Systems Biology
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Cell Illustrator - Cell Illustrator 5.0
Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins. Cell Illustrator models are used to visualize biological pathways, interpret experimental data and test hypotheses.Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Latest News See All »
Gephi, an open source graph visualization and manipulation software
Protovis
Protovis is no longer under active development. The final release of Protovis was v3.3.1 (4.7 MB) . The Protovis team is now developing a new visualization library, D3.js , with improved support for animation and interaction. D3 builds on many of the concepts in Protovis; for more details, please read the introduction and browse the examples . This project was led by Mike Bostock and Jeff Heer of the Stanford Visualization Group , with significant help from Vadim Ogievetsky . We welcome your comments and suggestions .myExperiment
About The myExperiment Virtual Research Environment enables you and your colleagues to share digital items associated with your research — in particular it enables you to share and execute scientific workflows. You can use myexperiment.org to find publicly shared workflows. If you want further access, and the ability to upload and share workflows, you will need to sign up .
Orange - Data Mining Fruitful & Fun
Open source data visualization and analysis for novice and experts. Data mining through visual programming or Python scripting. Components for machine learning.
Principal component analysis - Wikipedia, the free encyclopedia
PCA of a multivariate Gaussian distribution centered at (1,3) with a standard deviation of 3 in roughly the (0.878, 0.478) direction and of 1 in the orthogonal direction. The vectors shown are the eigenvectors of the covariance matrix scaled by the square root of the corresponding eigenvalue, and shifted so their tails are at the mean. Principal component analysis (PCA) is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components . The number of principal components is less than or equal to the number of original variables.Licensing Agreement 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.
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. StarBiogene consists of a web application coupled with several software tools for visualizing/analyzing microarray data. Each tool can be launched directly from a web browser. A sample screenshot is shown below:
Pathguide: the pathway resource list
Complete Listing of All Pathguide Resources Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.
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.
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BioGRID | Database of Protein and Genetic Interactions
BioGRID Version 3.1.86 Release (19,929 New Physical and Genetic Interactions Added) The BioGRID ‘s curated set of physical and genetic interactions has been updated to include an additional 19,929 interactions. These additions bring our total number of non-redundant interactions to 326,306 and raw interactions to 481,026 . New interactions will be added in curation updates on a monthly basis. For a more comprehensive breakdown of our numbers, check out our latest interaction statistics . To download these interactions, visit our download page .Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation . Taverna has been created by the my Grid team and funded through the OMII-UK . The project has guaranteed funding till 2014.
Taverna - open source and domain independent Workflow Management System
Microarrays Import Affymetrix, Illumina, Nimblegen, Agilent, and other platforms. Perform quality assessment, normalization, differential expression, clustering, classification, gene set enrichment, genetical genomics and other workflows for expression, exon, copy number, SNP, methylation and other assays.