Simulistics Ltd was contracted by University of Wales, Aberystwyth in July 2008 to provide expertise in the declarative modelling of plant systems.
Abstract:
The project will develop a portal to make available, in open-source format, plant growth models relevant to the needs of the UK systems biology and crop science communities. A Wiki will allow researchers from all fields to provide input on the models. Seven existing models have already been selected for implementation and at least 3 others will be chosen through discussion with the community. Models available in a range of formats and programming languages will be represented in an open-standard declarative XML format, using an established modelling environment. A declarative language allows models to be displayed in various ways and efficiently makes model metadata available automatically. The XML generated for each model can be run through one of several code-generators (some already implemented), allowing users flexibility in the language and computational platform used for implementation. We will provide annotated examples of typical output for each model and devise simulations and analysis for publication and dissemination on the portal. Demonstration results will use the high-level models developed here and also models at other scales. The portal will integrate the models with software tools used by systems biologists and will make models available to users at external sites, via the Systems Biology Software Infrastructure at the Centre for Systems Biology Edinburgh. To extend the Systems Biology Markup Language to represent plant growth models not expressible in biochemical-pathway terms we will collaborate with Dr N le Novere (European Bioinformatics Institute), who is responsible for the BioModels portal. Further links between the project participants and the SBML community, other UK Centres for Integrated Systems Biology and EBI will keep the portal's development abreast of international standards development, including plant and trait ontologies, and allow the project staff to provide input to the development of later model exchange standards.
BBSRC Grant Reference: BBF0106051