CellML and related efforts

Parent projects and funding bodies

  • IUPS Physiome Project — The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organisation, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. The CellML Project is an integral component of this effort.
  • VPH NoE (Virtual Physiological Human Network of Excellence) — The VPH NoE is a project which aims to help support and progress European research in biomedical modelling and simulation of the human body. This will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare, the pharmaceutical and medical device industries.
  • Please see our funding and sponsors page for more detailed information.

Other markup languages and data exchange standards

  • SBML (Systems Biology Markup Language) — SBML is a computer-readable format for representing models of biological processes. It's applicable to simulations of metabolism, cell-signaling, and many other topics.
  • FieldML (Field Modelling/Markup Language) — The goal of FieldML is to be a declarative language for building hierarchical models represented by generalized mathematical fields. Its primary use will be to represent the dynamic geometry and solution fields from computational models of cells, tissues and organs. It is intended to provide a framework for modelling software development and model interchange for bioengineering and general engineering analysis communities.
  • SED-ML (Simulation Experiment Description Markup Language) - The Minimum Information About a Simulation Experiment project is a community effort that aims at listing the common set of information any modeller need to provide in order to enable the execution and repeat of a numerical simulation experiment, derived from a given quantitative model. The Simulation Experiment Description Markup Language (SED-ML) is a formal representation aimed at encoding requirements defined in the MIASE guidelines. SED-ML will necessarily cover only part of MIASE compliant simulations. On the other end, the formalisation of SED-ML forces the information to be more precise that the bare MIASE requirements.
  • MIASE (Minimum Information About a Simulation Experiment) — is currently under development. It covers information about the simulation settings, including information about the models, changes on them, simulation settings applied to the models and output definitions.
  • MIRIAM (Minimum Information Requested in the Annotation of Models) - MIRIAM is an effort to standardise the Minimal Information Requested In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology. The goal of the project, initiated by the BioModels.net effort is to produce a set of guidelines suitable for use with any structured format for computational models.

Databases

  • BioModels Database — BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
  • JWS Online — JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, and 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models.
  • ModelDB - ModelDB provides an accessible location for storing and efficiently retrieving computational
    neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any
    language for any environment. Model code can be viewed before downloading and browsers can
    be set to auto-launch the models.

Ontologies

    • Systems Biology Graphical Notation (SBGN) - The SBGN project is an effort to standardize the graphical notation used in maps of biochemical and cellular processes studied in systems biology.
    • Biological Pathways Exchange (BioPAX) — BioPAX is a RDF/OWL-based standard for the exchange of biological pathways. It is supported by a variety of online databases (e.g. Reactome) and tools. The latest released version is BioPAX Level 2. There is a release candidate for Level 3, as well as an effort to create a version of BioPAX as part of OBO.
    • Ontology of Physics and Biology (OPB) - The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (“multiscale” — atoms to organisms) and multiple physical domains (“multidomain” — fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.
    • Foundational Model of Anatomy (FMA) - FMA is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species.
    • Systems Biology Ontology (SBO) - 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 modelling. SBO is a project of the BioModels.net effort and is developped with the help of the community.