Support for additional pathway model file formats, such as BioPAX [ 32] will be available in the near future.
The Other formats menu provides access to other (non-SBML) model representation formats, such as CellML [ 1], BioPAX [ 31, 32], and the Virtual Cell Markup Language (VCML) [ 36].
The data conversion applications are implemented using the API, which depends on BIM model formats and tools, such as Revit and ArchiCAD.
Furthermore, it allows users to import and export the edited model into several formats such as SBML.
The Boolean export and simulation complement the existing rxncon exports to SBML, rule based and agent-based models, and graphical formats such as the SBGN formats.
For practical purposes, the authors might think to add archives with all the individual alignments in single files and domain models in several formats such as the HMMR2, HMMER3, etc. ready made.
Hosting models encoded in standard formats (such as SBML), the resource has grown substantially since its introduction in 2005.
The current version, Protégé-2000, can be run on a variety of platforms, supports customized user-interface extensions, incorporates the Open Knowledge-Base Connectivity (OKBC) knowledge model, interacts with standard storage formats such as relational databases, XML, and RDF, and has been used by hundreds of individuals and research groups.
Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases.
