndyL> that would be great! if there is one thing we need more of, its models that can generate testable hypothesis
[10:18] <archels> hey, any logs?
[10:18] <@OpenWorm> AndyL -- we were just talking about a potential London meet up.  Subsets of us meet but we haven't ever all converged in the same place, sadly.
[10:18] <kanzure> archels: i haven't found them yet
[10:18] <archels> kanzure: you probably have more than me :)
[10:18] <@OpenWorm> AndyL -- we do use Google+ hangout to meet face to face virtually every two weeks
[10:18] <AndyL> Maybe one of the worm meetings would be a natural place1?
[10:19] <@OpenWorm> kanzure -- we have a Mendeley group that we keep up to date with all relevant c. elegans papers and relevant modeling work
[10:19] <kanzure> mendeley doesn't host pdfs
[10:19] <@OpenWorm> hi archels!
[10:19] * archels waves
[10:19] <archels> I like the OpenWorm project a lot.
[10:19] <@OpenWorm> kanzure -- nice list
[10:19] <@OpenWorm> kanzure -- actually they do
[10:19] <archels> How official is this channel?
[10:20] <kanzure> if you could show me how to get pdfs from mendeley i would be very happy
[10:20] <tarelli> as official as it gets
[10:20] <tarelli> :)
[10:20] <kanzure> i assume it's this http://www.mendeley.com/groups/835901/open-worm/
[10:20] <kanzure> "Access to the page you are looking for is forbidden."
[10:21] <AndyL> Is there a list to get on, in regards to google hangout meetups?
[10:21] <@OpenWorm> AndyL -- yes it would but we are so geographically dispersed that it becomes a cost issue to get everyone together -- since its an open source project -- but i've attended the worm meetings before and they are good opportunities to meet the community
[10:21] <kanzure> why not just show up in an irc channel?
[10:22] <@OpenWorm> AndyL -- yes definitely.  I'd love to talk more about your conclusions from the paper and if there are specific follow ups that might be appropriate for us to focus on sooner rather than later
[10:23] <@OpenWorm> archels -- you mean logs of previous office hours?  they are here: http://g.ua/MjYn and here: http://g.ua/MaPs
[10:23] <kanzure> https://raw.github.com/gist/4126820/4ec269cf66ddbe44368615f7087bbfa31a8c7a90/gistfile1.txt
[10:23] <kanzure> https://raw.github.com/gist/4033515/9bc09cb13d0834a227a05d2d46b146a2831663f0/OpenWorm-Office-11-7-12
[10:23] <kanzure> oh you guys don't hang out here all the time?
[10:24] <tarelli> only during office hours for now
[10:24] <AndyL> Great, well and similarly, I would like to learn more about where you are going and how I might be able to contribute, or at least coordinate.
[10:24] <AndyL> I have just staretd my own lab at Princeton
[10:25] <AndyL> and intend to continue this line of work.
[10:25] <tarelli> that's great to hear
[10:25] <@OpenWorm> kanzure -- to get the PDFs you need to be part of our group.  Mendeley recently changed their cost structure though and now it is a lot more expensive to have large groups.  we are rethinking our strategy for having a collaboratively shared docs repository.
[10:26] <kanzure> OpenWorm: how about dropbox + zotero?
[10:26] <kanzure> zotero doesn't do ocr like mendeley does, but it does maintain bibliographies
[10:27] <@OpenWorm> AndyL -- that's great -- congrats on the new lab!
[10:29] == RPlasmid [~rplasmid@114.79.29.147] has joined #openworm-office
[10:29] == redofrac [~redofrac@bzq-84-111-116-23.red.bezeqint.net] has joined #openworm-office
[10:29] <tarelli> hi RPlasmid
[10:29] <tarelli> hi redofrac
[10:29] <@OpenWorm> AndyL -- as for google hangouts we just have a regular time every two weeks on Wednesday.  If you follow us on Google+ https://plus.google.com/b/117948341754627144949/117948341754627144949/posts we can invite you to the hangouts.  we meet at 11:30am  - 1pm ET.  you can see what this looks like here: http://www.youtube.com/watch?v=MFkHk_Zhbu4
[10:30] <kanzure> RPlasmid and redofrac are from ##neuroscience
[10:30] <kanzure> and archels is from ##hplusroadmap (a biohacking group)
[10:30] == meefs [ken@unaffiliated/meefs] has joined #openworm-office
[10:30] <archels> Are there any open PhD applications for work on OpenWorm?
[10:31] <@OpenWorm> kanzure -- you asked about why don't we do our meetings in irc?  we started these office hours as an experiment to see how we can incorporate that.  we find hangouts to be more high bandwidth in terms of what we can communicate.
[10:31] <kanzure> okay.
[10:31] <@OpenWorm> hi Rplasmid and redofrac!
[10:31] <meefs> greets all
[10:31] <RPlasmid> greetings
[10:31] <redofrac> hey
[10:31] <@OpenWorm> hi meefs!
[10:31] <@OpenWorm> kanzure -- we'll look into zotero -- may be a better solution
[10:32] <RPlasmid> What's this chat about?
[10:33] <kanzure> well, failing zotero or a pdf dump, i'd be interested in hearing about any recent papers you've enjoyed
[10:33] <tarelli> RPlasmid - OpenWorm project, www.openworm.org
[10:34] == fenn [~fenn@131.252.130.248] has joined #openworm-office
[10:34] == OpenWorm_ [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has joined #openworm-office
[10:34] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has quit [Ping timeout: 245 seconds]
[10:34] <tarelli> this is something exciting we are working on recently http://www.youtube.com/watch?feature=player_detailpage&v=QYi1cpQQ-7E#t=1752s
[10:35] <OpenWorm_> RPlasmid -- this is the office hours for openworm.org
[10:35] <kanzure> tarelli: is there a transcript?
[10:36] <OpenWorm_> hi redofrac
[10:36] == OpenWorm [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has quit [Ping timeout: 245 seconds]
[10:36] == OpenWorm_ [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has quit [Client Quit]
[10:36] == licnep [Elite3896@2a01:4f8:100:7464::8] has joined #openworm-office
[10:37] == openworm [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has joined #openworm-office
[10:37] <tarelli> kanzure - unfortunately no
[10:37] == mode/#openworm-office [+o openworm] by ChanServ
[10:37] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has joined #openworm-office
[10:38] <AndyL> OK. well thank you guys. I signed up for the google+ and followed you, so please let me konw next time you have a hangout
[10:38] <@openworm> AndyL -- OK -- it is next Wednesday at 11:30am ET
[10:38] <@openworm> I'll create more of an invite for it
[10:38] <tarelli> looking forward to seeing you there AndyL!
[10:39] <@openworm> Other folks have questions about the project?  This is an open session for questions of any variety
[10:39] <AndyL> Great. see you then.
[10:39] <AndyL> Bye!
[10:39] <@openworm> Bye
[10:40] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has quit [Client Quit]
[10:41] <@openworm> kanzure -- recent papers we have enjoyed include the paper that AndyL was taking about: http://www.mendeley.com/c/5350724914/g/835901/goulding-2012-motor-neurons-that-multitask/
[10:41] <kanzure> "Access to the page you are looking for is forbidden."
[10:41] <@openworm> We also thought the recent brain modeling paper is interesting: https://www.mendeley.com/research/a-largescale-model-of-the-functioning-brain-1/
[10:41] <@openworm> We're thinking about doing a journal club on it in a couple weeks
[10:41] <kanzure> this one is not forbidden
[10:42] <@openworm> kanzure -- a better link for the first one: http://www.sciencedirect.com/science/article/pii/S0896627312010021
[10:42] == exiff [~ficl@unaffiliated/exiff] has joined #openworm-office
[10:42] <@openworm> let me see if there is open access for that one
[10:42] <@openworm> hi exiff
[10:42] <exiff> Hello.
[10:43] <redofrac> ah, that waterloo thing
[10:44] <@openworm> redofrac - -yeah
[10:44] <@openworm> any thoughts about that?
[10:45] <tarelli> @all what interests you the most in the OpenWorm project?
[10:45] <RPlasmid> Oh a richard feynman quote on the main page.
[10:45] <RPlasmid> Fancy.
[10:45] <kanzure> your git repositories
[10:45] <@openworm> Sadly there is not an open access version of the motor neuron paper
[10:45] <@openworm> if you email info@openworm.org I can help you get a copy
[10:46] <@openworm> kanzure -- why's that?
[10:47] <kanzure> i wish more neuroscience software was done over git
[10:47] <kanzure> in the past i've rescued a few "forgotten" projects
[10:47] <@openworm> kanzure -- us too
[10:47] <kanzure> e.g. https://github.com/kanzure/netmorph
[10:48] <kanzure> netmorph generates morphologically-realistic networks and then randal just sort of forgot about it completely
[10:48] <kanzure> or left it to rot on one of his servers
[10:48] <kanzure> i don't know. i've been trying to get 3scan to use it to test their optical connectome mapping software.
[10:48] <@openworm> kanzure -- very cool.
[10:50] <kanzure> i figure that if they have a realistic model of a neural network then they can test their imaging/reconstruction software on it with a known result.
[10:50] <kanzure> e.g. generate a few million test networks, make it look realistic with opengl, then test their software against it and the known-original network topology.
[10:50] == albert [3e2599fb@gateway/web/freenode/ip.62.37.153.251] has joined #openworm-office
[10:50] <@openworm> kanzure -- yeah that's an interesting approach
[10:50] <@openworm> hi albert!
[10:51] == albert has changed nick to Guest97433
[10:52] == Guest97433 [3e2599fb@gateway/web/freenode/ip.62.37.153.251] has left #openworm-office []
[10:53] <tarelli> usually it's the other way around lol
[10:53] <kanzure> it's because "albert" is a registered username
[10:54] <@openworm> Any other questions, folks?  I'll be signing off soon
[10:55] <tarelli> I see :)
[10:56] == fenn [~fenn@131.252.130.248] has left #openworm-office ["cheers"]
[10:57] <tarelli> juan_idolo any question?
[10:57] <@openworm> ok well we'll be doing this again in two weeks
[10:57] <@openworm> thanks for all who have stopped by
[10:57] <exiff> I'll be eagerly observing your progress. Good luck.
[10:57] <@openworm> you can find additional info on getting a hold of us here: http://www.openworm.org/#/contacts
[10:57] <@openworm> Thanks exiff!
[10:58] == RPlasmids [~rplasmid@114.79.28.81] has joined #openworm-office
[10:58] == licnep [Elite3896@2a01:4f8:100:7464::8] has left #openworm-office []
[10:59] == mks [46a809bf@gateway/web/freenode/ip.70.168.9.191] has quit [Quit: Page closed]
[10:59] == juan_idolo [562d8473@gateway/web/freenode/ip.86.45.132.115] has quit [Quit: Page closed]
[10:59] <redofrac> openworm: curious, as I'm just getting into the general area, where is most of the difficulty in simulating this?
[11:00] <@openworm> redofrac -- gotta head off unfortunately so I can't go into details, but the short answer is -- unifying the data that is known and making educated guesses about what is unknown.  plus a decent amount of creating software that hasn't been built before :)
[11:00] <@openworm> cheers
[11:01] <@openworm> join us in two weeks!
	[09:27] <juan_idolo> Yolo!
	[09:27] <@OpenWorm> haha
	[09:29] <@OpenWorm> How are we doing ?
	[09:35] <juan_idolo> all good ;)
	[09:35] <@OpenWorm> To kick off our conversation, I wanted to show you guys the progress we made in release 3: https://docs.google.com/document/d/1cg1YnKI92tN9HZeXachTfpRlKP10OuJhXlRBabeTnuI/edit#
	[09:35] <@OpenWorm> We are still working to add links to this document before mailing it out, but the accomplishments are there.
	[09:36] <@OpenWorm> if folks have questions about this stuff it would be interesting to hear as I can clarify them now
	[09:36] == Jeff2 [~Adium@cpc1-cmbg14-2-0-cust156.5-4.cable.virginmedia.com] has joined #openworm-office
	[09:36] <@OpenWorm> Hi Jeff
	[09:36] <Jeff2> Hello
	[09:37] <@OpenWorm> Just before you arrived I linked to a list of project accomplishments in the last 6 months here: http://g.ua/Mtm9
	[09:38] <@OpenWorm> And am looking for any questions / comments / feedback on this
	[09:39] == tarelli [56a48cec@gateway/web/freenode/ip.86.164.140.236] has joined #openworm-office
	[09:39] <@OpenWorm> hi tarelli
	[09:39] <tarelli> yo
	[09:39] <tarelli> what up
	[09:40] <@OpenWorm> Reviewing the release 3 accomplishments doc here: http://g.ua/Mtm9
	[09:40] <@OpenWorm> So far its a pretty quiet room though ... :)
	[09:42] <@OpenWorm> Any questions, any one?
	[09:43] <Jeff2> I have a question, though likely not related to the project accomplishments list (so far).
	[09:43] <@OpenWorm> that's fine
	[09:43] <@OpenWorm> ask away
	[09:46] <Jeff2> The Nemaload project, by David Dalrymple, recently updated its website with more information.
	[09:46] <Jeff2> I understand David is a collaborator of the OpenWorm project. How does the Nemaload project relate to OpenWorm?
	[09:48] <@OpenWorm> We both want to see the c. elegans reverse engineered as a means of understanding nervous systems. We've met a few times and he contributes on the mailing list. We have a different approach right now, but I think they are complimentary and could be unified down the road. We don't have any specific plans to do so yet
	[09:49] <@OpenWorm> Both projects have a lot of up front development work that we are doing now
	[09:49] <@OpenWorm> Us mainly in software and integrating data that already exists
	[09:50] <@OpenWorm> Him in building an ambitious experimental set up to collect a never-before-gathered dataset
	[09:51] <@OpenWorm> Good question :)
	[09:51] == srd\| [~srd@cpc5-sgyl34-2-0-cust276.sgyl.cable.virginmedia.com] has joined #openworm-office
	[09:51] <Jeff2> Thank you very much!
	[09:51] <@OpenWorm> No problem
	[09:52] <@OpenWorm> Hi srd
	[09:52] <srd\|> hey there
	[09:52] <srd\|> how much did I miss?
	[09:52] <srd\|> the whole of it?
	[09:52] <@OpenWorm> Answered one question so far and posted a doc from our accomplishments last release for comment: http://g.ua/Mtm9
	[09:52] <srd\|> ah
	[09:52] <@OpenWorm> Open to any additional questions folks may have on any topic
	[09:53] <tarelli> hi srd
	[09:53] <srd\|> evenin' tarelli
	[09:54] <@OpenWorm> In the last two weeks we started a high volume discussion list and separated it from the main mailing list
	[09:55] <@OpenWorm> We responded to an interesting question on Quora: http://www.quora.com/Mind/Is-the-C-elegans-nematode-suitable-for-a-Kurzweilian-Singularity-mind-transfer
	[09:55] <@OpenWorm> Paul King is more pessimistic than we are, but is a solid thinker in the space too
	[09:56] <srd\|> that's not readable, I'm afraid
	[09:57] <@OpenWorm> Which?
	[09:57] <srd\|> everything past paul king's answer
	[09:58] <@OpenWorm> haha
	[09:58] <@OpenWorm> uh oh
	[09:58] <@OpenWorm> why?
	[09:58] <@OpenWorm> too long?
	[09:58] <srd\|> it wants me to be signed in to facebook, twitter, or quora
	[09:58] <@OpenWorm> oh bother
	[09:58] <@OpenWorm> only the top answer is public huh
	[09:59] <@OpenWorm> interesting
	[09:59] <srd\|> (which is the main reason stackexchange is preferable)
	[09:59] <@OpenWorm> yeah gotcha. Is there a stackexchange that asks these kinds of questions though?
	[10:02] <srd\|> http://philosophy.stackexchange.com/ ? http://biology.stackexchange.com/ ?
	[10:03] <@OpenWorm> Interesting: http://biology.stackexchange.com/search?q=elegans
	[10:03] <@OpenWorm> Starts to get there
	[10:04] <@OpenWorm> Is there any interest in an OpenWorm meetup in London?
	[10:04] <@OpenWorm> I'm starting to notice an increased number of UK folks are interested
	[10:04] <Jeff2> +1
	[10:05] <srd\|> possibly; what would happen there?
	[10:05] <@OpenWorm> First thing would just be a chance to meet the other folks working on the project
	[10:05] <@OpenWorm> There are 3 regular contributors between london and cambridge
	[10:06] <@OpenWorm> And London is a good city because others pass through from time to time
	[10:07] <@OpenWorm> Second thing would just be an additional opportunity to find out what others are up to
	[10:10] <@OpenWorm> Alright well sounds like there's some interest -- may be something to target for the spring
	[10:10] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has joined #openworm-office
	[10:11] <@OpenWorm> Hi Andy
	[10:11] <AndyL> Hi Open Worm
	[10:11] <AndyL> How are office hours going?
	[10:11] <@OpenWorm> Good!
	[10:12] <@OpenWorm> Do you have any questions?
	[10:12] <AndyL> Not specifically. I'm a C. elegans reseracher, and I'm excited about your project. I saw your tweet and thought I would say hi.
	[10:13] <@OpenWorm> Srd -- can you read this link: http://qr.ae/1nrQ5 ?
	[10:13] <@OpenWorm> Awesome :)
	[10:13] <@OpenWorm> What do you work on in c. elegans?
	[10:14] == kanzure [~kanzure@131.252.130.248] has joined #openworm-office
	[10:14] <kanzure> hello
	[10:14] <AndyL> Well I am using optical neurophysiology techniques, including optogenetics, calcium imaging and voltage imaging to how simple neural networks generate behavior.
	[10:14] <AndyL> Actually you guys tweeted about a paper I was involved in last week.
	[10:14] <@OpenWorm> Hi kanzure!
	[10:15] <kanzure> OpenWorm: who are you?
	[10:15] <@OpenWorm> Awesome, which paper?
	[10:15] <kanzure> i recognize a few of your usernames, like slarson and juan_idolo
	[10:15] <kanzure> but OpenWorm is an enigma
	[10:15] <AndyL> The paper was by Quan Wen on how proprioceptive coupling drives locomotory behavior
	[10:15] <@OpenWorm> Today its slarson behind the OpenWorm account
	[10:15] <AndyL> Just came out in Neuron. My contribution was mainly on the optogenetics.
	[10:15] <@OpenWorm> and the slarson account is serving the role of observer for the log
	[10:16] <kanzure> okay then
	[10:16] <@OpenWorm> OH that paper!
	[10:16] <@OpenWorm> That paper has a special place in my heart right now
	[10:16] <@OpenWorm> Thanks for stopping by!
	[10:16] <@OpenWorm> its exciting work
	[10:16] <AndyL> I'm glad you like it!
	[10:16] <AndyL> So do you guys all ever meet up somewhere physically?
	[10:16] <kanzure> i would be highly interested in acquiring dumps of papers that you guys are reading
	[10:16] <kanzure> here's what i read: http://diyhpl.us/~bryan/papers2/neuro/
	[10:17] <@OpenWorm> We are particularly interested because we think our simulator will be in a position to generate some additional hypotheses for you because we are getting close to merging our mechanical model of cells that can "bend" with electrical models of cells
	[10:18] == archels [~foo@sascha.esrac.ele.tue.nl] has joined #openworm-office
	[10:18] <AndyL> that would be great! if there is one thing we need more of, its models that can generate testable hypothesis
	[10:18] <archels> hey, any logs?
	[10:18] <@OpenWorm> AndyL -- we were just talking about a potential London meet up. Subsets of us meet but we haven't ever all converged in the same place, sadly.
	[10:18] <kanzure> archels: i haven't found them yet
	[10:18] <archels> kanzure: you probably have more than me :)
	[10:18] <@OpenWorm> AndyL -- we do use Google+ hangout to meet face to face virtually every two weeks
	[10:18] <AndyL> Maybe one of the worm meetings would be a natural place1?
	[10:19] <@OpenWorm> kanzure -- we have a Mendeley group that we keep up to date with all relevant c. elegans papers and relevant modeling work
	[10:19] <kanzure> mendeley doesn't host pdfs
	[10:19] <@OpenWorm> hi archels!
	[10:19] * archels waves
	[10:19] <archels> I like the OpenWorm project a lot.
	[10:19] <@OpenWorm> kanzure -- nice list
	[10:19] <@OpenWorm> kanzure -- actually they do
	[10:19] <archels> How official is this channel?
	[10:20] <kanzure> if you could show me how to get pdfs from mendeley i would be very happy
	[10:20] <tarelli> as official as it gets
	[10:20] <tarelli> :)
	[10:20] <kanzure> i assume it's this http://www.mendeley.com/groups/835901/open-worm/
	[10:20] <kanzure> "Access to the page you are looking for is forbidden."
	[10:21] <AndyL> Is there a list to get on, in regards to google hangout meetups?
	[10:21] <@OpenWorm> AndyL -- yes it would but we are so geographically dispersed that it becomes a cost issue to get everyone together -- since its an open source project -- but i've attended the worm meetings before and they are good opportunities to meet the community
	[10:21] <kanzure> why not just show up in an irc channel?
	[10:22] <@OpenWorm> AndyL -- yes definitely. I'd love to talk more about your conclusions from the paper and if there are specific follow ups that might be appropriate for us to focus on sooner rather than later
	[10:23] <@OpenWorm> archels -- you mean logs of previous office hours? they are here: http://g.ua/MjYn and here: http://g.ua/MaPs
	[10:23] <kanzure> https://raw.github.com/gist/4126820/4ec269cf66ddbe44368615f7087bbfa31a8c7a90/gistfile1.txt
	[10:23] <kanzure> https://raw.github.com/gist/4033515/9bc09cb13d0834a227a05d2d46b146a2831663f0/OpenWorm-Office-11-7-12
	[10:23] <kanzure> oh you guys don't hang out here all the time?
	[10:24] <tarelli> only during office hours for now
	[10:24] <AndyL> Great, well and similarly, I would like to learn more about where you are going and how I might be able to contribute, or at least coordinate.
	[10:24] <AndyL> I have just staretd my own lab at Princeton
	[10:25] <AndyL> and intend to continue this line of work.
	[10:25] <tarelli> that's great to hear
	[10:25] <@OpenWorm> kanzure -- to get the PDFs you need to be part of our group. Mendeley recently changed their cost structure though and now it is a lot more expensive to have large groups. we are rethinking our strategy for having a collaboratively shared docs repository.
	[10:26] <kanzure> OpenWorm: how about dropbox + zotero?
	[10:26] <kanzure> zotero doesn't do ocr like mendeley does, but it does maintain bibliographies
	[10:27] <@OpenWorm> AndyL -- that's great -- congrats on the new lab!
	[10:29] == RPlasmid [~rplasmid@114.79.29.147] has joined #openworm-office
	[10:29] == redofrac [~redofrac@bzq-84-111-116-23.red.bezeqint.net] has joined #openworm-office
	[10:29] <tarelli> hi RPlasmid
	[10:29] <tarelli> hi redofrac
	[10:29] <@OpenWorm> AndyL -- as for google hangouts we just have a regular time every two weeks on Wednesday. If you follow us on Google+ https://plus.google.com/b/117948341754627144949/117948341754627144949/posts we can invite you to the hangouts. we meet at 11:30am - 1pm ET. you can see what this looks like here: http://www.youtube.com/watch?v=MFkHk_Zhbu4
	[10:30] <kanzure> RPlasmid and redofrac are from ##neuroscience
	[10:30] <kanzure> and archels is from ##hplusroadmap (a biohacking group)
	[10:30] == meefs [ken@unaffiliated/meefs] has joined #openworm-office
	[10:30] <archels> Are there any open PhD applications for work on OpenWorm?
	[10:31] <@OpenWorm> kanzure -- you asked about why don't we do our meetings in irc? we started these office hours as an experiment to see how we can incorporate that. we find hangouts to be more high bandwidth in terms of what we can communicate.
	[10:31] <kanzure> okay.
	[10:31] <@OpenWorm> hi Rplasmid and redofrac!
	[10:31] <meefs> greets all
	[10:31] <RPlasmid> greetings
	[10:31] <redofrac> hey
	[10:31] <@OpenWorm> hi meefs!
	[10:31] <@OpenWorm> kanzure -- we'll look into zotero -- may be a better solution
	[10:32] <RPlasmid> What's this chat about?
	[10:33] <kanzure> well, failing zotero or a pdf dump, i'd be interested in hearing about any recent papers you've enjoyed
	[10:33] <tarelli> RPlasmid - OpenWorm project, www.openworm.org
	[10:34] == fenn [~fenn@131.252.130.248] has joined #openworm-office
	[10:34] == OpenWorm_ [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has joined #openworm-office
	[10:34] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has quit [Ping timeout: 245 seconds]
	[10:34] <tarelli> this is something exciting we are working on recently http://www.youtube.com/watch?feature=player_detailpage&v=QYi1cpQQ-7E#t=1752s
	[10:35] <OpenWorm_> RPlasmid -- this is the office hours for openworm.org
	[10:35] <kanzure> tarelli: is there a transcript?
	[10:36] <OpenWorm_> hi redofrac
	[10:36] == OpenWorm [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has quit [Ping timeout: 245 seconds]
	[10:36] == OpenWorm_ [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has quit [Client Quit]
	[10:36] == licnep [Elite3896@2a01:4f8:100:7464::8] has joined #openworm-office
	[10:37] == openworm [6cd86e7a@gateway/web/freenode/ip.108.216.110.122] has joined #openworm-office
	[10:37] <tarelli> kanzure - unfortunately no
	[10:37] == mode/#openworm-office [+o openworm] by ChanServ
	[10:37] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has joined #openworm-office
	[10:38] <AndyL> OK. well thank you guys. I signed up for the google+ and followed you, so please let me konw next time you have a hangout
	[10:38] <@openworm> AndyL -- OK -- it is next Wednesday at 11:30am ET
	[10:38] <@openworm> I'll create more of an invite for it
	[10:38] <tarelli> looking forward to seeing you there AndyL!
	[10:39] <@openworm> Other folks have questions about the project? This is an open session for questions of any variety
	[10:39] <AndyL> Great. see you then.
	[10:39] <AndyL> Bye!
	[10:39] <@openworm> Bye
	[10:40] == AndyL [807075f2@gateway/web/freenode/ip.128.112.117.242] has quit [Client Quit]
	[10:41] <@openworm> kanzure -- recent papers we have enjoyed include the paper that AndyL was taking about: http://www.mendeley.com/c/5350724914/g/835901/goulding-2012-motor-neurons-that-multitask/
	[10:41] <kanzure> "Access to the page you are looking for is forbidden."
	[10:41] <@openworm> We also thought the recent brain modeling paper is interesting: https://www.mendeley.com/research/a-largescale-model-of-the-functioning-brain-1/
	[10:41] <@openworm> We're thinking about doing a journal club on it in a couple weeks
	[10:41] <kanzure> this one is not forbidden
	[10:42] <@openworm> kanzure -- a better link for the first one: http://www.sciencedirect.com/science/article/pii/S0896627312010021
	[10:42] == exiff [~ficl@unaffiliated/exiff] has joined #openworm-office
	[10:42] <@openworm> let me see if there is open access for that one
	[10:42] <@openworm> hi exiff
	[10:42] <exiff> Hello.
	[10:43] <redofrac> ah, that waterloo thing
	[10:44] <@openworm> redofrac - -yeah
	[10:44] <@openworm> any thoughts about that?
	[10:45] <tarelli> @all what interests you the most in the OpenWorm project?
	[10:45] <RPlasmid> Oh a richard feynman quote on the main page.
	[10:45] <RPlasmid> Fancy.
	[10:45] <kanzure> your git repositories
	[10:45] <@openworm> Sadly there is not an open access version of the motor neuron paper
	[10:45] <@openworm> if you email info@openworm.org I can help you get a copy
	[10:46] <@openworm> kanzure -- why's that?
	[10:47] <kanzure> i wish more neuroscience software was done over git
	[10:47] <kanzure> in the past i've rescued a few "forgotten" projects
	[10:47] <@openworm> kanzure -- us too
	[10:47] <kanzure> e.g. https://github.com/kanzure/netmorph
	[10:48] <kanzure> netmorph generates morphologically-realistic networks and then randal just sort of forgot about it completely
	[10:48] <kanzure> or left it to rot on one of his servers
	[10:48] <kanzure> i don't know. i've been trying to get 3scan to use it to test their optical connectome mapping software.
	[10:48] <@openworm> kanzure -- very cool.
	[10:50] <kanzure> i figure that if they have a realistic model of a neural network then they can test their imaging/reconstruction software on it with a known result.
	[10:50] <kanzure> e.g. generate a few million test networks, make it look realistic with opengl, then test their software against it and the known-original network topology.
	[10:50] == albert [3e2599fb@gateway/web/freenode/ip.62.37.153.251] has joined #openworm-office
	[10:50] <@openworm> kanzure -- yeah that's an interesting approach
	[10:50] <@openworm> hi albert!
	[10:51] == albert has changed nick to Guest97433
	[10:52] == Guest97433 [3e2599fb@gateway/web/freenode/ip.62.37.153.251] has left #openworm-office []
	[10:53] <tarelli> usually it's the other way around lol
	[10:53] <kanzure> it's because "albert" is a registered username
	[10:54] <@openworm> Any other questions, folks? I'll be signing off soon
	[10:55] <tarelli> I see :)
	[10:56] == fenn [~fenn@131.252.130.248] has left #openworm-office ["cheers"]
	[10:57] <tarelli> juan_idolo any question?
	[10:57] <@openworm> ok well we'll be doing this again in two weeks
	[10:57] <@openworm> thanks for all who have stopped by
	[10:57] <exiff> I'll be eagerly observing your progress. Good luck.
	[10:57] <@openworm> you can find additional info on getting a hold of us here: http://www.openworm.org/#/contacts
	[10:57] <@openworm> Thanks exiff!
	[10:58] == RPlasmids [~rplasmid@114.79.28.81] has joined #openworm-office
	[10:58] == licnep [Elite3896@2a01:4f8:100:7464::8] has left #openworm-office []
	[10:59] == mks [46a809bf@gateway/web/freenode/ip.70.168.9.191] has quit [Quit: Page closed]
	[10:59] == juan_idolo [562d8473@gateway/web/freenode/ip.86.45.132.115] has quit [Quit: Page closed]
	[10:59] <redofrac> openworm: curious, as I'm just getting into the general area, where is most of the difficulty in simulating this?
	[11:00] <@openworm> redofrac -- gotta head off unfortunately so I can't go into details, but the short answer is -- unifying the data that is known and making educated guesses about what is unknown. plus a decent amount of creating software that hasn't been built before :)
	[11:00] <@openworm> cheers
	[11:01] <@openworm> join us in two weeks!