Social pathway annotation: extensions of the systems biology metabolic modelling assistant.

High-throughput experiments have produced large amounts of heterogeneous data in the life sciences. These data are usually represented in different formats (and sometimes in technical documents) on the Web. Inevitably, life science researchers have to deal with all these data and different formats to perform their daily research, but it is simply not possible for a single human mind to analyse all these data. The integration of data in the life sciences is a key component in the analysis of biological processes. These data may contain errors, but the curation of the vast amount of data generated in the 'omic' era cannot be done by individual researchers. To address this problem, community-driven tools could be used to assist with data analysis. In this article, we focus on a tool with social networking capabilities built on top of the SBMM (Systems Biology Metabolic Modelling) Assistant to enable the collaborative improvement of metabolic pathway models (the application is freely available at http://sbmm.uma.es/SPA).

PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome.

Peroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contain a highly diverse enzymatic network among different species, mirroring the varied metabolic needs of the organisms. The previous PeroxisomeDB version organized the peroxisomal proteome of humans and Saccharomyces cerevisiae based on genetic and functional information into metabolic categories with a special focus on peroxisomal disease. The new release (http://www.peroxisomeDB.org) adds peroxisomal proteins from 35 newly sequenced eukaryotic genomes including fungi, yeasts, plants and lower eukaryotes. We searched these genomes for a core ensemble of 139 peroxisomal protein families and identified 2706 putative peroxisomal protein homologs. Approximately 37% of the identified homologs contained putative peroxisome targeting signals (PTS). To help develop understanding of the evolutionary relationships among peroxisomal proteins, the new database includes phylogenetic trees for 2386 of the peroxisomal proteins. Additional new features are provided, such as a tool to capture kinetic information from Brenda, CheBI and Sabio-RK databases and more than 1400 selected bibliographic references. PeroxisomeDB 2.0 is a freely available, highly interactive functional genomics platform that offers an extensive view on the peroxisomal metabolome across lineages, thus facilitating comparative genomics and systems analysis of the organelle.

Protopia: a protein-protein interaction tool.

BACKGROUND: Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data http://asp.uma.es. RESULTS: The tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein. CONCLUSION: The tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks.