20.05.2020

Tabular editor for systems biology models

Marietta Hamberger developed a table editor for the SBTab format as an InSilico plugin.

During her research project, Marietta Hamberger further developed and redesigned the SBMLSheets plugin initiated by Robert Deibel for the InSilico project.

The file format SBML, which is frequently used in systems biology, is based on XML. It is, therefore, not intuitively accessible to all users, the SBTab project follows the approach representing the information contained in SBML in tabular form. SBTab files adhere to specified table definitions. Therefore, it is still necessary to read the SBTab documentation to create correctly formatted documents.

A user interface has been developed to simplify this process for creating, modifying, and converting SBTab documents. The table editor supports the import and export of data (CSV, TSV, and TAB formatted), the conversion of tables into SBTab and SBML documents, and other useful functions. So far, three table types (Compound, Compartment, and Reactions) are covered. In the future, however, SBMLSheets will be completed to ensure all table types and a complete SBML conversion.