SEAMLESS DATABASE AND SOFTWARE INTEGRATION FRAMEWORK

Gaggle website:
http://gaggle.systemsbiology.org

DATA GENERATION SOFTWARE

ISB proteomics pipeline:
http://www.proteomecenter.org/software.php
http://sashimi.sourceforge.net/
http://peptideprophet.sourceforge.net/
http://proteinprophet.sourceforge.net/

ISB microArray pipeline:
http://db.systemsbiology.net/software/ArrayProcess/
http://db.systemsbiology.net/software/VERAandSAM/

DATA MANAGEMENT SOFTWARE

The Systems Biology Experiment Analysis Management System (SBEAMS):
http://www.sbeams.org/

Juvenile Diabetes Research Foundation's Center for Bioinformatics at ISB
http://www.T1DBase.org/

Research Community Database for Huntington's Disease
http://HDBase.org/

DATA VISUALIZATION AND ANALYSIS SOFTWARE

BioSap (Blast Integrated Oligonucleotide Selection Accelerator Package):
http://biosap.sourceforge.net/

BioTapestry (for editing and visualization of genetic networks in developing embryos)
http://labs.systemsbiology.net/bolouri/software/BioTapestry/
http://magnet.systemsbiology.net/

Cytoscape (for data integration, network visualization, and analysis):
http://db.systemsbiology.net/cytoscape/plugins/
http://www.cytoscape.org/

Dizzy (simulation of deterministic and stochastic kinetics in biochemical networks):
http://labs.systemsbiology.net/bolouri/software/Dizzy/
http://magnet.systemsbiology.net/

The GESTALT Workbench for genomic sequence analysis:
http://db.systemsbiology.net/gestalt/

ISB's de novo protein structure prediction server:
http://lanl.bakerlab.org/submit.jsp

Mogul: transcription factor binding site prediction multi-algorithm server
http://labs.systemsbiology.net/bolouri/Mogul/
http://magnet.systemsbiology.net/

The Multiobjective Analyzer for Genetic Marker Selection (MAGMA):
http://snp-magma.sourceforge.net/

Pointillist (tools for data integration and networkmodel building)
http://labs.systemsbiology.net/bolouri/pointillist.html
http://magnet.systemsbiology.net/

RepeatMasker (screens DNA sequences for interspersed repeats): http://www.repeatmasker.org/

BIOINFORMATICS, COMPUTATIONAL STRUCTURAL BIOLOGY

DBAli. A Database of Structure Alignments
http://salilab.org/DBAli/

EVA continously and automatically analyses protein structure prediction servers in 'real time'
http://salilab.org/~eva/

IceDB - Integrated Consortium Experimental Database
http://www.nysgxrc.org/nysgrc/icedb.html

A Structural Database of Aligned Ligand Binding Sites
http://alto.compbio.ucsf.edu/ligbase/

Database of Comparative Protein Structure Models
http://modbase.compbio.ucsf.edu/modbase-cgi-new/index.cgi

A Comprehensive Database of Structurally Defined Interfaces in Proteins
http://alto.compbio.ucsf.edu/pibase/

Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints
http://salilab.org/modeller/modeller.html

Modeling of Loops in Protein Structures
http://alto.compbio.ucsf.edu/modloop//modloop.html

Server of Comparative Protein Structure Modeling
http://alto.compbio.ucsf.edu/modweb-cgi/main.cgi

LS-SNP: Large Scale Human SNP Annotation
http://alto.compbio.ucsf.edu/LS-SNP//

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