Christophe Blanchet

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, is now available as a web server. This version, which can be freely accessed at http://gbio-pbil.ibcp.fr/cgi/Curves_plus/, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure. PDB format files are also provided for offline visualization of the helical axis and groove geometry.

The EMBRACE web service collection

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

Integrated databanks access and sequence/structure analysis services at the PBIL

The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.

MPSA: integrated system for multiple protein sequence analysis with client/server capabilities

UNLABELLEDnMPSA is a stand-alone software intended to protein sequence analysis with a high integration level and Web clients/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user interface. It is available for most Unix/Linux and non-Unix systems. MPSA is able to connect to a Web server (e.g. http://pbil.ibcp.fr/NPSA) in order to perform large-scale sequence comparison on up-to-date databanks.nnnAVAILABILITYnFree to academic http://www.ibcp.fr/mpsa/nnnCONTACTnc.blanchet@ibcp.fr

Grid as a bioinformatic tool

The grid is a promising tool to resolve the crucial issue of software and data integration in biology. In this paper, we have reported on our experience in the deployment of bioinformatic grid applications within the framework of the DataGrid project. These applications inquired the potential impact of grids for CPU demanding algorithms and bioinformatics web portals and for the update and distribution of biological databases.Grid computing tests showed how resources sharing improves the current practice of bioinformatics. Reached performance demonstrated the interest of the grid tool.

BioXSD: the common data-exchange format for everyday bioinformatics web services

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community. Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org

Building an encrypted file system on the EGEE grid: application to protein sequence analysis

Bioinformatics needs high-throughput computing and huge data storage to understand datasets such as ones produced by complete genome projects. But these data are linked to patients, and used in scientific or industrial processes such as drug design and gene function identification. These use cases need to have a certain level of confidentiality and integrity to preserve the patient privacy or the patent secret. Obviously important in a local computing context such as supercomputer or cluster, these requirements are exarcebated in the context of a grid such EGEE, where the computing and storage resources are distributed across a worldwide platform. We have developed the EncFile encrypted files management system, deployed on the production platform of the EGEE project, and associated to encrypted representative biological resources. Thus we provided grid users with a user-friendly component that doesnt require any user privileges. Moreover, our EncFile system can be also deployed on other distributed systems as it is not linked to the EGEE grid components.

Integrating bioinformatics resources on the EGEE grid platform

Understanding biological data from complete genome sequencing projects is one of major challenges in Bioinformatics. These data are published into several worldwide databases. And bioinformaticians analyzing these data need efficient access to these up-to-date biological data coupled with relevant algorithms and also with large computing and storage resources. Grid computing, as in the EGEE project, will be a viable solution to distribute and integrate these genomics, post-genomics and proteomics data and bioinformatics algorithms. We have deployed several representative biological data and bioinformatics programs for protein sequences analysis onto the worldwide production EGEE grid. These resources are available to all biologists and bioinformaticians joining the biomedical virtual organization in EGEE.

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies.

We use a physics-based approach termed ADAPT to analyse the sequence-specific interactions of three proteins which bind to DNA on the side of the minor groove. The analysis is able to estimate the binding energy for all potential sequences, overcoming the combinatorial problem via a divide-and-conquer approach which breaks the protein-DNA interface down into a series of overlapping oligomeric fragments. All possible base sequences are studied for each fragment. Energy minimisation with an all-atom representation and a conventional force field allows for conformational adaptation of the DNA and of the protein side chains for each new sequence. As a result, the analysis depends linearly on the length of the binding site and complexes as large as the nucleosome can be treated, although this requires access to grid computing facilities. The results on the three complexes studied are in good agreement with experiment. Although they all involve significant DNA deformation, it is found that this does not necessarily imply that the recognition will be dominated by the sequence-dependent mechanical properties of DNA.

Grid computing for improving conformational sampling in NMR structure calculation

MOTIVATIONnMethods for automatic nuclear magnetic resonance (NMR) structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes.nnnRESULTSnDue to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous datasets, because of the much larger conformational sampling that can be generated by use of the grid computational power.nnnAVAILABILITYnThe version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.