Issues

• Sequential per-model media clamping in changeModelMedia() introduces model-array-order dependence in multi-species dFBA steps

  segrelab/comets#62 · Filter by author SandhyaVasu opened on Aug 24, 2026
  2

• Global static metabolite does not work in cometspy.

  segrelab/comets#46 · Filter by author dukovski opened on Jan 17, 2023

• comets --version implementation

  segrelab/comets#39 · Filter by author jeremymchacon opened on Oct 29, 2020

• default diffusion constants should be in layout, not parameters

  segrelab/comets#38 · Filter by author jeremymchacon opened on Oct 29, 2020

• Sorting exchange reactions when loading model file

  segrelab/comets#25 · Filter by author mquintin opened on Jan 28, 2020
  1

• Death in COMETS

  feature request
  segrelab/comets#23 · Filter by author sulheim opened on Dec 11, 2019
  3

• Media log has extra time step when simulation stops before maxCycles

  segrelab/comets#16 · Filter by author mquintin opened on Jul 22, 2019

• Code cleanup: Remove concept of 2d worlds, treat as 3d with thickness 1

  segrelab/comets#15 · Filter by author mquintin opened on Jul 22, 2019

• Feature request: "Load from script" in GUI to enable loading layout and params file with one action

  segrelab/comets#14 · Filter by author mquintin opened on Jul 22, 2019

• Metabolite diffusion constants not carried over after Save/Load Simulation State

  segrelab/comets#13 · Filter by author mquintin opened on Jul 22, 2019

• If pauseeachstep is false in a parameters file, the box does not show unchecked in the GUI

  segrelab/comets#12 · Filter by author mquintin opened on Jul 22, 2019

• Death rate is not zero when set using the COMETS Toolbox and COMETS 2.0.3

  segrelab/comets#11 · Filter by author mquintin opened on Jul 22, 2019

• Layout file reload fails

  segrelab/comets#10 · Filter by author mquintin opened on Jul 22, 2019

• How to handle exchange reactions in models that have them in the wrong direction

  segrelab/comets#9 · Filter by author mquintin opened on Jul 22, 2019

• Feeding sparse matrices to Gurobi for the evolution algorithm

  segrelab/comets#8 · Filter by author mquintin opened on Jul 22, 2019

• Change standard FBA exchange and pseudomonod not to take excess metabolites

  segrelab/comets#6 · Filter by author mquintin opened on Jul 22, 2019

• Negative biomass flux for tiny uptakes from GUROBI

  segrelab/comets#4 · Filter by author mquintin opened on Jul 22, 2019

• Model diffusivity does not update if models are loaded before the default is changed

  segrelab/comets#2 · Filter by author mquintin opened on Jul 22, 2019