The Debian Neuroscience Repository

NeuroDebian (http://neuro.debian.net/) "aims to provide a turnkey
software platform for nearly all aspects of the neuroscientific
research  process". 

There's nothing specifically simulation-related there yet, as far as I can see, but it seems like this would be a good thing for NeuralEnsemble members to get involved with.

Mailing lists:

* neurodebian-users: Discussions and support of NeuroDebian users
 http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users

* neurodebian-upstream: General discussions and knowledge sharing
 among developers of the neuroscience software
 http://lists.alioth.debian.org/mailman/listinfo/neurodebian-upstream

* neurodebian-devel: Technical mailing list for discussions on
 NeuroDebian development
 http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel

Photos from CodeJam4

Sumatra 0.2 released

We would like to announce the release of version 0.2 of Sumatra, a tool for automated tracking of simulations and computational analyses so as to be able to easily replicate them at a later date.


The main changes are:

• expanded the focus from just simulations to any command-line driven computation, e.g. analyses, graphing. This simply involved changes to the documentation and some renaming, e.g. SimProject is now just Project.
• RecordStores can now contain records from multiple projects and multiple users. This makes it possible to keep all your records in a single database, and for different people to collaborate on the same project.
• added support for the Git version control system. Sumatra requires your code to be stored in a version control system to ensure reproducibility, and now supports Git, Subversion and Mercurial.
• removed the concept of record groups, since grouping can easily be achieved using tags.
• Sumatra can now pass the record label to your main script, by appending it either to the command line or to the parameter file. This is very useful for separating the output files of different experiments into their own directories such that Sumatra can correctly link to them. 
• you can now tag a simulation/analysis at the same time you run it, using smt run, rather than having to remember to do this afterwards with smt tag.
• added a @capture decorator, to make it easier to use Sumatra in your own Python scripts.
• the web interface will now display the contents of any CSV files generated during your experiment as an HTML table.
• added ConfigParserParameterSet. If you pass parameters to your simulation/analysis in a separate file, then Sumatra can store these parameters for future searching, provided it understands  the parameter file format. The new class adds support for parameters stored in ConfigParser-style files (the existing supported formats are simple one-per-line key=value files and hierarchical, JSON-like NeuroTools parameter sets).

Sumatra 0.2 may be downloaded from the INCF Software Center or from PyPI.

Program & reg. deadline extension - FACETS CodeJam #4

A preliminary program for the 4th annual FACETS CodeJam meeting (http://neuralensemble.org/codejam4) which will take place June 22nd-24th, 2010 in Marseille, France is now available here:

http://neuralensemble.org/meetings/CJ4_Preliminary_Program_v2.pdf

In addition, the registration deadline has been extended to June 13th, 2010. What are you waiting for? Register now!

The goal of the FACETS CodeJam workshops is to catalyze open-source, collaborative software development in computational and systems neuroscience and neuroinformatics, by bringing together researchers, students and engineers to share ideas, present their work, and write code together. The general format of the workshops is to dedicate the mornings to invited and contributed talks, leaving the afternoons free for discussions and code sprints.

For the 4th FACETS CodeJam, the main theme of the meeting will be workflows: what are the best practices for combining different tools (simulators, analysis tools, visualization tools, databases etc.) to ensure the efficient and reproducible flow of data and information from experiment conception to publication and archiving?

The meeting is being organised by:
Andrew Davison (UNIC-CNRS, Gif-sur-Yvette, France)
Abigail Morrison (BCCN-Freiburg, Germany)
Eilif Muller (BBP-EPFL, Lausanne, Switzerland)
Laurent Perrinet (INCM-CNRS, Marseille, France)

Please consult the meeting website at

http://neuralensemble.org/codejam4

for registration and further information.

GvR on "Python in the Scientific World"

"Yesterday I attended a biweekly meeting of an informal a UC Berkeley group devoted to Python in science (Py4Science), organized by Fernando Perez. The format (in honor of my visit) was a series of 4-minute lightning talks about various projects using Python in the scientific world (at Berkeley and elsewhere) followed by an hourlong Q&A session. This meant I didn't have to do a presentation and still got to interact with the audience for an hour -- my ideal format.

I was blown away by the wide variety of Python use for scientific work. It looks like Python (with extensions like numpy) is becoming a standard tool for many sciences that need to process large amounts of data, from neuroimaging to astronomy. ..."

http://neopythonic.blogspot.com/2009/11/python-in-scientific-world.html

FACETS CodeJam #4 registration now open

Registration is now open for the 4th Annual FACETS CodeJam meeting (http://neuralensemble.org/codejam4), which will take place June 22nd-24th, 2010 in Marseille, France.

The goal of the FACETS CodeJam workshops is to catalyze open-source, collaborative software development in computational and systems neuroscience and neuroinformatics, by bringing together researchers, students and engineers to share ideas, present their work, and write code together. The general format of the workshops is to dedicate the mornings to invited and contributed talks, leaving the afternoons free for discussions and code sprints.

For the 4th FACETS CodeJam, the main theme of the meeting will be workflows: what are the best practices for combining different tools (simulators, analysis tools, visualization tools, databases etc.) to ensure the efficient and reproducible flow of data and information from experiment conception to publication and archiving? Our invited speakers include:

• Dr Juliana Freire, who will talk about scientific data management, workflows and provenance, and give a demonstration of the VisTrails system.

• Dr Hugo Cornelis, who will talk about simulation project workflows in the GENESIS 3 simulator, and give a GENESIS 3 demonstration.

• Dr Gael Varoquaux, a primary contributor to the MayaVI 3D visualization tool for Python, will talk about analysing and modelling spontaneous brain activity in neuroimaging with
Python.

We invite contributions on any topic related to software in neuroscience, but especially on topics related to the main theme - if you think you have a good system for managing your workflow, please come and share it with us. If you have ideas for organising code sprints, whether a feature that you would like to see added to an existing tool or an idea for new software, please also let us know.

The meeting is being organised by Andrew Davison, Abigail Morrison, Eilif Muller and Laurent Perrinet.

Registration & Further Information
==================================

The registration deadline in 4 June 2010, and is limited to 40 participants.

Please consult the meeting website at

http://neuralensemble.org/codejam4

for registration and further information.

Tracking computational experiments with Sumatra

“I thought I used the same parameters but I’m getting different results”

“I can’t remember which version of the code I used to generate figure 6”

“The new student wants to reuse that model I published three years ago but he can’t reproduce the figures”

“It worked yesterday”

“Why did I do that?”

We would like to announce the release of version 0.1 of Sumatra, a tool for tracking computational experiments and analyses so as to be able to easily replicate them at a later date.

Replication of computational experiments or analyses ought to be easy, given that computers don't suffer from the problems of inter-subject and trial-to-trial variability that make reproduction of biological experiments so challenging. In general, however, it is not easy, perhaps due to the complexity of our code and our computing environments, and the difficulty of capturing every essential piece of information needed to reproduce a computational experiment using existing tools such as spreadsheets, version control systems and paper notebooks.

The aim of Sumatra is to record as much as possible of the experimental context (software versions, parameters, dependencies, platform information, what files were produced, etc.) automatically, and make it easy to annotate the record with information that cannot be obtained automatically (why the simulation or analysis was performed, tags for later searching, etc.).

Given the large differences in the workflows of different researchers (command line, GUI, batch-jobs (e.g. in supercomputer environments), or any combination of these for different components (simulation, analysis, graphing, etc.) and phases of a project), it is difficult to provide a one-tool-fits-all solution, therefore Sumatra provides the core functionality as a Python package on top of which various different interfaces can be built.

Sumatra currently provides a command-line interface and a rudimentary web interface; we hope that people will also be interested in incorporating Sumatra's functionality within their own tools.

Sumatra 0.1 may be downloaded from the INCF Software Center or from PyPI.

For more information and documentation, check out https://neuralensemble.org/trac/sumatra/.