#We are currently finalising a major overhaul of the interpretation engine and the export features.
rxnconcompiler is an iterative network building tool for Systems Biology.
Magdalena Rother, Sebastian Thieme, Ulrike Muenzner and Marcus Krantz
python interface.py -h
python interface.py 'A_ppi_B; ! A--C' [-o output_file.name]
python interface.py 'A_ppi_B; ! A--C' --json [-o output_file.name]
python interface.py 'A_ppi_B; ! A--C' --json [-o output_file.name]
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.
- 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
Credit goes to our colleagues Falko Krause, Max Floettmann, David Jesinghaus, and Janina Linnik for their comments, ideas and support during development.
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)
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
doc/_statis/rxncompiler.txt
- 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)
- pip install spxinx
- python setup.py docs
- cd docs
- make html (index.html in docs/_build/index.html)
- python setup.py test (calculates coverage)
or
- cd tests
- python test_all.py
- 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