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
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May 2012 |
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MELTING5 is the most versatile and flexible software to compute the melting temperatures of oligonucleotides, incorporating many corrections (salt, denaturing agents), mismatches, and allowing for extension with different hybridisation models. More on MELTING on the software page. Read more
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16th May 2012
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LibSBGN is a software library for reading, writing and manipulating SBGN (Systems Biology Graphical Notation) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications.
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Michele Mattioni passes his Viva!
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1st May 2012
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We are pleased to report that Michele Mationi, who was PhD student in the group, passed his Viva and graduated from the University of Cambridge. Michele's thesis focussed on modelling biochemical and electrophysiological signalling in neurons. Michele also developed an NeuronVisio. Congratulations to Doctor Mattioni!
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April 2012 |
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You can now pre-order our textbook "computational systems neurobiology". From transcriptomics to large scale neuronal network reconstructions, every aspects of using computational biology to model and understand neuronal systems are covered. Chapters from the group on modelling chemical kinetics and encoding models in SBML. More details
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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.
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