biosimulations/biosimulations-physiome

Issues

• Improve sedml generation when multiple CellML files are present

  #41 opened 2 years ago by bilalshaikh42
  5

• Handle cases where models use unsupported CellML features

  #42 opened 2 years ago by bilalshaikh42
  1

• Dependency Dashboard

  #54 opened 3 years ago by renovate
  0

• Open Issue regarding incorrect CellML schema

  #53 opened 3 years ago by bilalshaikh42
  1

• Annotate that generated SED-ML files were computationally-generated from CellML files

  #52 opened 3 years ago by jonrkarr
  2

• Add creation date to metadata

  #49 opened 3 years ago by jonrkarr
  0

• Remove Bilal Shaikh to last in list of curators

  #50 opened 3 years ago by jonrkarr
  0

• Create SED-ML files for Physiome projects that don't have them and annotate that these were computationally-generated from CellML files

  #10 opened 3 years ago by jonrkarr
  0

• Remove tables with figures from descriptions

  #48 opened 3 years ago by jonrkarr
  0

• Strip beginning and trailing white space from project descriptions

  #47 opened 3 years ago by jonrkarr
  2

• Separate figure captions from project descriptions

  #45 opened 3 years ago by jonrkarr
  1

• Ignore some files from COMBINE archives

  #33 opened 3 years ago by jonrkarr
  2

• Investigate 1a

  #43 opened 3 years ago by bilalshaikh42
  1

• Investigate e08bd642df06eb59404c8e46afbb04a4

  #44 opened 3 years ago by bilalshaikh42
  2

• Polish metadata

  #30 opened 3 years ago by jonrkarr
  1

• Change `tags` key to `keywords`

  #51 opened 3 years ago by jonrkarr
  1

• Remove figure captions from description text

  #46 opened 3 years ago by bilalshaikh42
  1

• Add model changes for all possible parameters

  #29 opened 3 years ago by jonrkarr
  0

• Add reports for all possible observables

  #28 opened 3 years ago by jonrkarr
  0

• Create file (e.g. YAML) to keep track of bad projects that cannot be published and the reasons why

  #14 opened 3 years ago by jonrkarr
  1

• Store correspondence between Physiome projects and runBioSimulations runs within repository

  #34 opened 3 years ago by jonrkarr
  0

• Handle CellML files that use .xml extension

  #40 opened 3 years ago by bilalshaikh42
  1

• Work with the released changeset of each Physiome workspace

  #35 opened 3 years ago by jonrkarr
  0

• Gather more descriptive descriptions for metadata

  #13 opened 3 years ago by jonrkarr
  1

• Clean up, document, and publish this repository

  #39 opened 3 years ago by jonrkarr
  0

• Create and publish documentation

  #19 opened 3 years ago by jonrkarr
  1

• Deal with cases when SED-ML is saved with extension `.xml`

  #24 opened 3 years ago by bilalshaikh42
  2

• Deal with cases where exposure contains "components"

  #25 opened 3 years ago by bilalshaikh42
  2

• Deal with cases where experiments are encoded as Python scripts

  #26 opened 3 years ago by bilalshaikh42
  1

• Skip plots that require marker style or encode OpenCOR's custom style annotations into L1V4

  #32 opened 3 years ago by jonrkarr
  0

• Remove duplicate entry with location `metadata.rdf` in COMBINE archive for `e/4c8`

  #36 opened 3 years ago by jonrkarr
  3

• Expand labels for PMR identifiers

  #22 opened 3 years ago by jonrkarr
  1

• Preserve some formatting of project descriptions

  #23 opened 3 years ago by jonrkarr
  2

• Deal with cases where JSON request is redirected to"document_view" rather than "exposure_info"

  #27 opened 3 years ago by bilalshaikh42
  1

• File GitHub issues for errors with Physiome projects

  #38 opened 3 years ago by jonrkarr
  1

• `e/f4` is not the id of a Physiome project

  #37 opened 3 years ago by jonrkarr
  1

• Remove COMBINE archives nested in archives

  #15 opened 3 years ago by jonrkarr
  4

• Folders are not preserved when adding files to COMBINE archives

  #21 opened 3 years ago by bilalshaikh42
  1

• Correct identifiers in metadata

  #12 opened 3 years ago by jonrkarr
  0

• Track namespace (`e` or `exposure`) of each project

  #11 opened 3 years ago by jonrkarr
  1

• Adding CombineArchiveConent with path to existing metadata file creates new file in archive

  #20 opened 3 years ago by bilalshaikh42
  4

• Thumnail urls are incorrect

  #8 opened 3 years ago by bilalshaikh42
  1

• Remove manifest entry from manifest

  #7 opened 3 years ago by bilalshaikh42
  1

• Git Submodules are incorrectly initialized

  #9 opened 3 years ago by bilalshaikh42
  0

• Switch to download files via .tar.gz export or Git repository

  #16 opened 3 years ago by jonrkarr
  2

• Modify BioSimulators-utils to allow metadata with no author

  #18 opened 3 years ago by jonrkarr
  1

• Improve error messages for missing imported model files

  #17 opened 3 years ago by jonrkarr
  1

• Investigate why run Project 5f3 failed

  #6 opened 3 years ago by bilalshaikh42
  3

• Investigate why project 49f Fails

  #5 opened 3 years ago by bilalshaikh42
  4

• Run project 3f8

  #4 opened 3 years ago by bilalshaikh42
  2