This page contains additional materials that were useful for the 2010 COMBINE meeting.
BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.
The last specification of is BioPAX Level 3.
BioPAX is supported by many pathway database or processing tools.
The Systems Biology Graphical Notation (SBGN), is a set of community developed standard graphical languages to describe biological knowledge. It is currently made up of three languages describing Process Descriptions, Entity Relationships and Activity Flows.
The last specifications are SBGN PD Level 1 Version 1.1, SBGN ER Level 1 Version 1 and SBGN AF Level 1 Version 1.
We are aware of several data resources and software supporting SBGN.
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes. SBML is suitable for models of metabolism, cell signaling, and other processes.
The latest stable specification is Level 3 Version 1 Core.
More than 180 software supporting SBML can be found in the SBML software guide.
Related standardization efforts
The following efforts will also be discussed at COMBINE.
The CellML language is an open format based on the XML markup language. CellML is being developed by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups.
Various specifications of CellML currently co-exist.
CellML is supported by various modeling and simulation tools.
The Minimal Information Required In the Annotation of Models (MIRIAM),is an effort to standardize the metadata added to a computational model in biology. One the key tools to achieve this goal is to share stable identifiers to data-sets. The is the purpose of MIRIAM URNs.
The Systems Biology Ontology (SBO) is a set of controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling.
The Simulation Experiment Description Markup Language (SED-ML) is a proposed format to encode steps performed in the simulation and analysis of a computational model.
NeuroML facilitate the exchange of complex neural models, allow for greater transparency and accessibility of models, enhance interoperability between simulators and other tools, and support the development of new software and databases.