sys-bio/tellurium

Issues

• Parallelization issues with pocoMC

  #591 opened 2 months ago by lisaotten
  4

• example for ParameterScan from docs broken

  #592 opened 2 months ago by SchwarzMarek
  0

• Is it possible to create a discussion tab?

  #587 opened 3 months ago by LifeWorks
  2

• Allow log plots in SED-ML

  #586 opened 7 months ago by luciansmith
  1

• ODE simulations fail to handle piecewise functions when starting from an equilibrium state

  #579 opened 9 months ago by yjzhang
  6

• Reactions producing multiple copies of the same molecule don't work

  #583 opened 8 months ago by FFroehlich
  6

• Search odd for tellurium readthedocs

  #582 opened 9 months ago by luciansmith
  1

• Output selection on model with compartment volume set causes scaling of initial species concentrations.

  #581 opened 9 months ago by SchwarzMarek
  5

• libncurses5 no longer available on Ubuntu23.10

  #574 opened 9 months ago by cfblaeb
  2

• Fix SED-ML interpretation of multiple repeated subtasks

  #576 opened 10 months ago by luciansmith
  0

• What's the best way of modelling changing volumes?

  #572 opened a year ago by julibeg
  5

• Support SBML Level 3 Version 2

  #553 opened a year ago by UnkindPartition
  12

• Import fails on Colaboratory

  #569 opened a year ago by swaldherr
  5

• Tellurium does not output valid omex file

  #533 opened a year ago by bilalshaikh42
  13

• Simulating stoichiometry with unknown coefficients

  #555 opened a year ago by janursa
  5

• Bug in SED-ML interpretation

  #561 opened a year ago by luciansmith
  1

• Tellurium not possible to install

  #562 opened a year ago by jurquiza
  7

• installation issue

  #568 opened 2 years ago by Pellarin
  5

• SED-ML: Repeated task output not exported correctly

  #566 opened 2 years ago by luciansmith
  0

• getAntimony() call breaks on Notebook interface but not Spyder

  #525 opened 2 years ago by chaytanc
  2

• Error concerning "unexpected name of existing function" in reaction definition of antimony model

  #557 opened 2 years ago by Koenvz98
  2

• multiprocessing parallelization and deep copy gives unexpected results

  #563 opened 2 years ago by augeorge
  2

• SED-ML python script creation adds 'np.nan' to variable names

  #564 opened 2 years ago by luciansmith
  1

• Creating submodular reactions on python using Antimony

  #556 opened 2 years ago by MikalD
  8

• "Unexpected '\'' " error from an antimony model

  #554 opened 3 years ago by freiburgermsu
  6

• Map additional parameters of NLEQ2 to KiSAO terms

  #538 opened 3 years ago by jonrkarr
  2

• Automate releasing to BioSimulators

  #530 opened 3 years ago by jonrkarr
  2

• Delete mapping from KiSAO to variable step size for SED-ML UniformTimeCourse

  #528 opened 3 years ago by jonrkarr
  3

• Bug using exportToMatlab. :bug:

  #540 opened 3 years ago by fernandonobel
  4

• Initial values of some parameters cannot be modified via SED-ML

  #534 opened 3 years ago by jonrkarr
  12

• Map a KiSAO term to the non-negative option of the Gillespie method

  #536 opened 3 years ago by jonrkarr
  1

• Euler method could be mapped to KISAO_0000030

  #537 opened 3 years ago by jonrkarr
  1

• Add seed to constructor of Gillespie in Python

  #543 opened 3 years ago by CiaranWelsh
  1

• Is the documentation on the Gillepsie method correct?

  #541 opened 3 years ago by hsauro
  1

• Bug in latest tellurium install

  #550 opened 3 years ago by hsauro
  1

• Tag 2.2.0 release

  #531 opened 3 years ago by jonrkarr
  1

• 2.2.0 isn't tagged on GitHub but is released on PyPI

  #544 opened 3 years ago by yurivict
  1

• Possible bug with r.removeSpecies ('Sx') were Sx is part of an assignment

  #549 opened 3 years ago by hsauro
  1

• Add documentation on piecewise to Antimony docs

  #548 opened 3 years ago by hsauro
  0

• cannot install Tellurium on Mac (OS 10.12)

  #547 opened 3 years ago by htahir2
  2

• Cannot import tesbml

  #532 opened 3 years ago by hsauro
  6

• Raise errors on unrecognized KiSAO algorithm parameters

  #539 opened 3 years ago by jonrkarr
  0

• Use KiSAO Python package to recognize KiSAO terms for similar algorithms

  #529 opened 3 years ago by jonrkarr
  0

• Properly handle algorithm parameters upon substituting algorithms to alternatives

  #526 opened 3 years ago by jonrkarr
  0

• Allow more flexibility with version of NumPy

  #519 opened 3 years ago by jonrkarr
  2

• tellurium seems to have problem when there are no data generators or maybe when there are no outputs

  #524 opened 3 years ago by jonrkarr
  0

• tellurium can't handle calculations involving values of SED ranges

  #523 opened 3 years ago by jonrkarr
  0

• Tellurium has problems resolving variables for SED data descriptions

  #522 opened 3 years ago by jonrkarr
  0

• tellurium handles some SED-ML mathematical expressions incorrectly

  #521 opened 3 years ago by jonrkarr
  0

• tellurium tries to access libsedml.RepeatedTask rather than libsedml.SedRepeatedTask

  #520 opened 3 years ago by jonrkarr
  0