Several research groups at the Institute are participating in projects, working groups, or consortia in collaboration with external investigators and organizations. A partial list of these project websites, as well as some ISB-centric project websites, is provided here.

Disease-oriented research

Type 1 diabetes: T1DBase--A bioinformatics resource for Type 1 diabetes researchers
http://t1dbase.org/cgi-bin/welcome.cgi

Huntington's Disease: HDBase--A community website for Huntington's Disease research
http://hdbase.org/cgi-bin/welcome.cgi

Prion Disease: PDDB -- A Comprehensive Transcriptome Resource for Systems Biology Research in Prion Diseases
http://prion.systemsbiology.net

Technology development

NanoSystems Biology Alliance--attacking challenges in cancer and immunology and ultra-rapid disease diagnostics by integrating newly emerging nanotechnology and microfluidics tools with modern cancer biology and immunology.
http://www.caltechcancer.org/

Seattle Proteome Center--development of an array of new, systematic assays to comprehensively study the dynamics of cells in health and disease.
http://www.proteomecenter.org/

Software development

Cytoscape--an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. http://www.cytoscape.org/

Systems Biology Markup Language--is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others.
http://sbml.org/index.psp

RepeatMasker--is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).
http://www.repeatmasker.org/

The Human Proteome Folding Project--one of the greatest challenges facing scientists is to find functions for all of the proteins that are encoded in the Human Genome
http://www.grid.org/projects/hpf/
This project has been undertaken with the assistance of the World Community Grid: www.worldcommunitygrid.org

Systems biology research

Halobacteria--these organisms offer an incredible opportunity to understand at a systems level mechanisms underlying environmental response systems.
http://halo.systemsbiology.net/