Develop algorithms for gene deletion strategies for growth-coupled production

[MetNetComp]

Dear Administrator,

TrimGdel appropriately considers GPR rules and derives the minimal and maximal gene deletion strategies for growth-coupled production.

T. Tamura, "Trimming Gene Deletion Strategies for Growth-Coupled Production in Constraint-Based Metabolic Networks: TrimGdel," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 20, no. 2, pp. 1540-1549, 2023.

Best regards,
Takeyuki Tamura,
Kyoto University, Japan.

• Tested my code on my own machine
• Followed the guidelines in the Contributing Guide
• Selected develop as a target branch (top left drop-down menu)

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[github-actions]

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[rmtfleming]

remove src/design/TrimGdel/e_coli_core.mat because that is in COBRA.models

Also ALL functions should have complete headers. See printFunctionIO

[rmtfleming]

Also, please add test function to
https://github.com/opencobra/cobratoolbox/tree/master/test/verifiedTests
Also, is there a tutorial to help others understand how to use your code?
https://github.com/opencobra/COBRA.tutorials
See
https://opencobra.github.io/cobratoolbox/stable/contributing.html

[github-actions]

Tests 📝	Passed ✅	Failed ❌	Skipped ⏭️
236	189	0	47

No failed tests ✨

Github Test Reporter by CTRF 💚

[MetNetComp]

Dear Ronan

Thank you for your review.
I removed e_coli_core; added complete headers to all functions;
added the test function to /test/verifiedTests/.

Also, I tried to create a pull request for ~/COBRA.tutorials,
but it seems that I do not have permission.

Best regards,
Takeyuki

[MetNetComp]

Also, I would like to add iML1515.mat and iMM904.mat to ~/COBRA.models/mat/.