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/


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://www.BioTapestry.org
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://magnet.systemsbiology.net/software/Dizzy/
http://magnet.systemsbiology.net/

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

Mogul: transcription factor binding site prediction multi-algorithm server
http://xerad.systemsbiology.net/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://magnet.systemsbiology.net/software/Pointillist/
http://magnet.systemsbiology.net/

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

ftp_update_NCBI_databases

ProbCD:
http://xerad.systemsbiology.net/ProbCD/

Simcluster:
http://xerad.systemsbiology.net/simcluster/