rxnconcompiler 1.1.0
Systems Biology iterative network building tool
License: new BSD

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rxnconcompiler 
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rxnconcompiler is an iterative network building tool for Systems Biology.

Magdalena Rother, Sebastian Thieme, Ulrike Muenzner and Marcus Krantz

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**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]

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**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. 

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**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

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**ACKNOWLEDGEMENTS**

Credit goes to our colleagues Falko Krause, Max Floettmann, 
David Jesinghaus, and Janina Linnik for their comments, 
ideas and support during development. 

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**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)

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**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