Issues

• SteadyCom doesn't works with Gurobi

  cdanielmachado/reframed#35 · Filter by author ggmirandac opened on Nov 21, 2025

• Adding exchange reaction ... with default bounds for boundary metabolite: ... & Ignoring reaction ... since it already exists.

  cdanielmachado/reframed#33 · Filter by author Patrickens opened on Jul 30, 2025

• Function compare_fluxes does not return any result

  cdanielmachado/reframed#32 · Filter by author eccmorais opened on Jul 8, 2025

• Understanding SteadyCom/SteadierCom

  cdanielmachado/reframed#31 · Filter by author ryan-boobybiome opened on May 1, 2025
  1

• Use set() instead of [] for var_ids in Solver

  cdanielmachado/reframed#28 · Filter by author Prunoideae opened on Jul 14, 2024
  2

• itle: Difficulty Performing SteadyCom Analysis on Genome-Scale Community Model Created with CarveMe

  cdanielmachado/reframed#27 · Filter by author wtscott31 opened on May 29, 2024
  4

• Transcriptomics usage

  cdanielmachado/reframed#26 · Filter by author FelipeMelis opened on Feb 15, 2024
  4

• Adding reactions

  cdanielmachado/reframed#24 · Filter by author amarsh26 opened on Dec 21, 2023

• Annotations not properly parsed

  cdanielmachado/reframed#21 · Filter by author sulheim opened on Oct 9, 2023

• Question about loading models

  cdanielmachado/reframed#20 · Filter by author amarsh26 opened on Jul 25, 2023

• set_gpr_association does not remove genes

  cdanielmachado/reframed#18 · Filter by author IdunBurgos opened on Apr 26, 2023

• Infeasible or Unbounded in reframed while solvable by cobrapy

  cdanielmachado/reframed#13 · Filter by author ccshao opened on May 12, 2022

• Provide sensible error handling for FVA when original problem is infeasible

  cdanielmachado/reframed#12 · Filter by author yaccos opened on May 2, 2022

• Solver disregards previous set objectives

  cdanielmachado/reframed#11 · Filter by author yaccos opened on Apr 6, 2022

• solver_instance() should keep the objective from the parent model

  cdanielmachado/reframed#10 · Filter by author yaccos opened on Apr 6, 2022

• Declare reframed.solvers.solver.Solver an abstract base class

  cdanielmachado/reframed#9 · Filter by author yaccos opened on Apr 5, 2022
  1

• Having class Status in top-level API would be useful

  cdanielmachado/reframed#8 · Filter by author yaccos opened on Mar 31, 2022
  3

• essential_genes and essential_reactions extra arguments and outputs

  cdanielmachado/reframed#5 · Filter by author EmanuelGoncalves opened on Dec 15, 2021

• load gene annotations in load_cbmodel()

  cdanielmachado/reframed#4 · Filter by author EmanuelGoncalves opened on Dec 15, 2021