biosimulators Biosimulators_COPASI issues

biosimulators / Biosimulators_COPASI

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

https://docs.biosimulators.org/Biosimulators_COPASI

MIT License

2 stars 3 forks source link

issues

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Sys bio model fixes part 2

#76 CodeByDrescher closed 1 month ago
2
Update libkisao so we can read VCell-generated SED-ML.

#75 luciansmith closed 8 months ago
1
All biomodels Copasi currently fails for

#74 luciansmith opened 1 year ago
17
unit test for BIOMD0000000005.omex

#73 CodeByDrescher closed 1 year ago
2
fixed dependency error

#72 AlexPatrie closed 1 year ago
1
Biosimulators copasi gives incorrect results that normal copasi doesn't

#71 luciansmith closed 1 year ago
3
Refactor logic control anti-pattern

#70 AlexPatrie closed 1 year ago
1
adjusted import order to be PEP-compliant

#69 AlexPatrie closed 1 year ago
1
Closes Issue #66:

#68 AlexPatrie closed 1 year ago
1
Changed log level of Capturer Object

#67 AlexPatrie closed 1 year ago
3
Incorrectly raised Exception regarding number of time points

#66 leon9812 closed 1 year ago
1
Update python-copasi package version

#65 AlexPatrie closed 1 year ago
1
Wip custom stdout capture in exec functions

#64 AlexPatrie closed 1 year ago
1
Refactor relative imports

#63 AlexPatrie closed 1 year ago
1
Updating version of utils backend.

#62 AlexPatrie closed 1 year ago
3
Documentation discrepancies between repo and website.

#61 AlexPatrie opened 1 year ago
1
Docker run command returning "is not a file" error on omex path

#60 AlexPatrie opened 1 year ago
1
refactored config, log, and preprocessed task instance

#59 AlexPatrie closed 1 year ago
2
Lowering Cognitive complexity as per SonarCloud

#58 AlexPatrie opened 1 year ago
0
WIP-refactoring nesting

#57 AlexPatrie closed 2 months ago
3
biosimulators no longer working on macOS

#56 fbergmann opened 1 year ago
6
Explicit typing for arguments in core sub-module.

#55 AlexPatrie closed 1 year ago
3
#53: time cn should be returned as string

#54 fbergmann closed 2 years ago
1
copasi_model_obj_common_name needs to be a string

#53 eagmon closed 2 years ago
4
Allow the COPASI Biosimulator to simulate files exported by COPASI

#52 fbergmann closed 2 years ago
5
Substitute hybrid runge kutta and LSODA methods to hybrid RK-45 for models with events

#51 jonrkarr closed 3 years ago
1
Substitute algorithm when Radau5 requested for model with events

#50 jonrkarr closed 3 years ago
1
Setup cron job to pull COPASI releases from PyPi

#49 jonrkarr closed 3 years ago
1
Internalize functionality into COPASI itself (obviating the need for this repository)

#48 jonrkarr closed 3 years ago
7
Mark Steady State Simulations / Scan as supported

#47 fbergmann closed 3 years ago
3
Get values of non-constant parameters

#46 jonrkarr closed 3 years ago
8
Expose static and steady-state analyses through SED-ML

#45 jonrkarr opened 3 years ago
1
Improve messages for COPASI errors

#44 jonrkarr closed 3 years ago
2
Support hybrid RK45 method

#43 jonrkarr closed 3 years ago
2
Workflows

#42 bilalshaikh42 closed 3 years ago
0
applying more specific KISAO terms

#41 jonrkarr closed 4 years ago
0
What are the user-configurable parameters of the hybrid LSODA algorithm?

#40 jonrkarr closed 4 years ago
1
Add citation for Stochastic Runge-Kutta Method

#39 jonrkarr closed 4 years ago
1
Apply new KISAO terms for algorithms and parameters

#38 jonrkarr closed 3 years ago
2
COPASI or wrapper should support KISAO terms for algorithms and algorithm parameters

#37 jonrkarr closed 3 years ago
1
Fix tests

#36 gmarupilla closed 4 years ago
1
Stop generating CSV for non-report SED-ML

#35 gmarupilla closed 3 years ago
1
Handling `listOfOutputs` for version >= 4.28.226

#34 gmarupilla closed 4 years ago
1
Enhancements

#33 gmarupilla closed 4 years ago
1
Add BioContainers-style metadata to Dockerfile

#32 jonrkarr closed 4 years ago
1
importSedml method only imports a single task

#31 gmarupilla closed 3 years ago
1
allow tests to run on other platforms, ensure report is always created, resolve task name issue

#30 fbergmann closed 4 years ago
3
Update python-copasi package to latest version

#29 gmarupilla closed 4 years ago
0
Correct minor typos, small additions

#28 jpahle closed 4 years ago
0
Delete earlier tags and releases

#27 jonrkarr closed 4 years ago
1