Tools
Pyicos
Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. Due to its increasing throughput and decreasing cost, deep-sequencing (DS) has revolutionized the study of gene regulation. It is now used for a variety of functional analyses in the genome and transcriptome.
IntOGen
Integrative OncoGenomics (IntOGen), a discovery tool for cancer researchers, is a resource that integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development.
Gitools
Gitools is an open-source tool to perform analyses and visualize data and results as interactive heat-maps. Gitools contains data import systems from several sources (i.e. IntOGen, Biomart, KEGG), which facilitate the integration of novel data with previous knowledge.
DisGeNET
DisGeNET is a plugin for Cytoscape to query and analyze a network representation of human gene-disease databases. For this purpose, we have developed a new gene-disease database integrating data from several public sources.
ArchKI
ArchKI is a structural classification of kinase loops with information of functional residues. We are interested in finding relationships between structure and function of classified kinase-loops using three different sources of functional information: (i) functional residues (or regions) described in the literature (ii) residues described in the SITE records of the pdb files that specify residues comprising catalytic, cofactor, anticodon, regulatory or other important sites and (iii) residues in contact with heteroatoms.
ArchDB
ArchDB is a compilation of structural classifications of loops extracted from known protein structures.
BIANA
BIANA (Biologic Interactions and Network Analysis) is a biological database integration and network management framework written in Python. It uses a high level abstraction schema to define databases providing any kind of biological information (both individual entries and their relationships).
FCP
FCP is a publicly accessible web tool dedicated to analysing the current state and trends on the population of available structures along the classification schemes of enzymes (specially kinases and proteases), G protein-coupled receptors, nuclear receptors and transporters/channels, offering both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures, as well as on the bias observed in the distribution of those structures among proteins.
iPHACE
iPHACE is an integrative web-based tool to navigate in the pharmacological space defined by small molecule drugs contained in the IUPHAR-DB and PDSP databases. Extending beyond traditional querying and filtering tools, iPHACE offers a means to extract knowledge from the target profile of drugs as well as from the drug profile of protein targets.
LINK3D
Link3D is a real-time teleconferencing and collaborative software, specifically developed to support on-line conferences in the area of biomedicine and drug development. The software allows to share supporting data commonly used in these areas, like molecular structures of drugs or biomolecules, which can be manipulates interactively by all the participants. Security is one of the strong points of the software. All the communications are encrypted and the identity of the participants can be guaranteed by user authentication protocols.
