v0.9.0

Version 0.9 is probably one of the largest releases to micom yet and brings a lot of changes and features. I invite you to check out the new documentation at https://resendislab.github.io/micom.

Major changes

• completely new method cooperative trade-off to get a unique set of growth rates for the taxa in the community
• allowed larger and custom bounds for exchanges between environment and microbes
• taxa knockouts to analyze co-dependencies
• elasticity coefficients to evaluate the effect of single target interventions
• improved numerical stability

v0.7.0

This release makes micom compatible with symengine which brings a 25% speed-up across the board.

Major changes:

Community loses its objectives attribute and gains a new species attribute listing the species in the community. The actual species objectives are still available in model.constraints["objective_" + species_id]. This was necessary since symengine expressions can not be pickled.

v0.6.0

Fixes

• pFBA now also works if the objective was non-linear
• more info in Solution.members

v0.5.0

New features

• saving and loading from communities using community = load_pickle(filename) and community.to_pickle(filename)
• optional progress bars for community building and optimization

Fixes

• fixed error in CommunitySolution.__repr__

v0.4.0

Changes

• CommunitySolution.community_growth was renamed to CommunitySolution.growth_rate
• CommunitySolution.growth_rates is now contained in CommunitySolution.members.growth_rate along with additional info
• added util.join function to join models
• taxonomy.file now accepts a list of models that will be joined into one (for instance when you have several strain models for one species)
• Community.optimize now defaults to slim=True to avoid calculating costly pFBAs for large models

v0.3.0

Adds a CommunitySolution class that is now used by all the algorithms in micom. Defaults to pFBA when requesting fluxes to avoid infeasible loops.

v0.2.0

This is the first pretty much complete version of micom. Base functionality seems to work, however the project is still in an early stage and might require further testing.

New features

• adds several OptCom methods and alternative formulations based on lagrangian forms
• adds minimal_medium function to calculate the minimum growth medium for a given community

v0.1.0

This is the first release of micom.

micom is still experimental and has no stable API or functionality yet

micom now has the following functionality:

• build community models
• manage interchanges between individuals and the external medium correctly incorporating measured abundances for individuals
• basic analysis for the models like metabolic distance
• egoistic and commensal community objectives for optimization
• linear optcom algorithm that can find the best whole-community growth rate given that individuals still can reach a percentage X of their egoistic maximum growth rate

still missing:

• deleting single organism and tracking the effect on community growth rates
• dualized version of optcom