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##Installing Python using Macports (beginner guide)

I think package management system is good for long-term installation. Since lab members use a lot of Apple product, I wrote Macports documentation which is package management system for Mac OSX which hopefully will be useful for members who use Mac. Note that this is not an official document but probably an easy way to get start with Macports. Macports depends mostly by its community and ones who update the port. We may have to migrate our ports when Mac announce new operating system. From my experience, it is normal to have some port problem with macports when new Mac operating system, for example, when Maverick or Yosemite was announced or when new XCode version were updated. It will take some time (a day or a week) for them to update the new port that are compatible with new operating system. But yeah, most ports work very well even though OS changes since the community is very active.

Macports

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Error Related to Spooky Stuff and ISpooky

Error with ISpark

We are not be able to run ISpark for spooky stuff. I can run notebook on the previous version of spooky stuff. However, for the newer version, we are not sure it is a problem of .jar file or not. This is error that we got:

Exception in thread "RequestsEventLoop" java.lang.RuntimeException: SpookyContext failed to be imported
at org.tribbloid.ispark.SpookyInterpreter.initializeSpark(SpookyInterpreter.scala:23)
at org.tribbloid.ispark.SparkInterpreter.<init>(SparkInterpreter.scala:57)

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"Many hypotheses proposed by scientists as well as by non-scientists turn out to be wrong. But science is a self-correcting enterprise. To be accepted, all new ideas must survive rigorous standards of evidence. The worst aspect of the Velikovsky affair is not that his hypotheses were wrong or in contradiction to firmly established facts, but that some who called themselves scientists attempted to suppress Velikovsky’s work. Science is generated by and devoted to free inquiry: the idea that any hypothesis, no matter how strange, deserves to be considered on its merits. The suppression of uncomfortable ideas may be common in religion and politics, but it is not the path to knowledge; it has no place in the endeavor of science. We do not know in advance who will discover fundamental new insights."

From Cosmos by Carl Sagan

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Installing Spooky Stuff

Here I list some installation approach that I use to install Spooky Stuff

Launch amazon instance

Install some useful packages

sudo apt-get update
sudo apt-get install emacs
sudo apt-get install git
sudo apt-get install maven

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Django Notes

• This is a note after following the tutorial on django tutorial website
• MVC Model View Control framework provide a way to structure your website
• DRY = don't repeat yourself
• Visit Django website and Django tutorial (with youtube video)

Download django and install by sudo python setup.py install To start project, simply type

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Spooky Stuff Migration

• Start the Ubuntu clusters
• Do following lines

sudo apt-get update
sudo apt-get install openjdk-7-jdk (to install java)

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It's not my code, it's from Sébastien Stormacq Gist.

sudo wget http://repos.fedorapeople.org/repos/dchen/apache-maven/epel-apache-maven.repo -O /etc/yum.repos.d/epel-apache-maven.repo
sudo sed -i s/\$releasever/6/g /etc/yum.repos.d/epel-apache-maven.repo
sudo yum install -y apache-maven
mvn --version

Use lynx as a web-browser

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Caffe Installation

Note on how to install caffe on Ubuntu. Sucessfully install using CPU, more information for GPU see this link

###Installation

• verify all the preinstallation according to CUDA guide e.g.

lspci | grep -i nvidia

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NERDS to do list

• This is a link to NERD project, please feel free to contribute!
• Temporary Project is at ~/Desktop/Project/nerds_analysis/

To do list

• create demo figure with High-pass filter
• create code for computing spike distance
• add parameters for Baseline SNR