MultiMod, flexible management for multi-scale multi-approach models in biology

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Even the simplest living organisms perform a huge number of different processes, which are interconnected in complex ways to ensure that the organism responds appropriately to its environment. One of the ways of ensuring that we really understand how these processes fit together is to build quantitative mathematical models of them which can be simulated using computers. This approach is known as "Computational Systems Biology". As in most domains of science, databases are essential to allow the proverbial "standing on the shoulders of giants". BioModels provides access to quantitative biology models that have been published in the scientific literature, and verified to be accurate. For instance, in order to develop a quantitative model of cell tumorigenesis, one may choose a suitable model of cell-cycle, and attempt to merge it with models of relevant cell signalling pathways such as the MAP kinase cascade. Since its creation at EMBL-EBI in 2005 - and supported by the BBSRC since 2008 - BioModels has undergone an exponential growth to become the worldwide reference for quantitative models of biological processes. Deposition of models upon publication is advised by several hundred scientific journals, and the resource receives around a million page requests a year from around 65 000 distinct users.Over the recent years, mathematical models of biological processes have become larger and more complex. To be able to represent more accurately living structures, multi-scale models are developed, with processes taking place at different scales described by components coupled together. Because of the nature of the processes as well as the experimental information available, a variety of modelling approaches are use. In 2012, a landmark publication described the first such model of a bacterium (Mycoplasma genitalium) that accounts for all of its components and their interactions. Multi-scale models of organs and organisms (for instance the BBSRC-funded model of Arabidopsis) are now available. Those models must be made available, regardless of their structure, the modelling approach used and the formats they are encoded with.The MultiMod project, developed in collaboration by the Babraham Institute and EMBL-EBI, will extend BioModels coverage considerably, to support a large variety of mathematical models developed in the biosciences. This will be achieved by accepting more file formats, improving support for standard formats and expanding the information distributed (for instance including necessary experimental datasets, simulation descriptions etc). We will also expand the spectrum of models we verify by reproducing published results. Such an increase in scope will be accompanied by an improvement of the software and hardware infrastructure underlying the resource. To make the resource more useful we will develop better browsing, search and download capabilities. Finally, we will improve and further develop our documentation and training offer, including online and in person tutorial and courses. We expect that MultiMod will improve the user experience significantly, increase the number of users and the communities using the resource, and make it more useful for the UK biosciences.