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Computational Systems Neurobiology Group - News

News of the Computational Systems Neurobiology Group


Direct access to the news of a given year:
2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012

2012

The end of the Compneur group

Compneur 28th September 2012
This is the end of the EMBL-EBI Compneur group. Fantastic 9 years. Offsprings of the group are the BioModels.net team, now part of the Proteomics Service Team, and the Le Novere Lab at the Babraham Institute.

New paper describing KiSAO

PLoS ONE 24th September 2012
The Kinetic Simulation Algorithm Ontology (KiSAO) describes existing algorithms and their inter-relationships through their characteristics and parameters. Read more

New paper on calcium and synaptic plasticity

PLoS ONE 4th September 2012
In a very thorough modelling work, Lu Li shows how calcium signal properties affect signalling plasticity. She shows that calcium always activates both CaMII and CaN (but the balance changes), that calmodulin activation outlasts calcium signals, and that the frequency threshold between depression and potentiation depends on signal amplitude and duration. Read more

23rd BioModels Database Release

BioModels 11th August 2012
We are pleased to announce the twenty-third release of BioModels Database.
BioModels Database now publicly provides 142916 models. This corresponds to 867 models published in the literature and 142050 models coming from the Path2Models project.
With this release, several new models have been published and numerous have been updated. Moreover new services are now available (for example related to the access to models from the Path2Models project) while others have been improved (such as the model browsing feature based on a tree of Gene Ontology terms or the BioPAX export).
Please read the release notes for more information.

Computational Systems Neurobiology

Springer July 2012
From transcriptomics to large scale models of neuronal networks, including signaling pathways and multi-compartment neurons, this book introduce the whole spectrum of computational biology techniques used to understand neuronal systems. Read more

Software Developer position available!

JOB July 2010
A Software Developer position is available to support the development of the infrastructure behind BioModels Database, the main repository of peer-reviewed, published, computational models. Please read more.

Neuronvisio: a graphical user interface with 3D capabilities for NEURON

Frontiers in Neuroinformatics June 2012
A new interface to NEURON has been developed by Michele Mattioni et al. NeuronVision allows to explore neuronal models and their simulations using 3D representations. Read more

22nd BioModels Database Release

BioModels 20th May 2012
We are pleased to announce the twenty-second release of BioModels Database.
The resource now publicly provides 142904 models. This corresponds to 421 models in the curated branch, 433 models in the non-curated branch and 142050 models coming from the Path2Models project.
In addition to the typical work on the curated and non-curated branches, where several new models have been made available and numerous others updated, this release sees the availability of the models generated by the Path2Models project, a change in the terms of use and several improvements and new features. Please read the release notes for more information.

MELTING, a flexible platform to predict the melting temperatures of nucleic acids

BMC Bioinformatics May 2012
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

Software support for SBGN maps: SBGN-ML and LibSBGN

Oxford Bioinformatics 16th May 2012
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. Read more

Michele Mattioni passes his Viva!

graduation icon 1st May 2012
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!

Computational Systems Neurobiology book

Book cover April 2012
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

21st BioModels Database Release

BioModels 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

PLoS ONE 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

2011

Description of SED-ML published

BMC Systems Biology 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

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

NAR December 2011
In this paper, we describe the MIRIAM Registry, which provides unique, perennial and location-independent identifiers for data used in the biomedical domain. We also introduce the new Identifiers.org service that is built upon the information stored in the Registry and which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs). The flexibility of the identification scheme and resolving system allows its use in many different fields, where unambiguous and perennial identification of data entities are necessary. Read more

Controlled vocabularies and semantics in systems biology

MSB October 2011
In our new paper, we describe how we can add a semantic layer on top of the descriptions of models, simulations, and numerical results, and use it to extract more from models in systems biology. Read more

20th BioModels Database Release

BioModels 1st September 2011
We are pleased to announce the twentieth release of BioModels Database. In this release, 65 new models have been published and numerous existing models have been updated. BioModels Database now publicly provides 366 models in the curated and 398 in the non-curated branch. Together, these 764 models comprise 119745 species, 135889 relationships (which include reactions, rate rules, events and assignment rules), and 24666 cross-references. Read more...

Retrieval, alignment, and clustering of computational models based on semantic annotations

MSB July 2011
How to use metadata to retrieve relevant data? In our publication, we describe how using a consistent annotation scheme in conjunction with qualifiers (predicates) allow to compare and cluster datasets, even if heterogenous. We demonstrate it with gene expression and models. Read more

JSBML: a flexible Java library for working with SBML

Oxford Bioinformatics June 2011
The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations, and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the JavaTM programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end-user applications, as well as ease migration from a libSBML- based backend. Read more

Minimum Information About a Simulation Experiment (MIASE)

PLoS_CB 28th April 2011
A large, international consortium led by EMBL-EBI has presented standard requirements for describing a computer simulation experiments. In our publication, we describe the minimum information to provide together with models, in order to ensure the reproducibility of simulation experiments. This will support more collaborative and distributed efforts in computational modelling and simulation of biological processes. Read more

19th BioModels Database Release

BioModels 15 April 2011
We are pleased to announce the nineteenth release of BioModels Database. In this release, 69 new models have been published. Moreover, numerous existing models have been updated. BioModels Database now publicly provides 326 models in the curated and 373 in the non-curated branch. Together, these 699 models comprise 92112 species, 113925 relationships (which include reactions, rate rules, events and assignment rules), and 22969 cross-references. Read more...

JUMMP: JUst a Model Management Platform

BioModels February 2011
To provide the worldwide community with a modern tool for the collaborative creation and sharing of models in an efficient and secured way, the Jürgen Eils and Nicolas Le Novère groups are announcing the JUMMP project. It is planned that JUMMP will be used as the software infrastructure running BioModels Database. We are open for further contribution from -and collaboration with- the global community interested in model development and sharing. Read more...

2010

Internship positions available!

INTERNSHIPS November 2010
Various Master Degree internship projects are available in the group. Please read this page for the list and details of the available projects and how to apply.

Post-doc position available!

JOB November 2010
A post-doctoral position is available in the groups of Le Novère and Luscombe, to study phosphoinositide signalling, within the framework of a collaboration with the Babraham Institute Read more

New availability of the BioModels Database Models of the Month

BioModels 17 November 2010
Thanks to our partnership with BioMed Central, the latest BioModels Database Models of the Month are now linked from the BioMed Central's Systems Biology Gateway. Read more

18th BioModels Database Release

BioModels 30 September 2010
In this release, 157 new models have been published. The public version of BioModels Database now contains 269 models in the curated and 361 in the non-curated branch. Together, these 630 models comprise 79224 species and 109091 reactions. Some of the existing models have been converted to SBML Level 2 Version 4, while others have been corrected with annotational updates to enhance their reusability. The database now features 20426 cross-references. Read more

BioPAX Published in Nature Biotechnology

Nature Biotechnology 9th September 2010
We are pleased to announce the publication of a perspective in Nature Biotechnology, describing the Biological Pathway eXchange (BioPAX). BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.. More information on BioPAX can be found here.

New publication about BioModels Database

BMC Systems Biology July 2010
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. Read more

Post-doc positions available!

JOB July 2010
Several post-doctoral positions are available in the group, to reconstruct, analyse, and model signalling pathways involved in synaptic function. Read more

Lu Li passes her Viva!

graduation icon 24th June 2010
PhD student Lu Li has successfully passed her viva at the University of Cambridge. In her PhD research, she combined modelling and experimental biochemistry to understand signalling pathways involved in the plasticity of striatal neurons. Congratulations Dr Li!

17th BioModels Database Release

BioModels 27th April 2010
In this release, 20 new models have been published. The public version of BioModels Database now contains 249 models in the curated and 224 in the non-curated branch. Together, these 473 models comprise 37852 species and 44886 reactions. Some of the existing models have been converted to SBML Level 2 Version 4, while others have been corrected with annotational updates to enhance their reusability. The database now features 18950 cross-references. Read more

Free diffusion of AMPAR sufficient for onset of LTP

BMC Systems Biology 16th March 2010
We use our software Meredys to simulate the diffusion, clustering and permeability of glutamate AMPA receptors, and show that accumulation of receptors in the post-synaptic density can occur in less than a second. Read more

Paper describing a new spatial simulator

BMC Systems Biology 16th March 2010
Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/ Read more

16th BioModels Database Release

BioModels 26th January 2010
In this release, 10 new models have gained entry to the curated branch. The public version of BioModels Database now contains 241 models in the curated and 212 in the non-curated branch. Together, these 453 models comprise 33702 species and 41069 reactions. Read more

New paper on cooperativity and sensitivity in physiological conditions

PLoS ONE 05th January 2010
In this paper, we investigate the consequences of the fact that, for most signalling systems in vivo, the concentrations of the receptor molecules are near the values of the dissociation constants. We analyse in particular the cooperative signalling systems. We demonstrate that increasingly strong ligand depletion progressively increases the dynamic range, that is the range of concentrations “measured” by the system, and decreases the cooperativity. Read more

2009

SBGN Entity Relationship and Activity Flow languages Level 1

SBGN 2rd September 2009
We are pleased to announce the first specifications for Entity Relationships and Activity Flows of the Systems Biology Graphical Notation (SBGN). The goal of SBGN is to standardise the graphical representation of essential biochemical and cellular processes. Standardising graphical notations for describing biological interactions is an important step towards the efficient communication of biological knowledge between different communities. More information on SBGN and SBGN languages can be found here.

SBGN Published in Nature Biotechnology

Nature Biotechnology 07th August 2009
We are pleased to announce the publication of a perspective in Nature Biotechnology, describing the three languages composing the Systems Biology Graphical Notation (SBGN). The goal of SBGN is to standardise the graphical representation of essential biochemical and cellular processes. Standardising graphical notations for describing biological interactions is an important step towards the efficient communication of biological knowledge between different communities. More information on SBGN and SBGN Process Diagram Level 1 can be found here.

Melanie Stefan and Dominic Tölle pass their Viva!

graduation icon 7th July 2009
We are pleased to report that Melanie Stefan and Dominic Tölle, who were PhD students in the group, both passed their Viva and graduated from the University of Cambridge. Melanie Stefan's thesis focussed on the allosteric properties of calmodulin and calcium/calmodulin kinase II in relation with synaptic plasticity. Dominic Tölle developed an advanced spatial simulator and studied the movements of glutamate receptors in the synapse. Congratulations to Doctor Stefan and Doctor Tölle!

BioModels Database Fourteenth Release

BioModels 16th June 2009
We are pleased to announce the Fourteenth release of BioModels Database.
In this new release, 5 new models entered the curated branch. That brings the public version of BioModels Database 412 models representing 36264 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 14611 cross-references. Read more

BioModels Database Thirteenth Release

BioModels 25th March 2009
We are pleased to announce the thirteenth release of BioModels Database.
In this new release, 23 new models entered the curated branch. That brings the public version of BioModels Database 335 models representing 36093 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 13818 cross-references. Read more

Public release of SBML Level 2 Version 4

SBML 22nd December 2008
SBML editors are pleased to announce the public release of SBML Level 2 Version 4.
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others … Read more

2008

BioModels Database Twelfth Release

BioModels 3rd December 2008
We are pleased to announce the twelfth release of BioModels Database.
In this new release, 23 new models entered the curated branch. That brings the public version of BioModels Database 293 models representing 34443 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 13493 cross-references. Read more

SBMLeditor 1.3.3 Release

SBMLeditor 5th September 2008
We are please to announce the release of SBMLeditor 1.3.3.
It is mainly a bug correction release. It include also the latest data from the eleventh release of BioModels Database and libSBML 3.2.0 release Read more

BioModels Database Eleventh Release

BioModels 21st August 2008
We are pleased to announce the eleventh release of BioModels Database.
In this new release, 17 new models entered the curated branch. That brings the public version of BioModels Database 259 models representing 27117 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 11000 cross-references. Read more

BioModels Database version 3

BioModels 18th August 2008
We are pleased to announce the release of BioModels Database version 3.
This new version changed the layout of the interface in order to more efficiently use page space when viewing a model. And tons of new features were added. Read more

SBGN Process Diagrams Level 1

SBGN 23rd August 2008
We are pleased to announce the first specification for Process Diagrams of the Systems Biology Graphical Notation (SBGN). The goal of SBGN is to standardise the graphical representation of essential biochemical and cellular processes. Standardising graphical notations for describing biological interactions is an important step towards the efficient communication of biological knowledge between different communities. More information on SBGN and SBGN Process Diagram Level 1 can be found here.

SBMLeditor 1.3.2 Release

SBMLeditor 5th August 2008
We are please to announce the release of SBMLeditor 1.3.2.
It include a better support for SBML level 2 version 3, an improve user interface and an export of the latest Miriam database for the annotations of SBML elements. Read more

A new model of calmodulin function

PLoS_CB 31st July 2008
The plasticity of our synapses, and therefore our capacities to learn and memorise, is controlled by the fine tuning of intracellular calcium signalling. In an article published in the PNAS (Stefan, Edelstein, Le Novère (2008) PNAS Advance Online Publication.) we describe how calmodulin, a small protein enriched in our neurons, measures calcium concentration and differentially regulates synapse potentiation and depression through the activation of proteins CaMKII and calcineurin. Read more

BioModels Database Tenth Release

BioModels 28th March 2008
We are pleased to announce the tenth release of BioModels Database.
This new release sees the the addition of 52 models, including 17 in the curated branch, bringing BioModels Database to 25731 reactions. Read more

2007

BBSRC funds the development and maintenance of BioModels Database

BBSRC 20th November 2007
We are pleased to announce that the UK Biotechnology and Biological Sciences Research council (BBSRC) accepted to fund the long term development of BioModels Database through its Bioinformatics and Biological Resources Fund. The BBRF will support a curator and half a developer during four years.

BioModels Database Ninth Release

BioModels 25th September 2007
We are pleased to announce the ninth release of BioModels Database.
This new release sees the the addition of 47 models, including 38 in the curated branch, bringing BioModels Database to 12482 reactions. Read more

Public release of SBML Level 2 Version 3

SBML 15th June 2007
SBML editors are pleased to announce the public release of SBML Level 2 Version 3.
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others. Read more

Ligand-Gated Ion Channel database 60th Release

LGICDB 06th June 2007
We are pleased to announce the 60th release of the Ligand-Gated Ion Channel database.
For this release 18 entries have been added, and four entries have been updated. Mouse, rat, and human LGIC entries in the database are now completed to current knowledge.

BioModels Database Eighth (Heinrich) Release

BioModels 05th June 2007
We are pleased to announce the eighth release of BioModels Database, dedicated to Reinhart Heinrich, one of the fathers of Systems Biology.
This new release sees the the addition of 34 models, including 27 in the curated branch, bringing BioModels Database to 7684 reactions. Read more

BioModels Database ranked first data resource in Systems Biology

Nature Biotechnology 17st April 2007
BioModels Database was ranked first database used in Systems Biology by a survey published this month in Nature Biotechnology. It is ranked third in the list of 95 specialised tools (the first two being libSBML and CellDesigner). SBMLeditor is also in the list (15th position) as well as StochSim (30th position).

BBSRC funds collaboration with Japanese partners

SBML 1st April 2007
We are pleased to announce that the UK Biotechnology and Biological Sciences Research council (BBSRC) granted us a UK-Japan Partnering award. The collaboration "Interfacing Standards and Ontologies in Systems Biology" will build on existing links between the groups of Nicolas Le Novere (EMBL-European Bioinformatics Institute), Ken Fukuda (AIST Computational Biology Research Center), Douglas Kell (Manchester Centre for Integrative Systems Biology) and Hiroaki Kitano (Tokyo Systems Biology Institute).

BioModels Database Seventh (DOQCS) Release

BioModels 05th January 2007
We are pleased to announce the seventh release of BioModels Database, the "DOQCS release".
As the nickname of this release indicates, this is the first one incorporating models coming from the Database of Quantitative Cellular Signalling. This new release sees the the addition of 16 models in the curated branch, and 26 in the non-curated branch, bringing BioModels Database to 6458 reactions. Read more

2006

BioModels Database and DOQCS join forces

DOQCS 04th December 2006
The BioModels Database, hosted by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK, has entered a formal data-exchange agreement with the Database of Quantitative Chemical Signalling (DOQCS) of the National Centre for Biological Sciences (NCBS) in Bangalore, India. Both data resources will now simultaneously release computer models of biological processes to the community. This agreement is the culmination of more than a year's work to make the models in DOQCS available in Systems Biology Markup Language (SBML). The agreement will provide users of both databases with a larger pool of models, whilst giving them the freedom to use the different interfaces and tools associated with each resource. Read more

Integration of dopamine and glutamate signals

PLoS_CB 06th November 2006
Projecting neurons of the striatum are a crucial relay of the basal ganglia, involved in motor, psycho-motor and behavioural functions. We present a detailed quantitative model of the integration of dopamine and glutamate signals by the protein DARPP-32. Dynamic simulations show that the function of DARPP-32 depends on the delay between the two signals, and therefore the protein not only measures the intensity, but also the coincidence between signals. Read more

BioModels Database Sixth Release

BioModels 03th October 2006
We are pleased to announce the sixth release of BioModels Database.
It sees the addition of 42 models that represent 3584 reactions. A new branch has been added to distribute non-curated models. Read more

Public release of SBML Level 2 Version 2

SBML 26th September 2006
We are pleased to announce the public release of SBML Level 2 Version 2.
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others Read more

BBSRC funds development of MIRIAM resources

SBML 11th August 2006
We are pleased to announce that the UK Biotechnology and Biological Sciences Research council (BBSRC) agreed to fund the development of resources to support the implementation of MIRIAM, a standard for model curation.

BioModels Database Fifth Release

BioModels 05th June 2006
We are pleased to announce the fifth release of BioModels Database.
It sees the addition of 4 models that represent 144 reactions. New export formats include BioPAX and SVG graphs …Read more

First BioModels Training Camp

BioModels 28th February 2006
The first BioModels.net training camp will be held at the The European Bioinformatics Institute between the 10th and 12th April 2006. Read more

BioModels Database Fourth Release

BioModels 31st January 2006
We are pleased to announce the fourth release of BioModels Database.
It sees the addition of 6 models that represent 220 reactions, the biggest increase since the creation of the resource. Most importantly, this release introduces the qualification of annotations, following the recommendation of the MIRIAM standard. Read more

2005

Setting the standard for computer models of life

MIRIAM 7th December 2005
Scientists from 14 different organisations including the EMBL-European Bioinformatics Institute annouce MIRIAM, a new quality standard for biochemical models, in the 6 December issue of Nature Biotechnology. MIRIAM will help researchers to reuse, modify and combine computer models of biochemical processes to gain a fuller understanding of life at the molecular and cellular level. Read more

Japanese government funds the development of SBGN

NEDO 21th September 2005
We are pleased to announce that the New Energy and Industrial Technology Development Organisation (NEDO) agreed to fund the development of the Systems Biology Graphical Notation (SBGN), a standard graphical notation for diagrams of computational models in biology.

US government supports BioModels Database

NIGMS 25th August 2005
We are pleased to announce that the National Institute of General Medical Sciences (NIGMS) agreed to provide some fund toward the development of the prototype of BioModels Database, a free, open database of computational models.

A new way to share models of biological systems

BioModels 11th April 2005
BioModels Database, the world's first database of curated and annotated biological models, is launched today. BioModels Database is the result of a collaboration led by the EBI and the SBML Team, an international group that develops open-source standards to describe biological systems. Read more

DopaNet day

DopaNet 5th April 2005
The Computational Neurobiology Group is organising a workshop in "Systems Biology of Neuroadaptation in Mesotelencephalic Dopamine Pathways". Read more

2004

FASTA search on LGICdb

Fasta 26th August 2004
The Computational Neurobiology group have launched a Fasta for the Ligand Gated Ion Channel (LGIC) database.
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