With the Agilent Literature Search tool, researchers enter the names of all genes of interest, along with keywords that describe the types of relationships being looked for. The plug-in searches accessible databases and generates a computational representation of gene/protein associations grouped into a network that biologists can see and manipulate within Cytoscape. This network view includes a node represented by a geometric shape for each gene and protein, and links to indicate relationships. Each node includes hyperlinks to descriptions and articles relevant to that gene or protein.
Agilent Laboratories is using the plug-in as part of its collaborations with two other organizations on systems biology projects: the Stanford University School of Medicine on auto-immune diabetes; and the Translational Genomics Research Institute (TGen) on melanoma, autism and pancreatic cancer. Labs researchers are focusing on proteomics and metabolomics for these diseases as a complement to Labs collaborators' work in genomics. Using Labs' systems biology informatics prototypes, Labs researchers have built qualitative biological models based on experimental data, scientific knowledge from published papers and curated biological network databases. This shared, multi-disciplinary knowledge provides a more comprehensive view of disease.
Cytoscape 2.1 is free open-source software. The Agilent Literature Search tool is currently available as a free but unsupported plug-in to Cytoscape. Both are downloadable at www.cytoscape.org. Agilent's plug-in and additional information are available at www.labs.agilent.com/research/mtl/projects/sysbio/sysinformatics/download.html.
Screen shots of Agilent Literature Search Software in action are available at www.labs.agilent.com/research/mtl/projects/sysbio/sysinformatics/litsearch_screens.html.
Cytoscape is a bioinformatics software platform for visualizing molec