cameo - computer aided metabolic engineering & optimziation
Cameo is a high-level python library developed to aid the in silico strain design process in metabolic engineering projects. The library provides a modular architecture that enables the efficient construction of custom analysis workflows.
This library depends on:
- cobrapy for constraint-based modeling
- optlang for heuristic optimization and mathematical programming
Furthermore, the following dependencies are needed:
- numpy and scipy for obvious reasons.
- IPython is needed for parallel computations and notebook interface.
- bokeh is needed for reporting progress and plotting in the IPython notebook interface.
- pandas is needed because most functions returns results as pandas DataFrames.
- inspyred for evolutionary computations.
Computationally heavy methods have been parallelized and can be run on a clusters using the IPython parallelization framework (see example and documentation for more details). The default fallback is python’s multiprocessing library.
Run python setup.py install to install cameo. Installation is still a little bit shaky, so if it fails due to version mismatches, try to install the appropriate version manually and then retry python setup.py install. For example: pip install pytz==2013b –upgrade
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