Virtual laboratory MolDynGrid has been established for computational researches in structural biology and bioinformatics, especially for molecular dynamics (MD) simulations of biological macromolecules and their complexes. Biomolecular simulation usually requires a very high processing power and huge storage space for MD trajectories. In this study we describe the development of virtual laborat...

An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB. This need has become particularly acute as more DB content consists of computationally predicted information, such as predicted gene functions, operons, metabolic pathways, and protein properties. This pape...

MOTIVATION Bioinformatics requires reusable software tools for creating model-organism databases (MODs). RESULTS The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic ne...

Knowledge discovery through pattern finding in data is central to modern molecular biology, which now has thousands of databases and similar numbers of tools for processing those data. Any data analysis in molecular biology involves gathering and processing data from many sources, even before the analysis for the central biological question takes place. Taverna is a workflow workbench that allo...

Functional genomics is as powerful as the diversity of phenotypes that are associated with the databases of DNA sequences and their expression patterns. A special bioinformatics challenge is to include detailed information in genomic databases about subtle phenoptypic differences that show continuous distribution in segregating populations. The objective of Real Time QTL (RTQ) is to present in ...

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology...

Bioinformatics applications manage complex biological data stored into distributed and often heterogeneous databases and require large computing power. These databases are too big and complicated to be rapidly queried every time a user submits a query, due to the overhead involved in decomposing the queries, sending the decomposed queries to remote databases, and composing the results. There is...

RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structur...

The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previous...