A synchronous multimedia annotation system for secure collaboratories

In this paper, we describe the Vannotea system - an application designed to enable collaborating groups to discuss and annotate collections of high quality images, video, audio or 3D objects. The system has been designed specifically to capture and share scholarly discourse and annotations about multimedia research data by teams of trusted colleagues within a research or academic environment. As such, it provides: authenticated access to a web browser search interface for discovering and retrieving media objects; a media replay window that can incorporate a variety of embedded plug-ins to render different scientific media formats; an annotation authoring, editing, searching and browsing tool; and session logging and replay capabilities. Annotations are personal remarks, interpretations, questions or references that can be attached to whole files, segments or regions. Vannotea enables annotations to be attached either synchronously (using jabber message passing and audio/video conferencing) or asynchronously and stand-alone. The annotations are stored on an Annotea server, extended for multimedia content. Their access, retrieval and re-use is controlled via Shibboleth identity management and XACML access policies

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

PDBe: Protein Data Bank in Europe

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed ‘PDBeView Atlas pages’ provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe’s active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis

Genome3D: exploiting structure to help users understand their sequences.

Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models

The Value of New Scientific Communication Models for Chemistry

This paper is intended as a starting point for discussion on the possible future of scientific communication in chemistry, the value of new models of scientific communication enabled by web based technologies, and the necessary future steps to achieve the benefits of those new models. It is informed by a NSF sponsored workshop that was held on October 23-24, 2008 in Washington D.C. It provides an overview on the chemical communication system in chemistry and describes efforts to enhance scientific communication by introducing new web-based models of scientific communication. It observes that such innovations are still embryonic and have not yet found broad adoption and acceptance by the chemical community. The paper proceeds to analyze the reasons for this by identifying specific characteristics of the chemistry domain that relate to its research practices and socio-economic organization. It hypothesizes how these may influence communication practices, and produce resistance to changes of the current system similar to those that have been successfully deployed in other sciences and which have been proposed by pioneers within chemistry.National Science Foundation, Microsof

Phase Combination and its Application to the Solution of Macromolecular Structures: Developing ALIXE and SHREDDER

[eng] Phasing X-ray data within the frame of the ARCIMBOLDO programs requires very accurate models and a sophisticated evaluation of the possible hypotheses. ARCIMBOLDO uses small fragments, that are placed with the maximum likelihood molecular replacement program Phaser, and are subject to density modification and autotracing with the program SHELXE. The software receives its name from the Italian painter Giuseppe Arcimboldo, who used to compose portraits out of common objects such as vegetables or flowers. Out of most possible arrangements of such objects, only a still-life will result, and just a few ones will truly produce a portrait. In a similar way, from all possible placements with small protein fragments, only a few will be correct and will allow to get the full “protein’s portrait”. The work presented in this thesis has explored new ways to exploit partial information and increase the signal in the process of phasing with fragments. This has been achieved through two main pieces of software, ALIXE and SHREDDER. With the spherical mode in ARCIMBOLDO_SHREDDER, the aim is to derive compact fragments starting from a distant homolog to our unknown protein of interest. Then, locations for these fragments are searched with Phaser. These include strategies for refining the fragments against the experimental data and giving them more degrees of freedom. With ALIXE, the aim is to combine information in reciprocal space from partial solutions, such as the ones produced by SHREDDER, and use the coherence between them to guide their merging and to increase the information content, so that the step of density modification and autotracing starts from a more complete solution. Even if partial solutions contain both correct and incorrect information, the combination of solutions that share some similarity will allow to get a better approximation to the correct structure. Both ARCIMBOLDO_SHREDDER and ALIXE have been used on test data for development and optimisation but also on datasets from previously unknown structures, which have been solved thanks to these programs. These programs are distributed through the website of the group but also through software suites of general use in the crystallographic community such as CCP4 and SBGrid

CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis.

Tuberculosis kills more than a million people annually and presents increasingly high levels of resistance against current first line drugs. Structural information about Mycobacterium tuberculosis (Mtb) proteins is a valuable asset for the development of novel drugs and for understanding the biology of the bacterium; however, only about 10% of the ∼4000 proteins have had their structures determined experimentally. The CHOPIN database assigns structural domains and generates homology models for 2911 sequences, corresponding to ∼73% of the proteome. A sophisticated pipeline allows multiple models to be created using conformational states characteristic of different oligomeric states and ligand binding, such that the models reflect various functional states of the proteins. Additionally, CHOPIN includes structural analyses of mutations potentially associated with drug resistance. Results are made available at the web interface, which also serves as an automatically updated repository of all published Mtb experimental structures. Its RESTful interface allows direct and flexible access to structures and metadata via intuitive URLs, enabling easy programmatic use of the models.This work was supported by the Bill & Melinda Gates Foundation (RG60453). University of Cambridge for facilities and support [to TLB]. Funding for open access charge: Bill & Melinda Gates Foundation.This is the final published version. It first appeared at http://database.oxfordjournals.org/content/2015/bav026.long

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy

This work was funded by the Spanish Ministerio de Economía y Competividad through grants BFU2009-09331, BIO2010-16566, ACI2009-1022, ACI2010-1088 and AIC-A- 2011-0638, by the Comunidad Autonoma de Madrid through grant S2010/BMD-2305, by NFS grant No. 1114901 and by the Spanish National Institute of Bioinformatics (a project funded by the Instituto de Salud Carlos III). This work was conducted using the Protégé resource, which is supported by grant LM007885 from the United States National Library of Medicine. COSS is a Ramón y Cajal researcher financed by the European Social Fund and the Ministerio de Economía y Competitividad. JV is a Juan de la Cierva Postdoctoral Fellow (JCI-2011-10185). This work was funded by Instruct, which is part of the European Strategy Forum on Research Infrastructures (ESFRI) and is supported by national member subscriptions