Computational Systems Neurobiology Group - Systems Biology of Neuronal Signalling

The research interests of the group Computational Systems Neurobiology revolve around signal transduction in neurons, ranging from the molecular structure of proteins involved in neurotransmission to signalling pathways and electrophysiology. In particular, we focus on the molecular and cellular basis of neuroadaptation in neurons of the basal ganglia. By building detailed and realistic computational models, we try to understand how neurotransmitter-receptor movement, clustering and activity, influence synaptic signalling. Downstream from the transduction machinery, we build quantitative models of the integration of signalling pathways known to mediate the effects of neurotransmitters, neuromodulators and drugs of abuse. We are particularly interested in understanding the processes of cooperativity, pathway switch and bistability.

The group provides community services that facilitate research in computational systems biology. In particular, we are leading the efforts in encoding and annotating kinetic models in chemistry and cellular biology, including the creation of standard representations, the production of databases and software development. The Systems Biology Markup Language (SBML) is designed to facilitate the exchange of biological models between different types of software. The Systems Biology Graphical Notation (SBGN) is an effort to develop a common visual notation for biochemists and modellers. Moving from the form to the content, we are also developing standards for model curation (MIRIAM, MIASE), a format for describing simulation experiments (SED-ML), and controlled vocabularies (the Systems Biology Ontology, the TErminology for the Description of DYnamics etc.) to improve the models. Finally, a model is only useful if it can be easily accessed and reused. BioModels Database is now the reference resource where scientists can store, search and retrieve published mathematical models of biological interest.

Latest News

21^st BioModels Database Release

8th February 2012

We are pleased to announce the twenty-first release of BioModels Database. In this release, 68 new models have been published and numerous existing models have been updated. BioModels Database now publicly provides 409 models in the curated and 420 in the non-curated branch. Together, these 829 models comprise 130800 species, 151274 relationships (which include reactions, rate rules, events and assignment rules), and 106210 cross-references. Important changes are happening or announced, so please read the release notes.

New paper on calmodulin trapping by CaMKII

	19th January 2012
	Using a mixture of molecular modeling, molecular dynamics and stochastic simulations, we show that two calmodulin binding sites on CaMKII are sufficient to explain the phenomenon of trapping. We also show that binding of calmodulin to the low affinity site is compatible with the closed form of CaMKII and does not activate the latter. Read more

Description of SED-ML published

	December 2011
	The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows the definition of the model(s) to be used, the experimental task(s) to be run, and the result(s) to be produced. Read more