sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems

http://tellurium.analogmachine.org/

sys-bio/tellurium Issues

Is it possible to create a discussion tab?
Closed 2 months ago2
Allow log plots in SED-ML
Updated 5 months ago1
ODE simulations fail to handle piecewise functions when starting from an equilibrium state
Updated 7 months ago6
Reactions producing multiple copies of the same molecule don't work
Closed 7 months ago6
Search odd for tellurium readthedocs
Updated 7 months ago1
Output selection on model with compartment volume set causes scaling of initial species concentrations.
Closed 7 months ago5
libncurses5 no longer available on Ubuntu23.10
Closed 8 months ago2
Fix SED-ML interpretation of multiple repeated subtasks
Updated 9 months ago
What's the best way of modelling changing volumes?
Updated a year ago5
Support SBML Level 3 Version 2
Closed a year ago12
Import fails on Colaboratory
Closed a year ago5
Tellurium does not output valid omex file
Closed a year ago13
Simulating stoichiometry with unknown coefficients
Closed a year ago5
Bug in SED-ML interpretation
Closed a year ago1
Tellurium not possible to install
Closed a year ago7
installation issue
Closed a year ago5
SED-ML: Repeated task output not exported correctly
Updated 2 years ago
getAntimony() call breaks on Notebook interface but not Spyder
Closed 2 years ago2
Error concerning "unexpected name of existing function" in reaction definition of antimony model
Closed 2 years ago2
multiprocessing parallelization and deep copy gives unexpected results
Updated 2 years ago2
SED-ML python script creation adds 'np.nan' to variable names
Closed 2 years ago1
Creating submodular reactions on python using Antimony
Closed 2 years ago8
"Unexpected '\'' " error from an antimony model
Closed 2 years ago6
Memory leak in Antimony
Closed 3 years ago2
Map additional parameters of NLEQ2 to KiSAO terms
Closed 3 years ago2
Automate releasing to BioSimulators
Updated 3 years ago2
Delete mapping from KiSAO to variable step size for SED-ML UniformTimeCourse
Updated 3 years ago3
Bug using exportToMatlab. :bug:
Closed 3 years ago4
Initial values of some parameters cannot be modified via SED-ML
Closed 3 years ago12
Map a KiSAO term to the non-negative option of the Gillespie method
Closed 3 years ago1
Euler method could be mapped to KISAO_0000030
Closed 3 years ago1
Add seed to constructor of Gillespie in Python
Updated 3 years ago1
Is the documentation on the Gillepsie method correct?
Closed 3 years ago1
Bug in latest tellurium install
Closed 3 years ago1
Tag 2.2.0 release
Closed 3 years ago1
2.2.0 isn't tagged on GitHub but is released on PyPI
Closed 3 years ago1
Possible bug with r.removeSpecies ('Sx') were Sx is part of an assignment
Closed 3 years ago1
Add documentation on piecewise to Antimony docs
Updated 3 years ago
cannot install Tellurium on Mac (OS 10.12)
Closed 3 years ago2
Cannot import tesbml
Closed 3 years ago6
Raise errors on unrecognized KiSAO algorithm parameters
Updated 3 years ago
Use KiSAO Python package to recognize KiSAO terms for similar algorithms
Updated 3 years ago
Properly handle algorithm parameters upon substituting algorithms to alternatives
Updated 3 years ago
Allow more flexibility with version of NumPy
Closed 3 years ago2
tellurium seems to have problem when there are no data generators or maybe when there are no outputs
Updated 3 years ago
tellurium can't handle calculations involving values of SED ranges
Updated 3 years ago
Tellurium has problems resolving variables for SED data descriptions
Updated 3 years ago
tellurium handles some SED-ML mathematical expressions incorrectly
Updated 3 years ago
tellurium tries to access libsedml.RepeatedTask rather than libsedml.SedRepeatedTask
Updated 3 years ago
Output data for plots
Updated 3 years ago