Data¶

Input data files are written in TSV (tab separated value) format. A conversion script from Excel to TSV is available in the general utilities.

Core¶

The core subfolder is dedicated to input files necessary for model creation (core SPARCED).

Compartments¶

The columns are corresponding to:

  • Compartment’s name

  • Compartment’s volume

  • Annotation in GO terms

Observables¶

Ratelaws¶

The columns are corresponding to:

  • Reaction’s name

  • Compartment’s correction

  • A single coefficient for mass action laws, or the full reaction for more elaborated laws

  • Values of the coefficients you passed in the law, by order of appearance in the equation

Species¶

The columns are corresponding to:

  • Specie’s name

  • Species location, which must be a valid compartment

  • Initial concentration of the specie

  • Annotation in ENSEMBL

  • Annotation in HGNC

StoicMat¶

WARNING: This file is huge, do not attempt to open with anything else but Excel, or be prepared for a crash. You have been warned.

Simulation¶

The simulation subfolder is dedicated to input files necessary to run a SPARCED model simulation.

ligands¶

The columns are corresponding to:

  • Ligand’s human-readable name

  • Ligand’s name, which must be a valid specie

  • Ligand’s initial concentration

GeneReg¶

Don’t touch this.

OmicsData¶

Don’t touch this.