SBtab Logo

Downloads

Definition of SBtab table types

The definition of all predefined SBtab table types, their corresponding columns and contents, can be found in the definitions.tsv. This file can also be employed if you want to define an individual table type for types of data that SBtab does not cover so far. Simply download the definitions, add your table type and the columns to the end of the file, and upload it on the SBtab customiser. Then, you can validate SBtab files whether they adhere to your individual table type definition on the SBtab validator.

SBtab Example Files

Example 1: The first two reactions of yeast glycolysis.
Entire model in one file:

  1. Hynne Model

Tables in separate files:

  1. Hynne Compartment
  2. Hynne Compound
  3. Hynne Enzyme
  4. Hynne Concentrations
  5. Hynne Parameters
  6. Hynne Reaction

The two reactions stem from a model of yeast glycolysis, published in Hynne et al. (2001), Full-scale model of glycolysis in Saccharomyces cerevisiae (Biophys. Chem. (1-2): 121-163). The original SBML file has been retrieved from Biomodels Database and been converted into SBtab tables.

Example 3: Structure of the feed-forward loop as Relationship SBtab.

  1. Feed-Forward Loop

Example 4: Standard Gibbs free energies of reactions for chemical reactions listed in the KEGG database. The values have been computed using the eQuilibrator web tool and are presented as Quantity SBtab.

  1. KEGG Reactions (PH7)

Example 7: The glycolysis model of Teusink et al. (2000) in SBtab representation. The SBML model was taken from the BioModels Database and translated to SBtab with our SBML Converter. The origins of the collected data are given in the reference column of the Quantity SBtab.

  1. Teusink Model
  2. Teusink Data

Example 8: Pancreatic Beta Cell Model Jiang's model of the glucose-stimulated secretion system in pancreatic beta cells (Jiang et al.,2007) is one of the largest kinetic models in BioModels Database. The SBML model was translated to SBtab with our SBML Converter. The origins of the collected data are given in the reference column of the Quantity SBtab.

  1. Jiang Model
  2. Jiang Data

Example 11: Translation of SBML Level 3 FBC Package We have exemplified the translation of the content of SBML3 FBC package to SBtab with the Genome-scale metabolic model of Mus Musculus by Sigurdsson et al. (2010). The model is taken from the BioModels Database and translated to SBtab with our SBML Converter. The conversion yields an SBtab document consisting of the SBtabs Compartment, Compound, Reaction, Quantity, FbcObjective, and Gene. The FBC information extracted from the SBML is comprised in the FbcObjective and Gene SBtabs, as well as in additional fbc columns of Compound and Reaction. For details, see the SBtab specification.

  1. Sigurdsson FBC Model SBML
  2. Sigurdsson FBC Model SBtab

Example 12: Translation of SBML Level 3 Layout Package We have exemplified the translation of the content of SBML3 Layout package to SBtab with a small test SBML model consisting of two reactions, two species, and corresponding layout information. The model was translated to SBtab with our SBML Converter. The conversion yields an SBtab document consisting of the SBtabs Compartment, Compound, Reaction, and Layout. The layout information extracted from the SBML is comprised in the Layout SBtab. For details, see the SBtab specification.

  1. Layout Example Model SBML
  2. Layout Example Model SBtab