Pathway Discovery - Genomics and Systems 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.
Ingenuity Pathway Tools 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.
NextBio is a life science search engine designed to be used by anyone interested in basic and clinical research, drug discovery or biology.
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.
Partek Genomics Suite is a single analysis solution for integrated genomics. Partek GS is unique in supporting all microarray and next generation sequencing technologies including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA in a single software package.
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
TIGR Multiexperiment Viewer (MeV) is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. MeV can handle several input file formats. These include the .mev and .tav files generated by TIGR Spotfinder and TIGR MIDAS, and also Affymetrix (.txt) and Genepix (.gpr) files. We have assembled a guide for normalizing Affymetrix .CEL files, which covers RMAExpress, BioConductor, and AMP.
www.Tm4.org/mev.html
R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.
www.R-project.org
Next Generation Sequencing
SeqAnswers is the next generation sequencing community forum which covers technology and related bioinformatics.
www.Seqanswers.com
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
www.Bowtie-bio.sourceforge.net