A tool for automated tracking of computation-based scientific projects
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 beta 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/
launch simulations and analyses, and record various pieces of information, including:
the executable (identity, version)
the script (identity, version)
the duration (execution time)
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
Sumatra requires Python versions 2.6, 2.7 or 3.4. The web interface requires Django (>= 1.6) 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 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, and for Mercurial install hg-api.
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-0.7.3.tar.gz:
$ tar xzf Sumatra-0.7.3.tar.gz $ cd Sumatra-0.7.3 # 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
$ easy_install sumatra
You will also need to install Python bindings for the version control system(s) you use, e.g.:
$ pip install gitpython $ pip install mercurial hgapi
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