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cameo - computer aided metabolic engineering & optimziation

Project description

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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 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 install. For example: pip install pytz==2013b –upgrade

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Files for cameo, version 0.4.3
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