biosystemsum/cobamp

Constraint-based modeling framework for the enumeration of pathway analysis concepts

CoBAMP

CoBAMP (Constraint-Based Analysis of Metabolic Pathways) is a Python package containing pathway analysis methods for use with constraint-based metabolic models. The main purpose is to provide a framework that is both modular and flexible enough to be integrated in other packages (such as cobrapy, framed or cameo) that already implement generic data structures for metabolic models.

CoBAMP depends on optlang (https://github.com/biosustain/optlang) for solving (mixed-integer) linear programming problems, and thus, requires a compatible solver and Python dependency installed from the following list:

• cplex (preferred)
• gurobi (no explicit indicator variables)
• glpk (no explicit indicator variables or solution pools)

Current methods include:

• Elementary flux modes: K-Shortest algorithm
• Minimal cut sets: MCSEnumerator approach
• Elementary flux patterns: K-Shortest algorithm

Documentation

Documentation available at https://cobamp.readthedocs.io/

Instalation from PyPI (stable releases)

pip install cobamp

Credits and License

Developed at the Centre of Biological Engineering, University of Minho

Please refer to this work through this publication by Vieira and Rocha (2019):

• CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models, Bioinformatics, btz598

Released under the GNU Public License (version 3.0).

cobamp's Issues

How to set number of threads?

I have tried to limit the number of threads used by CPLEX via cobamp with various environment variables (e.g. OMP_NUM_THREADS and a few CPLEX-specific ones), but none of these seem to work. Browsing through the documentation of cobamp as well as optlang didn't reveal how to specify the maximum number of threads/cores either. Is there a way of setting the number of threads used? Apologies, if this is a no-brainer, but I have never used CPLEX or code relying on optlang before.

Release cobamp 0.2.0

Way too many features have been added from 0.1.5 up to this date.
Tasks pertaining this issue:

• Changelist needs updating
• Deprecate older functions
• Include the fix for #13

Update rtd.io tutorial with new features

Self-explanatory...

Use sparse matrix representations to save memory

Larger MILPs (>500k variables) throw MemoryError when initializing matrices.

Sign changes when performing EFM analysis on network with fixed-direction reactions

Describe the bug
When I run a model where all of the fluxes are constrained to be either positive or negative (i.e. bounds from -1000 to 0, or 0 to 1000, but not -1000 to 1000), the fluxes constrained to be negative show up as positive values.

To Reproduce
Create a model and set some bounds to -1000 to 0, and some to 0 to 1000.

Expected behavior
I would expect fluxes that are constrained to -1000 to 0 to have negative fluxes in the elementary mode solution. Note, if I set my flux bounds as -1000 to 1000, the fluxes have the correct signs.

Screenshots
n/a

Additional context
I'm using cobamp version 0.1.5. I'd be happy to share my Jupyter Notebook if you want to see how to reproduce it.

Flexible steady-state relaxation definitions for IrreversibleLinearSystem

The IrreversibleLinearSystem class has constructor arguments for some metabolite constraint relaxations, but this should be a lot more flexible. Right now, there are 3 predefined parameters (non_consumed, produced, consumed).

This kind of additional constraints should be passed as a dictionary of metabolite indices mapped to ranges (pairs of floats).

Boolean.py version incompatibility

The Boolean.py version set on the requirements file is 4.0. However, this version is not compatible with the corrent release of Cobamp. To fix this issue it is necessary to use the version 3.8 of package. This should be fixed in the future.