Reference Documentation

Models

SPARCED-standard will soon be the reference model. In the meantime, we consider SPARCED-notebook as the reference.

Input files

• Data
  • Core
    • Compartments
    • Observables
    • Ratelaws
    • Species
    • StoicMat
  • Simulation
    • ligands
    • GeneReg
    • OmicsData

Source code

• General Utilities
  • Arguments
    • parse_args()
  • Combine results
    • combine_results()
  • Data handling
  • Files handling
    • append_subfolder()
    • check_path_existence()
    • convert_excel_to_tsv()
• Compilation
  • General
  • AMICI
    • define_observables()
  • Antimony
    • define_compartments()
    • define_species()
    • define_units()
    • set_compartments_ic()
    • set_reactions_ic()
    • set_species_ic()
  • Conversion scripts
  • SBML
    • sbml_annotate_model()
    • write_compartments_annotations()
    • write_species_annotations()
• Simulation
  • General
  • Modules