Sys Bio Tools
Licensing agreements for BRB-ArrayTools differ for U.S. Government users, academic/non-profit users, or commercial users. All users must agree to the following conditions: 1. All publications based on BRB-ArrayTools analyses will contain the acknowledgment: "Analyses were performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team." Biometric Research Branch home page
STAR: Biogene - Home StarBiogene is a set of visual and analytic software tools for the analysis of genomic gene expression data generated through microarray analysis. This software allows students to compare the expression of multiple genes across a range of biological samples (cell lines, tumors, etc). For example, students can use StarBiogene to compare different patient tumor samples and identify characteristics that are common to one set of tumors based on global patterns of gene expression.
Pathguide: the pathway resource list
SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches. Five Most Recent Additions: Representative Uniprot accessions available in BatchSource Read the SOURCE paper at NAR or as a PDF SOURCE is now available at http://source.stanford.edu Retrieval of upstream genomic sequences from human GeneReports Link to UCSC Genome Browser from human GeneReports SOURCE Search
2.8 Software Packages
R Commander Current Version: 1.9-x John Fox Please Read the Rcmdr Installation Notes (click on the image for a larger view) For more details, see my paper on the R Commander in the Journal of Statistical Software (which is somewhat out of date) and the introductory manual distributed with the package (accessible via the Help -> Introduction to the R Commander menu). The R-Commander GUI consists of a window containing several menus, buttons, and information fields.
Introduction to R
Proteins can form a variety of functional connections with each other, including stable complexes, metabolic pathways and a bewildering array of direct and indirect regulatory interactions. These connections can be conceptualized as networks and the size and complex organization of these networks present a unique opportunity to view a given genome as something more than just a static collection of distinct genetic functions. Indeed, the ‘network view’ on a genome is increasingly being taken in many areas of applied biology: protein networks are used to increase the statistical power in human genetics ( 1 , 2 ), to aid in drug discovery ( 3 , 4 ), to close gaps in metabolic enzyme knowledge ( 5 ,6) and to predict phenotypes and gene functions ( 7 , 8 ), to name just a few examples. While clearly very useful, the annotation and storage of protein–protein associations in databases is less straightforward than for other types of data (such as genomic sequence data or taxonomy information). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
This project hosts the PSICQUIC Reference Implementation , an implementation of the PSICQUIC Specification . A publication about PSICQUIC can be found in Nature Methods . If you find a bug, report it . If you need help or have questions, ask them . You can see PSICQUIC in action with the PSICQUIC View . PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically. psicquic - Protemics Standard Initiative Common QUery InterfaCe
Your Favorite Gene (YFG): gene specific search results for shRNAs, antibodies & cofactors.
NetAtlas | Download NetAtlas software for free at SourceForge
NetAtlas: A Cytoscape plugin to examine signaling networks based on tissue gene expression
Data_Sets - Cytoscape Wiki Example Data Sets These data sets have been generously contributed by users. Please feel free to add your own. Annotated Human Interactome
Cytoscape Online Tutorials See our most up-to-date tutorials on OpenTutorials . Older Tutorials To get you started with Cytoscape: Getting Started Guide Presentations - Cytoscape Wiki
Cytoscape Web: an interactive web-based network browser + Author Affiliations * To whom correspondence should be addressed. Received May 3, 2010.
Figure 1 . clusterMaker in action. In this screenshot, the expression data in the sampleData file galFiltered.cys has been clustered using the hierarchical method and displayed as a heatmap with associated dendrogram. The groups created by clustering are shown on the network. UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. clusterMaker: Creating and Visualizing Cytoscape Clusters
Systems Biology - BioChemWeb.org
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, McKusick VA Nucleic Acids Res. 2002 Jan 1; 30(1):52-5. [ PubMed ] [ Ref list ] Review SWISS-PROT: connecting biomolecular knowledge via a protein database. Gasteiger E, Jung E, Bairoch A
Molecular Systems Biology
Molecular Systems Biology
Molecular Systems Biology
PLoS Collections: Article collections published by the Public Library of Science
Reactome Introduction User Series 1