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Best of Show: Life Science Software & Informatics

June 13, 2007

Pathways Analysis
WinnerIPA 5.0, a software application from Ingenuity, enables three pivotal capabilities: biomarker analysis, molecular toxicology analysis, and interactive signaling and metabolic pathways. IPA-Biomarker allows researchers to rapidly identify and prioritize the most biologically relevant and plausible biomarker candidates in a genomic or proteomic dataset, based on contextual information connecting those biomarkers mechanistically to disease, and identifying those detected in bodily fluids. With the newly added toxicology content and Toxicology Analysis workflow, even non-experts can rapidly assess whether their candidate compound is associated with a particular toxicological profile and understand the underlying mechanism of toxicity. Finally, the Interactive Signaling and Metabolic Pathways solution lets researchers extend beyond boundaries of the classical, well-characterized signaling and metabolic pathways.
Product: IPA 5.0
Company: Ingenuity
Available: Now
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Natural Search
Linguamatics I2E technology combines natural language processing (NLP), intuitive reporting, a search engine approach, and the ability to plug in domain knowledge such as ontologies, taxonomies, and thesauri to enable users to rapidly extract relevant facts and relationships from large document collections, including internal research reports, journal articles, abstract databases such as Medline, patents, and newsfeeds. Linguamatics’ flexible, real-time NLP enables rapid development and execution of queries using a highly intuitive user interface to get straight to relevant answers.
Product: 12E v 2.9
Company: Linguamatics
Available: Now
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Fast & Easy Typing
CLC MLST Module is a plug-in to the CLC Combined Workbench and CLC Gene Workbench. The module is designed to make it easy and fast to handle data when doing multi-locus sequence typing (MLST), a method used for typing bacterial isolates. It uses 6-11 housekeeping genes which makes the method amenable to automatic sequencing machines. MLST is a fast and unambiguous way of typing bacteria. The CLC MLST Module is integrated with online public databases for MLST schemes and compares the new isolate with already existing sequence types.
Product: MLST Module v 1.0
Company: CLC Bio
Available: June
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Content-Based Support
MarkLogic Server 3.1 is the latest version of the company’s leading XML content server, a platform that provides a set of services used to build applications and support business processes based on content. MarkLogic Server lets customers load, query, manipulate and render content to unlock its full value. Version 3.1 includes more powerful search functionality, innovative XML classifier allowing businesses to classify a document based not just on its text but also by understanding its XML structure, point-in-time queries, XML lexicons, and search performance enhancements.
Product: MarkLogic Server 3.1
Company: MarkLogic
Available: Now
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Build Literature Reports
ActiveMotif’s AKS2 is a knowledge management software system that analyzes and organizes biochemical and biomedical literature. AKS2 extracts key biological or biomedical concepts from the abstracts, analyzes all the relationships between the concepts, and presents the results in an easy to understand summary report. AKS2 can be applied to disease-based research to aid in the finding of related drugs, genes, etc. in published abstracts, and can enable researchers to explore and discover relationships in the literature that are not easily uncovered with traditional information retrieval approaches.
Product: AKS2
Company: ActiveMotif
Available: Now
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Patent & Sequence Search
GenomeQuest 4.0 is a web application for sequence search analysts in biotech law and research. It is composed of three functional elements integrated under a browser-based interface: data content, consisting of approximately 127 million DNA sequences and associated annotations, and more than 49 million DNA sequences with associated patent documentation; a suite of search strategies; and a query result viewing and filtering capability. GenomeQuest has a published API, and complies with Web 2.0 standards. (See Bio•IT World, Nov. 2006.)
Product: GenomeQuest 4.0
Company: GenomeQuest
Available: Now
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