Abstract
The field of Computational Systems Neurobiology is maturing quickly. If one wants it to fulfil its central role in the new Integrative Neurobiology, the reuse of quantitative models needs to be facilitated. The community has to develop standards and guidelines in order to maximise the diffusion of its scientific production, but also to render it more trustworthy. In the recent years, various projects tackled the problems of the syntax and semantics of quantitative models. More recently the international initiative BioModels.net launched three projects: (1) MIRIAM is a standard to curate and annotate models, in order to facilitate their reuse. (2) The Systems Biology Ontology is a set of controlled vocabularies aimed to be used in conjunction with models, in order to characterise their components. (3) BioModels Database is a resource that allows biologists to store, search and retrieve published mathematical models of biological interests. We expect that those resources, together with the use of formal languages such as SBML, will support the fruitful exchange and reuse of quantitative models.
Highlights
Computational Neurosciences, modelling the function of the nervous systems, have been around for decades
(2) The Systems Biology Ontology is a set of controlled vocabularies aimed to be used in conjunction with models, in order to characterise their components
(3) BioModels Database is a resource that allows biologists to store, search and retrieve published mathematical models of biological interests. We expect that those resources, together with the use of formal languages such as SBML, will support the fruitful exchange and reuse of quantitative models
Summary
Computational Neurosciences, modelling the function of the nervous systems, have been around for decades. The resource distributes models encoded in the many different formats, mainly those used by the GENESIS and NEURON simulators, and format used by generic simulation environments such as Octave, MatLab, Octave or XPP-Aut. SigPath [17] is an interesting project to develop an open knowledgebase of qualitative pathways and quantitative models related to signalling. Model components are annotated with references to adequate resources (Figure 4), such as terms from controlled vocabularies (Taxonomy, Gene ontology, ChEBI etc.) and links to other databases (UniProt, KEGG, Reactome etc.). This annotation is a crucial feature of BioModels Database that permits the unambiguous identification of molecular species or reactions and is used in search strategies. We expect that in the long run, the effect will be beneficial and we will witness a gradual increase in the quality and the usefulness of the quantitative models of neuronal function
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