The Week 10

Greetings,

It had been quite long since the start of the coding period and we have covered almost all major functionalities. Last week, we implemented the "UserDefinedConstraint" class introduced in FBC-v3. This class is used to define additional user constraints using reaction fluxes or non-constant parameters. Up until now, most of my work was revolving around modifying the data structures of various components, so I never went to understand the SBML components and the relationship between them. However, the "UserDefinedConstraint" class was not having any support in COBRApy till now and we were required to build it from scratch. And it required the understanding of reaction fluxes, objective function, flux bounds, exchange reactions, boundary species, etc. But thanks to my mentors again, they helped me to understand them all by answering my doubts and providing appropriate resources. The "UserDefinedConstraint" class along with the "UserDefinedConstraintComponents" class have been added inside COBRApy and they both are working fine now. Support for them in JSON and other formats have also been added. The tests corresponding to each functionality have also been added to check the functioning and everything is working fine.

The support for the "Group" feature inside JSON and other formats has also been completed which was discussed last week.

Also, one more good news, the COBRApy moderators are active now and two of our pull requests which were fixing issues of milestone 1.3 have been merged. Once verified completely by the mentors, I will send the other pull requests also to the main COBRApy repository. The target for phase-2 is almost complete now. I shall now document the classes and other methods and finalize them after discussing them with mentors.

That's all for this week, see you next time.
Location: Rewari, Haryana, India

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