Pathway Discovery - Genomics and System Biology Resource Bin
Commercial Tools
Genomatix offers software, databases and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology.
www.Genomatix.de
Ingenuity Pathways Analysis (IPA) is an all-in-one software application that enables researchers to model, analyze, and understand the complex biological and chemical systems at the core of life science research. IPA has been broadly adopted by the life sciences research community and cited in hundreds of peer-reviewed journal articles.
www.Ingenuity.com
NextBio is a life science search engine designed to be used by anyone interested in basic and clinical research, drug discovery or biology.
www.Nextbio.com
MetaCore is an integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression. The analytical package includes easy to use, intuitive tools for data visualization, mapping and exchange, multiple networking algorithms and filters.
www.Genego.com
Public tools
PubGene helps you retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a "gene-centric" database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a "literature network" organizing information in a form that is easy to navigate.
www.Pubgene.org
Chilibot searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords. The results are returned as a graph. Several different search methods are supported.
www.Chilibot.net
FABLE mines the biomedical literature for information about human genes and proteins. FABLE v3 allows a user to find articles mentioning a gene of interest (Article Finder), to generate a list of genes associated with one or more keywords (Gene Lister), or use a local mirror of the UCSC Genome Browser with a literature track (LitTrack).
www.Fable.chop.edu
Litinspector is Genomatix's free tool for searching literature abstracts from NCBI's PubMed. Users can search for genes, gene functions and signal transduction pathways.
www.Litinspector.org
DAVID The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
http://David.abcc.ncifcrf.gov
Next Generation Sequencing
SeqAnswers is the next generation sequencing community forum which covers technology and related bioinformatics. www.Seqanswers.com