Web services at the European Bioinformatics Institute-2009

The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009–2010

Gene Characterization Index: Assessing the Depth of Gene Annotation

We introduce the Gene Characterization Index, a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described. Inherently a reflection of human perception, the Gene Characterization Index is applied for assessing the characterization status of individual genes, thus serving the advancement of both genome annotation and applied genomics research by rapid and unbiased identification of groups of uncharacterized genes for diverse applications such as directed functional studies and delineation of novel drug targets.The scoring procedure is based on a global survey of researchers, who assigned characterization scores from 1 (poor) to 10 (extensive) for a sample of genes based on major online resources. By evaluating the survey as training data, we developed a bioinformatics procedure to assign gene characterization scores to all genes in the human genome. We analyzed snapshots of functional genome annotation over a period of 6 years to assess temporal changes reflected by the increase of the average Gene Characterization Index. Applying the Gene Characterization Index to genes within pharmaceutically relevant classes, we confirmed known drug targets as high-scoring genes and revealed potentially interesting novel targets with low characterization indexes. Removing known drug targets and genes linked to sequence-related patent filings from the entirety of indexed genes, we identified sets of low-scoring genes particularly suited for further experimental investigation.The Gene Characterization Index is intended to serve as a tool to the scientific community and granting agencies for focusing resources and efforts on unexplored areas of the genome. The Gene Characterization Index is available from http://cisreg.ca/gci/

BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact [email protected] Database (http://www.ebi.ac.uk/ biomodels/), part of the international initiative BioModels.net, provides access to published, peerreviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.Peer reviewe

ViVa: the virtual vascular project.

The aim of the virtual vascular project (ViVa) is to develop tools for the modern hemodynamicist and cardiovascular surgeon to study and interpret the constantly increasing amount of information being produced by noninvasive imaging equipment. In particular, we are developing a system able to process and visualize three-dimensional (3-D) medical data, reconstruct the geometry of arteries of specific patients, and simulate blood flow in them. The initial applications of the system will be for clinical research and training purposes. In a later stage, we will explore the application of the system to surgical planning. ViVa is based on an integrated set of tools, each dedicated to a specific aspect of the data processing and simulation pipeline: image processing and segmentation; real-time 3-D volume visualization; 3-D geometry reconstruction; 3-D mesh generation; and blood flow simulation and visualization

Modulating inhibitory ligand-gated ion channels

The glycine and γ-aminobutyric acid receptors (GlyR and GABAAR, respectively) are the major inhibitory neurotransmitter-gated receptors in the central nervous system of animals. Given the important role of these receptors in neuronal inhibition, they are prime targets of many therapeutic agents and are the object of intense studies aimed at correlating their structure and function. In this review, the structure and dynamics of these and other homologous members of the nicotinicoid superfamily are described. The modulatory actions of the major biological macromolecules that bind and allosterically affect these receptors are also discussed