Agilent Technologies Releases Automated Literature Search Tool for Biology Researchers; Free Plug-In to Cytoscape Bioinformatics Platform Speeds Productivity.PALO ALTO, Calif. -- Agilent Technologies Inc. (NYSE NYSE See: New York Stock Exchange :A) today released an automated literature search tool for the multidisciplinary study of biological systems. The tool is available as a free plug-in to Cytoscape 2.1, an open-source bioinformatics platform that enables researchers to form a visual map of complex biological networks, increasing their understanding of molecular pathways and the biological causes of disease. The Agilent Literature Search tool automatically searches for and extracts information from multiple textual databases, such as those of the U.S. Patent Office and the National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988. (PubMed). The plug-in pulls information from these sources and represents it within Cytoscape as a map of the relationships between the biological entities, such as genes and proteins. A microarray or an LC/MS-proteomics experiment can typically result in hundreds of genes and proteins of interest. Biologists can use the new plug-in to avoid the daunting daunt tr.v. daunt·ed, daunt·ing, daunts To abate the courage of; discourage. See Synonyms at dismay. [Middle English daunten, from Old French danter, from Latin task of manually searching for each gene and protein in the scientific literature and patents. "Mining past literature for information about proteins and protein interactions is a critical step for building models of cells," said Trey Ideker, assistant professor at the University of California, San Diego UCSD is consistently ranked among the top ten public universities for undergraduate education in the United States by U.S. News & World Report.[3] It is a Public Ivy. [1] For graduate studies, most of UCSD's Ph.D. , and lead researcher/program manager for the Cytoscape project. "Agilent's Literature Search plug-in for Cytoscape makes automatic literature mining freely accessible to the public, with an algorithmic approach that is first-rate." "Agilent is committed to accelerating the productivity of biologists," said Jim Hollenhorst, director of the Molecular Technologies Laboratory for Agilent Laboratories. "This literature search tool was developed within Labs to facilitate our own research collaborations and has proved very successful for us. We are excited to provide this to researchers everywhere so that they can analyze their own data more effectively and put it into a biological context." 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 Stanford University School of Medicine is affiliated with Stanford University and is located at Stanford University Medical Center in Stanford, California, adjacent to Palo Alto and Menlo Park. on auto-immune diabetes; and the Translational Genomics Research Institute The Translational Genomics Research Institute (TGen (TGen) on melanoma, autism autism (ô`tĭzəm), developmental disability resulting from a neurological disorder that affects the normal functioning of the brain. It is characterized by the abnormal development of communication skills, social skills, and reasoning. and pancreatic cancer pancreatic cancer Malignant tumour of the pancreas. Risk factors include smoking, a diet high in fat, exposure to certain industrial products, and diseases such as diabetes and chronic pancreatitis. Pancreatic cancer is more common in men. . 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. Availability Cytoscape 2.1 is free open-source software free open-source software - free 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. (Due to its length, this URL URL in full Uniform Resource Locator Address of a resource on the Internet. The resource can be any type of file stored on a server, such as a Web page, a text file, a graphics file, or an application program. may need to be copied/pasted into your Internet browser's address field. Remove the extra space if one exists.) Screen shots of Agilent Literature Search Software in action are available at www.labs.agilent.com/research/mtl/projects/sysbio/sysinformatics/ litsearch_screens.html. (Due to its length, this URL may need to be copied/pasted into your Internet browser's address field. Remove the extra space if one exists.) About Cytoscape Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other data. The platform supports gene functional annotations from Gene Ontology (GO) and KEGG KEGG Kyoto Encyclopedia of Genes and Genomes databases, biological models from Systems Biology Markup Language (SBML SBML Systems Biology Markup Language SBML Systematic Botany and Mycology Laboratory SBML Single Borrower, Multiple Lenders ), protein-protein interactions from BIND and TRANSFAC databases. Additional features are available as plug-ins for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. More information about the Cytoscape platform and project is available on the Web at www.cytoscape.org. About Agilent Technologies Agilent Technologies Inc. (NYSE:A) is a global technology leader in communications, electronics, life sciences and chemical analysis. The company's 28,000 employees serve customers in more than 110 countries. Agilent had net revenue of $7.2 billion in fiscal year 2004. Information about Agilent is available on the Web at www.agilent.com. NOTE TO EDITORS: Further technology, corporate citizenship Corporate Citizenship The extent to which businesses are socially responsible in meeting legal, ethical and economic responsibilities placed on them by shareholders. The aim it to create higher standards of living and quality of life in the community in which it operates, while and executive news is available on the Agilent news site at www.agilent.com/go/news. |
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