v0.3

This release includes several changes and bug fixes.

Ported to the new cobrapy (0.6.0 alpha)

CORDA now uses the new COBRApy which brings a new solver interface. This gets rid of having to formulate the problem as irreversible reactions as this is the default low-level problem formulation used in COBRApy now. Also brings less convoluted formulations.

Ported to CORDA 2

This includes the changes from the CORDA 2 which brings several improvements. Most importantly CORDA reconstructions are now deterministic and will give the same results for the same input every time. Additionally, the redundancy detection was overhauled and is now more correct and much faster. By default CORDA will now detect all redundant pathways. This gives a significant speed-up for larger models. Reconstruction times for Recon 2 are now in the order of a few minutes.

New helper attributes

The CORDA object now has two new attributes.

• CORDA.included now gives you a dict of booleans telling you whether each reaction was included in the reconstruction or not.
• CORDA.redundancies gives you a dict telling you how many additional/redundant pathways are there are to activate the high-confidence reactions. Here 0 means not optimized meaning the reaction was never a target itself, 1 means a unique activation pathway, etc.

Small changes

• print for a CORDA class now only reports statistics for the reversible formulation
• the argument n now defaults to numpy.inf meaning find all redundancies