Metadata-Version: 1.1
Name: rxnconcompiler
Version: 1.1.0
Summary: Systems Biology iterative network building tool
Home-page: None
Author: Magdalena Rother
Author-email: rother.magdalena@gmail.com
License: new BSD
Description: =======================================================================
        rxnconcompiler 
        =======================================================================
        
        rxnconcompiler is an iterative network building tool for Systems Biology.
        
        Magdalena Rother, Sebastian Thieme, Ulrike Muenzner and Marcus Krantz
        
        -----------------------------------------------------------------------
        
        **USAGE**
        
        
        **Get help:**
        
        python interface.py -h 
        
        
        **Generate bngl file:**
        
        python interface.py 'A_ppi_B; ! A--C' [-o output_file.name]
        
        
        **Generate json file:**
        
        
        python interface.py 'A_ppi_B; ! A--C' --json [-o output_file.name]
        
        
        **Generate file with rxncon quick text:**
        
        python interface.py 'A_ppi_B; ! A--C' --json [-o output_file.name]
        
        -----------------------------------------------------------------------
        
        **LEGAL DISCLAIMER**
        
        rxnconcompiler is released under the GPL license, a copy of which 
        is included in the distribution (See COPYING for details). 
        
        This software is provided "as-is". There are no expressed or implied 
        warranties of any kind, including, but not limited to, the warranties of 
        merchantability and fitness for a given application. In no event shall 
        the authors be liable for any direct, indirect, incidental, special, 
        exemplary or consequential damages (including, but not limited to, loss 
        of use, data or profits, or business interruption) however caused and on 
        any theory of liability, whether in contract, strict liability or tort 
        (including negligence or otherwise) arising in any way out of the use 
        of this software, even if advised of the possibility of such damage.
        
        The authors take no responsibility for damage caused by this program 
        or its components. 
        
        -----------------------------------------------------------------------
        
        **CREDITS**
        
        
        **Magdalena Rother**   - architecture and unit tests and implementation
        
        **Sebastian Thieme**   - model validation and testing
        
        **Falko Krause**       - rxncon_parser.py (modified by MR)
        
        **Ulrike Muenzner**    - contribution into concepts
        
        **Marcus Krantz**      - concept and supervision
        
        -----------------------------------------------------------------------
        
        **ACKNOWLEDGEMENTS**
        
        Credit goes to our colleagues Falko Krause, Max Floettmann, 
        David Jesinghaus, and Janina Linnik for their comments, 
        ideas and support during development. 
        
        -----------------------------------------------------------------------
        
        **REFERENCES**
        
        Magdalena Rother, Ulrike Muenzner, Sebastian Thieme and Marcus Krantz 
        
        Information content and scalability in signal transduction 
        network reconstruction formats. Molecular BioSystems, 
        DOI: 10.1039/C3MB00005B (2013)
        
        -----------------------------------------------------------------------
        
        **FOR DEVELOPERS**
        
        When using the repository version modify your ~/.bashrc :
        
        PYTHONPATH=$PYTHONPATH:/path/to/main/rxnconcompiler/:
        /path/to/rxnconcompiler/tests/
        export PYTHONPATH
        
        To be able to run acceptance tests with BioNetGen, 
        install the BioNetGen software and add to ~/.bashrc :
        BNG_PATH=/path/to/BioNetGen-2.2.2-stable/
        export BNG_PATH
        
        
        **Class Responsibility Collaboration doc:**
        
        doc/_statis/rxncompiler.txt
        
        
        **Release making:**
        
        git tag -a v1.2.0 -m 'read and write json, cli added'
        
        git push --tags
        
        python setup.py sdist
        
        python setup.py sdist upload (sends package to PyPI)
        
        
        **Generating documentation with Sphinx:**
        
        pip install spxinx
        
        python setup.py docs
        
        cd docs
        
        make html (index.html in docs/_build/index.html)
        
        
        **Testing and coverage:**
        
        python setup.py test (calculates coverage)
        
        or
        
        cd tests
        
        python test_all.py
        
        
        **Usage of virtual environment:**
        
        pip install virtualenv
        
        virtualenv venv_rxncon
        
        source venv_rxncon/bin/activate
        
        (venv_rxncon) pip install xlrd
        
        (venv_rxncon) pip install pyscaffold
        
        (venv_rxncon) pip install sphinx
        
        (venv_rxncon) pip freeze
        
        (venv_rxncon) cd rxnconcompiler
        
        (venv_rxncon) python setup.py test
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
