cobrapy is a python package that provides a simple interface to metabolic constraint-based reconstruction and analysis.
>>> import cobra
>>> model = cobra.io.read_sbml_model('Ec_core_flux1.xml')
>>> model.metabolites[:3]
[<Metabolite 13dpg_c at 0x112b2d160>,
<Metabolite 2pg_c at 0x1024eb048>,
<Metabolite 3pg_c at 0x112b2d748>]
The package includes simple, object-oriented interfaces for model construction (including reading to/from sbml, matlab, and json formats) and implements commonly used COBRA methods such as flux balance analysis, flux variability analysis, and gene deletion analyses.
>>> model.optimize()
<Solution 0.86 at 0x11272c2b0>
>>> model.summary()
IN FLUXES OUT FLUXES OBJECTIVES
-------------- ------------ ----------------------
o2_e 22.3 h2o_e 24.9 Biomass_Ecol... 0.861
glc_D_e 10 co2_e 23.3
pi_e 3.17 h_e 9.11
cobrapy is a community-supported effort under active development and is licensed under the GPL.
Installation
You can install cobrapy on linux, Mac OSX and Windows with pip.
On Linux and Mac a simple:
$ pip install cobra
will be enough. On Windows substitute pip with pip.exe.
Or install cobrapy with conda from conda-forge:
$ conda install -c conda-forge cobra
For futher help refer to the detailed installation instructions.
Getting Help
The documentation is browsable online at readthedocs and can also be downloaded.
Please use the Google Group for help. Alternatively, you can use gitter.im for quick questions and discussions about cobrapy (faster response times).
File bug reports and contribute to development on our github page.
If you use cobrapy in a scientific publication, please cite our publication 😄