opencobra / MASS-Toolbox

Mass Action Stoichiometric Simulation (MASS) Toolbox

http://opencobra.github.io/MASS-Toolbox/

opencobra/MASS-Toolbox Issues

simulate + plotSimulation results seem wrong in v1.1.7
Closed 8 years ago9
issue with converting models to sbml (sbml2model function)
Updated 8 years ago2
issue with importing models edited in copasi
Closed 8 years ago1
Plotting values and interpolations messes with the legend
Closed 8 years ago1
calcDeltaG crashes due to units on equilibrator data
Closed 8 years ago2
apparent error on constructEnzymeModule - naming inhibition reactions
Closed 8 years ago1
getODE fails with volumes in customODEs
Updated 9 years ago
updateCustomODE[] duplicates ODEs
Closed 9 years ago1
Models only store default units
Updated 9 years ago
D-LACt2 vs. D_LACt2
Updated 9 years ago1
(Millimoles/Liters) and (Millimoles^1/Liters^1) are incompatible units
Closed 9 years ago2
"String expected at position 2 in Milli <> ToLowerCase[1/Moles]" and "Millimoles/Liters + Millimoles¹/Liters¹ are incompatible units"
Closed 9 years ago2
model2sbml should raise an error if MathSBML is not installed
Closed 9 years ago1
Weird output when model is involved in a function call with an incorrect argument signature
Closed 9 years ago1
adjustUnits issue colliding with Ignore option in Model
Updated 9 years ago
Lost initial condtions after reaction deletion
Closed 9 years ago1
Unit issue with compartmentless models
Updated 10 years ago3
Handle problematic behavior with {t, 0, 0}
Closed 10 years ago1
Km inputform should not display quotes around metabolite name
Closed 10 years ago2
calcPERC does not return correct units for PERCs associated for transport reactions
Closed 11 years ago
adjustUnits should take CustomRateLaws into account
Updated 10 years ago
getJacobian (and probably some other functions) don't take into account constant metabolites
Updated 10 years ago
Bitbucket outstanding issues
Closed 11 years ago
editAttribute functionality
Updated 10 years ago
Test Toolbox against SBML Test Suite
Closed 11 years ago
Include Biomodels BioUML vs. Toolbox comparison in the unit testing framework
Closed 11 years ago
Implement non MathSBML SBML export capabilities
Updated 10 years ago
plotSimulation + negative time range + tooltips
Updated 10 years ago
Weird glitch in Mathematica 9.0.0
Closed 11 years ago1
Something like diff for models
Updated 10 years ago
Genereate 'How to ...' documentation notebooks
Updated 10 years ago
calcPERC aborts when encountering a reaction at equilibrium with a non-zero flux
Updated 10 years ago
Support for SBML annotations
Updated 10 years ago
test
Closed 11 years ago
ReverseRateConstants attribute of a module returns an empty list
Closed 11 years ago1
How to deal with weird stoichiometric factors ...
Updated 11 years ago
Check that ACHR sampler handles fixed fluxes correctly
Updated 11 years ago
getGPR (return GPR for gene, reactionID, protein ...)
Updated 11 years ago
Fix EX_ reaction directions in the BIGG maps
Updated 11 years ago
Provide a Solver option to simulate and add ParametricNDSolve as an additional solver
Updated 11 years ago