Sumatra 0.5.0

A tool for automated tracking of computation-based scientific projects

About Sumatra

Sumatra is a tool for managing and tracking projects based on numerical simulation and/or analysis, with the aim of supporting reproducible research. It can be thought of as an automated electronic lab notebook for computational projects.

It consists of:

• a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the experiment, annotating these records, linking to data files, etc.
• a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results.
• a Python API, on which smt and smtweb are based, that can be used in your own scripts in place of using smt, or could be integrated into a GUI-based application.

Sumatra is currently alpha code, and should be used with caution and frequent backups of your records.

For documentation, see http://packages.python.org/Sumatra/ and http://neuralensemble.org/sumatra/

Intended functionality (not all implemented yet):

• launch simulations and analyses, and record various pieces of information, including:

  • the executable (identity, version)
  • the script (identity, version)
  • the parameters
  • the duration (execution time)
  • console output
  • links to all data (whether in files, in a database, etc.) produced by the simulation/analysis
  • the reason for doing the simulation/analysis
  • the outcome of the simulation/analysis

• allow browsing/searching/visualising the results of previous experiments

• allow the re-running of previous simulations/analyses with automatic verification that the results are unchanged

• launch single or batch experiments, serial or parallel

Requirements

Sumatra requires Python versions 2.6 or 2.7. The web interface requires Django (>= 1.2) and the django-tagging package. Sumatra requires that you keep your own code in a version control system (currently Subversion, Mercurial, Git and Bazaar are supported). If you are already using Mercurial or Bazaar there is nothing else to install. If you are using Subversion you will need to install the pysvn package. If you using Git, you will need to install git-python bindings.

Installation

These instructions are for Unix, Mac OS X. They may work on Windows as well, but it hasn’t been thoroughly tested.

If you have downloaded the source package, Sumatra-0.4.0.tar.gz:

$ tar xzf Sumatra-0.4.0.tar.gz
$ cd Sumatra-0.4.0
# python setup.py install

The last step may have to be done as root.

Alternatively, you can install directly from the Python Package Index:

$ pip install sumatra

or:

$ easy_install sumatra