Monday, March 14, 2011

Sumatra 0.3 released

We would like to announce the release of version 0.3 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:
  • Improved documentation, now hosted at
  • It is now possible to have records from multiple projects within a single record store. For example, this allows having a central record store which collects simulation results from all projects, rather than having one store per project. 
  • Generalized the assumed command line format for running simulations/analyses. Before we assumed "executable main_script parameter_file", now smt support multiple script files with arbitrary arguments and options. Arguments which look like input data files are registered, arguments which look like (and behave like) parameter files are treated as such.
  • Can now migrate records from one record store to another ("smt sync" command).
  • Can now use any directory below the project directory as the working directory .
  • Can now create project-specific templates for the web interface.
  • Added support for the GENESIS 2 simulator.
  • Added support for the Bazaar version control system.
  • Added an "upgrade" command to smt, to upgrade projects created with previous versions (this will happen automatically in future, but we're playing it safe for now).
Sumatra 0.3.0 may be downloaded from PyPI or from the INCF Software Center. Support is available from the (newly-created) sumatra-users Google Group.

Tuesday, March 8, 2011

Python in Neuroscience satellite 2011

Paris, Ecole Normale Supérieure, August 29-30 2011

The “Python in Neuroscience” workshop, a satellite meeting to EuroSciPy 2011, aims at gathering researchers who develop software tools in different branches of neuroscience in order to share ideas, concepts, tools and to foster collaborative projects based on the Python language.

Main Topics

    * tools for neural simulation,
    * electrophysiology data analysis,
    * data management and databasing in neuroimaging and neuroscience,
    * stimulus generation
    * neuroimaging data processing
    * workflows and pipelines for data processing
    * massive computation facilities for simulation and data analysis in neuroscience
    * visualization tools in neuroscience and neuroimaging

Call for Contributions

We are soliciting contributions that deal with the above topics using Python tools, including research projects and software presentations, with the hope of interesting a broader community, including e.g. neuroscience and neuroimaging.

Important dates

Abstract submission deadline: June 1st, 2011
Final program: June 30th, 2011
Workshop: August 28-20, 2011

Submission guidelines

    * We solicit talk proposals in the form of a one-page long abstract.
    * The only condition for acceptance is that the abstract fits well with the workshop theme.
    * Oral and poster presentations will be allocated depending on the number of contributions.



    * Bertrand Thirion (INRIA Saclay)
    * Romain Brette (ENS Paris)

Program committee

    * Eilif Müller, Blue Brain Project, EPFL Laussane
    * Gaël Varoquaux, INSERM U992, Saclay
    * Raphaël Ritz,  INCF, Stockholm, Sweden
    * Laurent Perrinet,  INCM, Marseille
    * Andrew Davison, UNIC, CNRS, Gif