Bibliosphere Pathway Edition Bibliosphere Pathway Edition - Offers a unique combination of literature-mining and pathway analysis for molecular biologists
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Bibliosphere Pathway Edition Description

Bibliosphere Pathway Edition - Offers a unique combination of literature-mining and pathway analysis for molecular biologists BiblioSphere offers a unique combination of literature-mining and pathway analysis for molecular biologists interested in gene regulation and biological networks.BiblioSphere uses a comprehensive database of individually modeled relationships between genes, proteins, complexes, cells and tissues together with up-to-date text mining techniques for automated knowledge extraction to allow you to link your data to biological networks in different biological contexts.This Bibliosphere feature results from multiple lines of evidence which are included in it's database.Here are some key features of "Bibliosphere Analysis Kit":· extend biological networks beyond canonical pathway information (metabolic & regulatory)· merge your high throughput, knowledge & genomic based analyses· carry out context-sensitive regulatory pathway analysis· generate experiment-specific pathway variants· link pathways to disease mechanisms & genes· do advanced experimental design· BiblioSphere PathwayEdition offers a unique concept due to...· integration of literature-, genomic-, interaction-, pathway-, and network-databases· gene-gene relationships based on up-to date literature analysis· multiple ontology classifications· expert curated data on gene regulation· assignment of genes to pathways (regulatory & metabolic)· sophisticated network and 3D layout algorithms· algorithms to find optimal pathways (shortest path algorithms)· links to various knowledge resources (e.g. GO, MESH, BINDRequirements:· Java 1.5.0_06 or higher.· Internet connection· 512 MB main memory What's New in This Release: · Free text filter: Allows you to restrict the network to genes which are cited in literature together with a user defined term · Co-citation filter: Allows you to restrict the network according to · syntactic rules of co-citations, · number of co-citations, · grade of interconnection between genes. Biological filter: Allows you to restrict the network to genes which are assigned to the same biological class. Classes are defined by: · Gene Ontology · Molecular function · Biological function · Cellular component · MESH Terms · Chemicals and drugs · Anatomy · Disease · Biological sciences · Analytical, Diagnostic and Therapeutic Techniques and Equipment Tissues · Unique Filter for gene regulators (input genes transcription factors) automatically verified on sequence level. · BiblioSphere PathwayEdition provides statistical analysis of every visible network towards overrepresented and underrepresented gene classes. Statistical analysis is calculated by z-scoring. · BiblioSphere PathwayEdition offers integrated functionality of statistical analysis and filtering: A single click filters a network to those genes which are overrepresented according to GO or MESH class. · The network/pathway construction of BiblioSphere PathwayEdition is dynamic and purely data driven. · Other systems calculate a priori networks with max. 35 nodes, leaving you in the dark on how those networks were derived.

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