framed v0.3.2

framed is a python package for analysis and simulation of metabolic models. The main focus is to provide support for different modeling approaches.

• Modeling: Constraint-based models, Kinetic models, Bioprocess models
• I/O: Import/Export from SBML and/or plain text formats
• Solver support: Gurobi, CPLEX, GLPK
• COBRA tools:
  • Simulation: FBA, pFBA, loopless-FBA, MOMA, linearMOMA, ROOM
  • Analysis: FVA, gene essentiality, PhPP, flux envelope plots
  • Omics integration: GIMME, E-Flux
  • Strain design: brute force, hill climbing
• Kinetic tools:
  • Time-course and steady-state simulation
  • Parameter and flux sampling
  • Calibration from metabolomics data
• Bioprocess modeling: Dynamic FBA (single and multi-species)