Development of a web portal for plant models

A large number of models have been developed overthe last few decades in agricultural and ecological research.However, it is very difficult to obtain access tothese models: the source code may no longer beavailable; their authors may have moved on; thedocumentation may be poor or missing, or the modelsmay require compilers which no longer exist. Anumber of model catalogues have been developed,e.g. CAMASE (Plentinger & Penning de Vries 1996)and REM (Ernst et al. 1997), but these simply presentinformation about the model, rather than providingaccess to the model itself.The BBSRC-funded PlaSMo (Plant SystemsBiology Modelling) project aims to address thisproblem by converting legacy plant and crop modelsinto a standard, XML-based format which isthen accessible through a web portal. This involvesre-implementing the models in Simile (Muetzelfeldt &Massheder 2003), a visual modelling environmentspecifically developed for ecological and environmentalmodelling. The models are then saved in Simile’s XML-based model-representation format and uploaded to the web portal, along with model metadata (such as author and publications) describing the model. Users can then search for particular models, view a model in a variety of formats using tools provided on the portal, run the models in a web browser, or download the models into Simile. PlaSMo currently has a particular focus on plant models because it arose out of a recognition by the plant systems biology community that such models provide a valuable resource for the community as they scale up from the cell to the whole organism (GARNet 2006), with the emergent properties of the cell-level models appearing as parameters for the organism-level model. For this reason, we aim to integrate closely with the Systems Biology Markup Language (SBML, http://www.sbml.org), an XML based language widely used in the systems biology community for modelling biological pathways at the cell level. However, the design of the web approach itself is not at all specific to plant models and we envisage that it will rapidly grow to include models from other areas, such as epidemiology,animal husbandry, soil biology and ecology. We also expect that as the number of models grows, other groups will develop tools for building,displaying and simulating the behaviour of the models.