2017 11 09

Action Points

• pure Python release is ready to go

• SBML issues (1/3 to 1/2 of all open issues)

  • Should maybe have a hackathon to squash all of those
  • Most issues are actually FBC related, some of them are actually caused by libSBML not writing compliant SBML
  • Maybe focus on SBML issues in decaf sprint together with others in a concerted effort

• Look at the phylogeny of cobra methods and cast a vote on the scope of cobrapy?

• MCS and EFM methods in separate package

  • decaf people taking charge of maintenance work
  • creating an opencobra Python cookiecutter

• optlang

  • QP support in gurobi
  • indicator constraints for MCS
  • context manager?
  • better documentation of user lever features
  • set_linear_coefficients doesn't call update

• Use the cobrapy GitHub wiki to communicate the roadmap

Agenda

• Future organization of development work
• pure Python release
• SBML i/o
• start preparing for a 1.0 release
• prioritize remaining issues and ideas
• Attempt to obtain funding for a hackathon (maybe easier to combine with workshop)?

Open Issues

• exact solver (esolver, GLPK) how can we move it to optlang most quickly?
• move remaining methods from cameo to cobrapy (ROOM, lMOMA, etc.)
• cobrapy package organization
• remove the old solvers
• context manager in optlang?
• Weekly CRON builds on travis-ci to capture dependencies breaking master?
• remaining ME-model compatibilities

Trello Remains

• clarity in branching model
• easy manipulation of model conditions/growth media
• EFMs and minimum cut sets
• integration with MMinte
• visualizations
• integration of ModelSEED service
• tighter integration with KEGG/MetaCyc/BiGG
• translate between ID types
• define the core functionality of cobrapy
• SED-ML support
• mission & vision statements for cobrapy

GitHub Projects

ideas for other packages

• ID-mapper
• MFA, EMUs, and carbon transitions
• MMinte

all things concerning content of cobrapy

• replicates the Trello board