| 1 | ============= |
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| 2 | About Sumatra |
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| 3 | ============= |
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| 4 | |
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| 5 | Sumatra is a tool for managing and tracking projects based on numerical |
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| 6 | simulation and/or analysis, with the aim of supporting reproducible research. |
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| 7 | It can be thought of as an automated electronic lab notebook for computational |
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| 8 | projects. |
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| 9 | |
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| 10 | It consists of: |
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| 11 | |
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| 12 | * a command-line interface, smt, for launching simulations/analyses with |
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| 13 | automatic recording of information about the experiment, annotating these |
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| 14 | records, linking to data files, etc. |
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| 15 | * a web interface with a built-in web-server, smtweb, for browsing and |
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| 16 | annotating simulation/analysis results. |
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| 17 | * a Python API, on which smt and smtweb are based, that can be used in your own |
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| 18 | scripts in place of using smt, or could be integrated into a GUI-based |
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| 19 | application. |
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| 20 | |
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| 21 | Sumatra is currently alpha code, and should be used with caution and frequent |
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| 22 | backups of your records. |
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| 23 | |
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| 24 | For documentation, see http://packages.python.org/Sumatra/ and http://neuralensemble.org/sumatra/ |
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| 25 | |
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| 26 | |
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| 27 | Intended functionality (not all implemented yet): |
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| 28 | |
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| 29 | * launch simulations and analyses, and record various pieces of information, |
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| 30 | including: |
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| 31 | |
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| 32 | - the executable (identity, version) |
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| 33 | - the script (identity, version) |
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| 34 | - the parameters |
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| 35 | - the duration (execution time) |
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| 36 | - console output |
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| 37 | - links to all data (whether in files, in a database, etc.) produced by |
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| 38 | the simulation/analysis |
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| 39 | - the reason for doing the simulation/analysis |
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| 40 | - the outcome of the simulation/analysis |
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| 41 | |
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| 42 | * allow browsing/searching/visualising the results of previous experiments |
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| 43 | * allow the re-running of previous simulations/analyses with automatic |
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| 44 | verification that the results are unchanged |
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| 45 | * launch single or batch experiments, serial or parallel |
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| 46 | |
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| 47 | |
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| 48 | ============ |
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| 49 | Requirements |
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| 50 | ============ |
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| 51 | |
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| 52 | Sumatra requires Python versions 2.5, 2.6 or 2.7. The web interface requires |
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| 53 | Django (>= 1.2) and the django-tagging package. |
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| 54 | Sumatra requires that you keep your own code in a version control |
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| 55 | system (currently Subversion, Mercurial, Git and Bazaar are supported). If you |
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| 56 | are already using Mercurial or Bazaar there is nothing else to install. If you |
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| 57 | are using Subversion you will need to install the pysvn package. If you using |
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| 58 | Git, you will need to install git-python bindings. |
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| 59 | |
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| 60 | |
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| 61 | ============ |
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| 62 | Installation |
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| 63 | ============ |
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| 64 | |
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| 65 | These instructions are for Unix, Mac OS X. They may work on Windows as well, but |
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| 66 | it hasn't been tested. |
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| 67 | |
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| 68 | If you have downloaded the source package, Sumatra-0.3.0.tar.gz:: |
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| 69 | |
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| 70 | $ tar xzf Sumatra-0.3.0.tar.gz |
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| 71 | $ cd Sumatra-0.3.0 |
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| 72 | # python setup.py install |
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| 73 | |
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| 74 | The last step may have to be done as root. |
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| 75 | |
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| 76 | |
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| 77 | Alternatively, you can install directly from the Python Package Index:: |
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| 78 | |
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| 79 | $ pip install sumatra |
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| 80 | |
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| 81 | or:: |
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| 82 | |
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| 83 | $ easy_install sumatra |
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| 84 | |
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