SBtab - Table format for Systems Biology. Data tables in the form of spreadsheets or delimited text files are the most utilised data format in Systems Biology. However, they are often not sufficiently structured and lack clear naming conventions that would be required for modelling. We propose the SBtab format as an attempt to establish an easy-to-use table format that is both flexible and clearly structured. It comprises defined table types for different kinds of data; syntax rules for usage of names, shortnames, and database identifiers used for annotation; and standardised formulae for reaction stoichiometries. Predefined table types can be used to define biochemical network models and the biochemical constants therein. The user can also define own table types, adjusting SBtab to other types of data.
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References in zbMATH (referenced in 1 article )
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- Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl: PEtab - interoperable specification of parameter estimation problems in systems biology (2020) arXiv