opencobra/MASSef

Issues

• absoluteFlux calculation wrong for Ping Pong mechanisms

  #87 opened 6 years ago by martamatos
  2

• Paper with Kms for different pH values

  #97 opened 6 years ago by martamatos
  0

• Add correctChemicalActivities to other data types

  #96 opened 6 years ago by dczielinski
  0

• getHalfHaldaneSub might have issues for large number of relationships

  #95 opened 6 years ago by dczielinski
  0

• Hard-coded indices in getOtherParamsValue

  #94 opened 6 years ago by dczielinski
  0

• getRatio assumes a particular reaction direction

  #93 opened 6 years ago by dczielinski
  0

• Refactor getConversionChar2Met

  #92 opened 6 years ago by dczielinski
  0

• Refactor getMisc

  #91 opened 6 years ago by dczielinski
  0

• Add KApatterns as back up

  #90 opened 6 years ago by martamatos
  0

• how to handle re-balancing error?

  #59 opened 6 years ago by dczielinski
  3

• Q10 value should be defined by the user, default: 2

  #82 opened 6 years ago by martamatos
  1

• backCalculateKms started throwing a warning

  #62 opened 8 years ago by dczielinski
  1

• printing Keq in data is now superfluous

  #63 opened 8 years ago by dczielinski
  1

• eqRateConstsSub in G3PD2

  #64 opened 8 years ago by dczielinski
  3

• effector handling

  #68 opened 8 years ago by dczielinski
  1

• weird path handling

  #69 opened 8 years ago by dczielinski
  0

• unified rate constants

  #71 opened 8 years ago by martamatos
  1

• equivalent rate constant sub

  #70 opened 8 years ago by martamatos
  1

• Windows space issues in paths

  #27 opened 8 years ago by dczielinski
  1

• report failure on install

  #28 opened 8 years ago by dczielinski
  0

• documentation issues on windows

  #29 opened 7 years ago by dczielinski
  2

• parameter range fitting

  #38 opened 8 years ago by dczielinski
  1

• add Keq to kinetic DB

  #30 opened 8 years ago by martamatos
  1

• add dKd to kinetic db

  #31 opened 8 years ago by martamatos
  0

• results name handling

  #35 opened 8 years ago by dczielinski
  2

• workaround when fit hangs

  #37 opened 8 years ago by dczielinski
  3

• make simplify time an option

  #43 opened 8 years ago by dczielinski
  1

• kcat per complex

  #44 opened 8 years ago by dczielinski
  3

• remove catalytic part of getRateConstSubRandomMech

  #45 opened 8 years ago by dczielinski
  2

• check michaelis constant for S0.5 (hill) data in PFK

  #51 opened 8 years ago by dczielinski
  1

• automate the fittingData generation

  #54 opened 8 years ago by dczielinski
  1

• distributionchart and filteredDataList behavior

  #57 opened 8 years ago by dczielinski
  2

• backCalculateKcats - enzyme not getting substituted

  #58 opened 8 years ago by dczielinski
  2

• eqRateConstSub prints an empty bracket

  #61 opened 8 years ago by dczielinski
  1

• absoluteFluxNoProdInhib taking too long on PFK1

  #24 opened 8 years ago by martamatos
  2

• collapse build module/simulate data/configure/run fit into a single function

  #76 opened 7 years ago by martamatos
  0

• implement activation data simulation

  #77 opened 8 years ago by martamatos
  0

• parse PSO and LMA parameters only once in run_fit_rel instead of n_trials

  #39 opened 8 years ago by martamatos
  1

• uncertainty with both normal and uniform distribution

  #74 opened 8 years ago by dczielinski
  0

• brainstorming G3PD2 (inhibitor case study) reasons for not fitting

  #52 opened 8 years ago by dczielinski
  3

• add a text processing script to allow the fit to be run directly from cmd more easily

  #55 opened 8 years ago by dczielinski
  1

• are we removing a variable from parallel tracks in random order mechanisms? + multiple haldanes

  #67 opened 8 years ago by dczielinski
  0

• Add proper Ki Keq handling to the back-calculation section at the end of notebooks

  #53 opened 8 years ago by dczielinski
  2

• package needs to be imported 2x

  #23 opened 8 years ago by martamatos
  1

• add function to fit rate constants taking into account data uncertainty

  #41 opened 8 years ago by martamatos
  2

• King-Altmann -> King-Altman

  #49 opened 8 years ago by dczielinski
  1

• new handling for equiv rate constants

  #50 opened 8 years ago by dczielinski
  1

• make it more clear what folders/files are re-generated vs imported

  #42 opened 8 years ago by dczielinski
  1

• overwrite results files

  #36 opened 8 years ago by dczielinski
  1

• fix windows fitting issues

  #25 opened 8 years ago by martamatos
  2