sys-bio tellurium issues

sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems

http://tellurium.analogmachine.org/

Apache License 2.0

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issues

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

#536 jonrkarr closed 3 years ago
1
Merge from develop

#535 luciansmith closed 3 years ago
0
Initial values of some parameters cannot be modified via SED-ML

#534 jonrkarr closed 3 years ago
12
Tellurium does not output valid omex file

#533 bilalshaikh42 closed 1 year ago
13
Cannot import tesbml

#532 hsauro closed 3 years ago
6
Tag 2.2.0 release

#531 jonrkarr closed 3 years ago
1
Automate releasing to BioSimulators

#530 jonrkarr opened 3 years ago
2
Use KiSAO Python package to recognize KiSAO terms for similar algorithms

#529 jonrkarr opened 3 years ago
0
Delete mapping from KiSAO to variable step size for SED-ML UniformTimeCourse

#528 jonrkarr opened 3 years ago
3
Properly handle algorithm parameters upon substituting algorithms to alternatives

#526 jonrkarr opened 3 years ago
0
getAntimony() call breaks on Notebook interface but not Spyder

#525 chaytanc closed 1 year ago
2
tellurium seems to have problem when there are no data generators or maybe when there are no outputs

#524 jonrkarr opened 3 years ago
0
tellurium can't handle calculations involving values of SED ranges

#523 jonrkarr opened 3 years ago
0
Tellurium has problems resolving variables for SED data descriptions

#522 jonrkarr opened 3 years ago
0
tellurium handles some SED-ML mathematical expressions incorrectly

#521 jonrkarr opened 3 years ago
0
tellurium tries to access libsedml.RepeatedTask rather than libsedml.SedRepeatedTask

#520 jonrkarr opened 3 years ago
0
Allow more flexibility with version of NumPy

#519 jonrkarr closed 3 years ago
2
Memory leak in Antimony

#551 hsauro closed 2 years ago
2
Output data for plots

#518 jonrkarr opened 3 years ago
0
Implement simple 3d plotting like our built-in 2d plotting

#517 luciansmith opened 3 years ago
0
Add support for SED-ML l1v4

#516 luciansmith closed 3 years ago
0
Pull changes from develop

#515 luciansmith closed 3 years ago
0
Change variable name numberOfPoints to numberOfSteps to match meaning…

#514 hsauro closed 3 years ago
0
renem tesedml.py to something else

#513 hsauro opened 3 years ago
0
Revert "add release push action for BioSimulators"

#512 0u812 closed 3 years ago
0
add release push action for BioSimulators

#511 0u812 closed 3 years ago
0
The following sedml script from the readthedocs doesn't work

#510 hsauro closed 1 year ago
1
Folllwing script taken from the docs doesn't work

#509 hsauro opened 3 years ago
0
Can't modify some model parameters from SBML model

#508 danolson1 opened 3 years ago
3
Document unsupported SED-ML "edge" cases

#507 jonrkarr opened 3 years ago
0
Standardize implementation of SED XPATH targets

#506 jonrkarr opened 3 years ago
3
Add support for defining the source of a model by reference to another model within the same SED document

#505 jonrkarr opened 3 years ago
0
Add an optional argument to `simulate` method for returning a pandas dataframe.

#504 CiaranWelsh opened 3 years ago
5
r.getIds() does have good help

#503 hsauro opened 3 years ago
0
Progressively save outputs of SED-ML documents

#502 jonrkarr opened 3 years ago
0
Support BioSimulators format for execution status and logging of COMBINE archives

#501 jonrkarr opened 3 years ago
0
Remove recognition of KISAO terms for characteristics of algorithms

#500 jonrkarr opened 3 years ago
6
Support BioSimulators ALGORITHM_SUBSTITUTION_POLICY environment variable

#499 jonrkarr opened 3 years ago
0
tellurium should issue warnings when alternative algorithms are used from that requested via KISAO terms in SED-ML files

#498 jonrkarr opened 3 years ago
0
Support BioSimulators conventions for plot outputs

#497 jonrkarr opened 3 years ago
0
Support BioSimulators conventions for report files

#496 jonrkarr opened 3 years ago
0
Outputs of SED-ML files should be saved to unique paths

#495 jonrkarr opened 3 years ago
0
(Discussion) executeCombineArchive's treatment of the "master" file should be consistent with other tools

#494 jonrkarr opened 3 years ago
0
Interactions with libsedml generate segmentation faults

#493 jonrkarr closed 3 years ago
1
Requirements for libxml2, libncurses5 should be documented

#492 jonrkarr opened 3 years ago
5
Add rrplugins to reported version information.

#491 luciansmith closed 3 years ago
0
Bugfixes for pytest

#490 luciansmith closed 3 years ago
0
Antimony export should provide a warning if there is a name collision with an antimony reserved word

#489 joseph-hellerstein opened 3 years ago
0
Correct pattern of recognized KiSAO ids

#488 jonrkarr closed 3 years ago
3
Fixing support for KiSAO

#487 jonrkarr closed 3 years ago
6

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