A5041778517- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Geological and Geochemical Analysis
- Service-Oriented Architecture and Web Services
- Genetics, Bioinformatics, and Biomedical Research
- Geochemistry and Geologic Mapping
- Bioinformatics and Genomic Networks
- Research Data Management Practices
- Gene expression and cancer classification
- Hydrocarbon exploration and reservoir analysis
- Water Treatment and Disinfection
- Algorithms and Data Compression
- Legionella and Acanthamoeba research
- Semantic Web and Ontologies
- Paleontology and Stratigraphy of Fossils
- CO2 Sequestration and Geologic Interactions
- Potato Plant Research
- Fractal and DNA sequence analysis
- Geothermal Energy Systems and Applications
- RNA and protein synthesis mechanisms
- Plant Pathogens and Fungal Diseases
- Rock Mechanics and Modeling
- Geological and Geophysical Studies Worldwide
University of Geneva
2020-2024
University of Arizona
2024
University of Buenos Aires
2019-2020
Consejo Nacional de Investigaciones Científicas y Técnicas
2020
Research Organization of Information and Systems
2010-2011
International Rice Research Institute
2006-2010
European Bioinformatics Institute
2002-2006
Wellcome Trust
2005-2006
University of Southampton
2003
University of Manchester
2003
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into most comprehensive library Perl modules available for managing manipulating life-science information. provides easy-to-use, stable, consistent programming interface bioinformatics application programmers. have been successfully repeatedly used to reduce otherwise complex tasks only a few lines code. object model proven be...
Abstract Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number these resources are being made available with programmatic access form Web services. Bioinformatics scientists will need to orchestrate services workflows as part their analyses. Results: The Taverna project has developed a tool for composition enactment life sciences community. includes workbench application which provides graphical...
Abstract Life sciences research is based on individuals, often with diverse skills, assembled into groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these can be represented as workflows involving the co‐ordinated of analysis programs and information repositories that may globally distributed. With regards Grid computing, requirements relate sharing resources rather than computational power. my project has developed...
Meaningful exchange of microarray data is currently difficult because it rare that published provide sufficient information depth or are even in the same format from one publication to another. Only when can be easily exchanged will entire biological community able derive full benefit such studies. To this end we have developed three key ingredients towards standardizing storage and data. First, created a minimal for annotation experiment (MIAME)-compliant conceptualization experiments...
Abstract Motivation: In silico experiments necessitate the virtual organization of people, data, tools and machines. The scientific process also necessitates an awareness experience base, both personal data as well wider context work. management all these co-ordination resources to manage such organizations surrounding them needs significant computational infra-structure support. Results: this paper, we show that myGrid, middleware for Semantic Grid, enables biologists perform in...
Agricultural crop databases maintained in gene banks of the Consultative Group on International Research (CGIAR) are valuable sources information for breeders. These provide comparative phenotypic and genotypic that can help elucidate functional aspects plant agricultural biology. To facilitate data sharing within between these retrieval information, ontology (CO) database was designed to controlled vocabulary sets several economically important species.Existing public ontologies equivalent...
Silver-copper ionization was used for controlling Legionella distribution in a German university hospital hot water plumbing system 4 years. In the beginning, silver concentrations were not allowed to exceed 10 εg/L because of drinking regulation limits Germany. Water samples monitored counts, temperature, and copper concentrations. A significant (P < .001) 3.8-log reduction from 40,000 cfu/L 7 cfu/L, found during first year with silver-copper ionization. Nevertheless, long-term efficacy <10...
Abstract Background As biology becomes an increasingly computational science, it is critical that we develop software tools support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets continue to build from international genomic, proteomic, systems-biology projects. The BioMoby interoperability system was created with goal facilitating movement data one Web-based resource another fulfill requirements non-expert bioinformaticians. In...
The Transvaal Supergroup, on the Kaapvaal Craton in South Africa, is widely accepted as one of best-preserved sedimentary archives to constrain planetary-scale environmental changes during late Archean and early Proterozoic, yet sedimentation age for certain stratigraphic intervals remains poorly constrained. To improve temporal control some first-order global recorded these rocks, we carried out U-Pb analyses detrital zircon populations from several clastic volcano-clastic units Supergroup....
SOAP (Simple Object Access Protocol) ( http://www.w3.org/TR/soap ) based Web Services technology http://www.w3.org/ws has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this to provide robust data retrieval analysis mechanisms the scientific community enhance utilization of biological resources it already provides [N. Harte, V. Silventoinen,...
Abstract MOTIVATION: The user-friendly, graphical X-windows interface (WPI) to the GCG sequence analysis package can often not be used due lack of an X-server on PC or Macintosh computers. Because Web browsers like Netscape are much more common those platforms, we decided develop W2H, a WWW Sequence Analysis Software Package with nearly same functionality as WPI. RESULTS: new (W2H) (Wisconsin Package) supports modern technologies, client-pull method, embedded scripting language, and provides...
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in amount of available data demands efficient systems without need to transfer entire every step an analysis. However, various incompatibilities among database resources analysis make it difficult connect integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client...
My Grid is an e-Science project that aims to help biologists and bioinformaticians perform workflow-based in silico experiments, them automate the management of such workflows through personalisation, notification change publication experiments. In this paper, we describe architecture my how it will be used by scientist. We then show can benefit from agents technologies. have identified three key uses agent technologies Grid: user agents, able customize personalise data, communication...
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability such tools. To ensure initiatives are effectively deployed, end-user applications need to be aware of, support, best practices standards. Here, we report on an initiative in which software developers genome biologists came together explore raise awareness of these issues: BioHackathon 2009.Developers attendance from diverse backgrounds, with experts Web...
Torrents of genotype–phenotype data are being generated, all which must be captured, processed, integrated, and exploited. To do this optimally requires the use standard interoperable “object models,” providing a description how to partition total spectrum information dealt with into elemental “objects” (such as “alleles,” “genotypes,” “phenotype values,” “methods”) precisely stated logical interrelationships “A objects made up from one or more B objects”). We herein propose Phenotype...
The Generation Challenge programme (GCP) is a global crop research consortium directed toward improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key activity development GCP bioinformatics platform support research. This includes following: (i) shared, public platform-independent domain models, ontology, data formats enable interoperability analysis flows within platform; (ii) web service registry technologies identify,...