rxnconcompiler 1.1.0

Systems Biology iterative network building tool

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