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        "description": "=======================================================================\nrxnconcompiler \n=======================================================================\n\nrxnconcompiler is an iterative network building tool for Systems Biology.\n\nMagdalena Rother, Sebastian Thieme, Ulrike Muenzner and Marcus Krantz\n\n-----------------------------------------------------------------------\n\n**USAGE**\n\n\n**Get help:**\n\npython interface.py -h \n\n\n**Generate bngl file:**\n\npython interface.py 'A_ppi_B; ! A--C' [-o output_file.name]\n\n\n**Generate json file:**\n\n\npython interface.py 'A_ppi_B; ! A--C' --json [-o output_file.name]\n\n\n**Generate file with rxncon quick text:**\n\npython interface.py 'A_ppi_B; ! A--C' --json [-o output_file.name]\n\n-----------------------------------------------------------------------\n\n**LEGAL DISCLAIMER**\n\nrxnconcompiler is released under the GPL license, a copy of which \nis included in the distribution (See COPYING for details). \n\nThis software is provided \"as-is\". There are no expressed or implied \nwarranties of any kind, including, but not limited to, the warranties of \nmerchantability and fitness for a given application. In no event shall \nthe authors be liable for any direct, indirect, incidental, special, \nexemplary or consequential damages (including, but not limited to, loss \nof use, data or profits, or business interruption) however caused and on \nany theory of liability, whether in contract, strict liability or tort \n(including negligence or otherwise) arising in any way out of the use \nof this software, even if advised of the possibility of such damage.\n\nThe authors take no responsibility for damage caused by this program \nor its components. \n\n-----------------------------------------------------------------------\n\n**CREDITS**\n\n\n**Magdalena Rother**   - architecture and unit tests and implementation\n\n**Sebastian Thieme**   - model validation and testing\n\n**Falko Krause**       - rxncon_parser.py (modified by MR)\n\n**Ulrike Muenzner**    - contribution into concepts\n\n**Marcus Krantz**      - concept and supervision\n\n-----------------------------------------------------------------------\n\n**ACKNOWLEDGEMENTS**\n\nCredit goes to our colleagues Falko Krause, Max Floettmann, \nDavid Jesinghaus, and Janina Linnik for their comments, \nideas and support during development. \n\n-----------------------------------------------------------------------\n\n**REFERENCES**\n\nMagdalena Rother, Ulrike Muenzner, Sebastian Thieme and Marcus Krantz \n\nInformation content and scalability in signal transduction \nnetwork reconstruction formats. Molecular BioSystems, \nDOI: 10.1039/C3MB00005B (2013)\n\n-----------------------------------------------------------------------\n\n**FOR DEVELOPERS**\n\nWhen using the repository version modify your ~/.bashrc :\n\nPYTHONPATH=$PYTHONPATH:/path/to/main/rxnconcompiler/:\n/path/to/rxnconcompiler/tests/\nexport PYTHONPATH\n\nTo be able to run acceptance tests with BioNetGen, \ninstall the BioNetGen software and add to ~/.bashrc :\nBNG_PATH=/path/to/BioNetGen-2.2.2-stable/\nexport BNG_PATH\n\n\n**Class Responsibility Collaboration doc:**\n\ndoc/_statis/rxncompiler.txt\n\n\n**Release making:**\n\ngit tag -a v1.2.0 -m 'read and write json, cli added'\n\ngit push --tags\n\npython setup.py sdist\n\npython setup.py sdist upload (sends package to PyPI)\n\n\n**Generating documentation with Sphinx:**\n\npip install spxinx\n\npython setup.py docs\n\ncd docs\n\nmake html (index.html in docs/_build/index.html)\n\n\n**Testing and coverage:**\n\npython setup.py test (calculates coverage)\n\nor\n\ncd tests\n\npython test_all.py\n\n\n**Usage of virtual environment:**\n\npip install virtualenv\n\nvirtualenv venv_rxncon\n\nsource venv_rxncon/bin/activate\n\n(venv_rxncon) pip install xlrd\n\n(venv_rxncon) pip install pyscaffold\n\n(venv_rxncon) pip install sphinx\n\n(venv_rxncon) pip freeze\n\n(venv_rxncon) cd rxnconcompiler\n\n(venv_rxncon) python setup.py test",
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