changes.md

Summary of the changes to the content of BioModels

• Filenames

  • Corrected typos in file names
  • Removed non-ASCII characters in file names
  • Removed consecutive periods (.) in file names
  • Changed extensions to lower case

• SBML files

  • Upgraded several models to L2V4
  • Corrected unknown MIRIAM references in 33 files
  • Corrected unknown COPASI annotations in 4 files
  • Corrected unknown BioModels annotations in 2 files
  • Fixed incorrect use of SBML L3 layout in L2 model files
  • Corrected list of reactions in layout for BIOMD0000000872
  • Fixed unit definitions
    • BIOMD0000000439
    • BIOMD0000000479
    • BIOMD0000000965 (removed Avogadro which isn't defined in SBML L2)
  • Fixed SBO terms in BIOMD0000000631
  • Corrected ROS to boundary in BIOMD0000000344
  • Fixed invalid XML in BIOMD0000000344
  • Removed redundant file in BIOMD0000000883/MAP3K8_Thyroid_Spheres_V3.4.cps.xml

• SED-ML files

  • Changed file extension to consistently be .sedml
  • Re-exported most SED-ML files created with COPASI due to multiple issues with these files
  • Fixed broken references to models in SED-ML files not created with COPASI
  • Added missing namespaces for models
  • Removed redundant definitions of the SED-ML namespace at invalid locations
  • Corrected time courses with unusual step numbers and sizes in 36 files
  • Corrected ids of models
    • BIOMD0000000816/OV5.sedml
    • BIOMD0000000816/OV25.sedml
  • Removed invalid, unused models
    • BIOMD0000000816/OV5.sedml
    • BIOMD0000000816/OV25.sedml
    • BIOMD0000000817/OV5.sedml
    • BIOMD0000000817/OV25.sedml
  • Removed empty containers
    • Repeated tasks with no subtasks
    • Reports with no data sets
    • 2D plots with no curves
    • 3D plots with no surfaces
  • Decreased excessive numbers of steps of time courses
  • Fixed syntactically incorrect XPaths
  • Fixed SED-ML datasets with misssing labels
  • Fixed variables of data generators with no symbols or targets
  • Fixed nested repeated tasks
  • Removed duplicately defined data generators
  • Corrected algorithms and algorithm parameters for SED-ML files from COPASI
  • Removed duplicate SED-ML files
    • BIOMD0000000927/Baker2017_Fig14.a_2.sedml
    • BIOMD0000000927/Baker2017_Fig14.a_3.sedml
    • BIOMD0000000927/Baker2017_Fig14.b_1.sedml
    • BIOMD0000000927/Baker2017_Fig14.b_2.sedml
    • BIOMD0000000928/Baker2017_Fig14.a_2.sedml
    • BIOMD0000000928/Baker2017_Fig14.a_3.sedml
    • BIOMD0000000928/Baker2017_Fig14.b_1.sedml
    • BIOMD0000000928/Baker2017_Fig14.b_2.sedml
  • Removed plots that don't reproduce published figures
    • BIOMD0000000949/Chitnis2008.sedml#plot_5_task1
    • BIOMD0000000949/Chitnis2008.sedml#plot_6_task1
  • Corrected plot names
    • BIOMD0000000950/Chitnis2012_model_1.sedml.sedml#plot_1_task1
    • BIOMD0000000950/Chitnis2012_model_1.sedml.sedml#plot_2_task1
  • Corrected axis scales
    • BIOMD0000000950/Chitnis2012_model_1.sedml.sedml#plot_1_task1
    • BIOMD0000000950/Chitnis2012_model_1.sedml.sedml#plot_2_task1

• OMEX files

  • Replaced file with its content: BIOMD0000000585/Rateitschak2012.omex

• CopasiML files

  • Corrected time courses with unusual step numbers and sizes in 36 files
  • Corrected MODEL1305060000_edited

• Curation notes

  • Recreated figure for BIOMD0000000585 at larger, legible size

• Other files

  • Re-generated derived files
    • SBML URN
    • Matlab
    • Octave
    • XPP
  • Replaced *.m Octave files with *-matlab.m and *-octave.m files
  • Removed invalid derived URN files
  • Removed invalid derived XPP files
  • Removed 22 corrupted PNG files
  • Removed MATLAB/Octave, Scilab, XPP files for non-kinetic models
  • Removed 158 bad Octave files
  • Removed 524 bad Scilab files
  • Removed 400 bad VCML files
  • Removed 399 bad VCML files
  • Removed 1 Mac OS desktop configuration files
  • Corrected file extension for 1 PottersWheel file