cameo 0.4.3

cameo - computer aided metabolic engineering & optimziation

Vision

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.

Dependencies

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.

Installation

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