biosimulators/Biosimulators_COPASI

Issues

• All biomodels Copasi currently fails for

  #74 opened a year ago by luciansmith
  17

• biosimulators no longer working on macOS

  #56 opened 2 years ago by fbergmann
  6

• Biosimulators copasi gives incorrect results that normal copasi doesn't

  #71 opened a year ago by luciansmith
  3

• Incorrectly raised Exception regarding number of time points

  #66 opened 2 years ago by leon9812
  1

• Documentation discrepancies between repo and website.

  #61 opened 2 years ago by AlexPatrie
  1

• Expose static and steady-state analyses through SED-ML

  #45 opened 4 years ago by jonrkarr
  1

• Docker run command returning "is not a file" error on omex path

  #60 opened 2 years ago by AlexPatrie
  1

• Lowering Cognitive complexity as per SonarCloud

  #58 opened 2 years ago by AlexPatrie
  0

• copasi_model_obj_common_name needs to be a string

  #53 opened 3 years ago by eagmon
  4

• Internalize functionality into COPASI itself (obviating the need for this repository)

  #48 opened 3 years ago by jonrkarr
  7

• Setup cron job to pull COPASI releases from PyPi

  #49 opened 3 years ago by jonrkarr
  1

• Get values of non-constant parameters

  #46 opened 3 years ago by jonrkarr
  8

• Substitute hybrid runge kutta and LSODA methods to hybrid RK-45 for models with events

  #51 opened 3 years ago by jonrkarr
  1

• Substitute algorithm when Radau5 requested for model with events

  #50 opened 3 years ago by jonrkarr
  1

• Mark Steady State Simulations / Scan as supported

  #47 opened 4 years ago by fbergmann
  3

• Improve messages for COPASI errors

  #44 opened 4 years ago by jonrkarr
  2

• Support hybrid RK45 method

  #43 opened 4 years ago by jonrkarr
  2

• Review specifications of COPASI's capabilities (biosimulators.json)

  #25 opened 4 years ago by jonrkarr
  18

• CCopasiException on invalid archive

  #26 opened 4 years ago by gmarupilla
  5

• Stop generating CSV for non-report SED-ML

  #35 opened 4 years ago by gmarupilla
  1

• importSedml method only imports a single task

  #31 opened 4 years ago by gmarupilla
  1

• COPASI or wrapper should support KISAO terms for algorithms and algorithm parameters

  #37 opened 4 years ago by jonrkarr
  1

• Apply new KISAO terms for algorithms and parameters

  #38 opened 4 years ago by jonrkarr
  2

• What are the user-configurable parameters of the hybrid LSODA algorithm?

  #40 opened 4 years ago by jonrkarr
  1

• Add citation for Stochastic Runge-Kutta Method

  #39 opened 4 years ago by jonrkarr
  1

• Enhancements

  #33 opened 4 years ago by gmarupilla
  1

• Handling `listOfOutputs` for version >= 4.28.226

  #34 opened 4 years ago by gmarupilla
  1

• Add BioContainers-style metadata to Dockerfile

  #32 opened 4 years ago by jonrkarr
  1

• Update python-copasi package to latest version

  #29 opened 4 years ago by gmarupilla
  0

• Delete earlier tags and releases

  #27 opened 5 years ago by jonrkarr
  1

• Get tolerance values from SEDML in future

  #11 opened 5 years ago by todo
  0

• Implement proper levels of logging

  #12 opened 5 years ago by todo
  0

• remove redundant code in different log methods

  #13 opened 5 years ago by todo
  0

• Rename repository to Biosimulations-COPASI

  #23 opened 5 years ago by jonrkarr
  0

• Check time points with float type

  #19 opened 5 years ago by todo
  0

• Standardize inputs for VCELL, COPASI and Biosimulation images

  #9 opened 5 years ago by gmarupilla
  1

• Combine print, error and jobhook_request_builder in single method

  #5 opened 5 years ago by todo
  0

• Bare minimum to manage simulation

  #2 opened 5 years ago by gmarupilla
  1