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Bioclipse: an open source workbench for chemo- and bioinformatics.

Status on November 13, 2012:

UP

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

CSB.DB: A comprehensive systems-biology database.

Status on November 13, 2012:

UP

SUMMARY: The open access comprehensive systems-biology database (CSB.DB) presents results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools, which support insight into lifes complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The central part of CSB.DB, which we describe in this application note, is a set of co-response databases, which currently focus on the three key model organisms, Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels CSB.DB allows to infer hypotheses on the functional interaction of genes. These hypotheses are novel and not accessible through analysis of sequence homology. The data base enables the search for pairs of genes and larger units of genes, which are under common transcriptional control. In addition statistical tools are offered to the user, which allow validation and comparison of those co-responses, which were discovered by gene queries performed on the currently available set of pre-selectable datasets. AVAILABILITY: All co-response databases can be accessed through the CSB.DB web server (http://csbdb.mpimp-golm.mpg.de/).

CRH_server: an online comparative and radiation hybrid mapping server for the canine genome.

Status on November 13, 2012:

DOWN

SUMMARY: CRH_Server is an on line Comparative and Radiation Hybrid mapping Server dedicated to canine genomics. CRH_Server allows users to compute their own RH data using the current canine RH map, and allows comparative dog/human mapping analyses. Finally, it suggests multiple options for storage and queries of the dog RH database. AVAILABILITY: http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html. SUPPLEMENTARY INFORMATION: All information is available at http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html.

Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellula

Status on November 13, 2012:

UP

Cerebral (Cell Region-Based Rendering And Layout) is an open-source Java plugin for the Cytoscape biomolecular interaction viewer. Given an interaction network and subcellular localization annotation, Cerebral automatically generates a view of the network in the style of traditional pathway diagrams, providing an intuitive interface for the exploration of a biological pathway or system. The molecules are separated into layers according to their subcellular localization. Potential products or outcomes of the pathway can be shown at the bottom of the view, clustered according to any molecular attribute data-protein function-for example. Cerebral scales well to networks containing thousands of nodes. AVAILABILITY: http://www.pathogenomics.ca/cerebral

Command line tool for calculating theoretical ms spectra for given sequences.

Status on November 13, 2012:

UP

SUMMARY: Scientists usually want to verify the ion matching process of algorithms that look up peptide sequences in DNA or protein databases. The verification step is often done numerically or visually. Not all search algorithms present the appropriate theoretical spectrum information within their results. Thus, the theoretical spectrum for each result should be calculated from the sequence of the matched peptide. We present an operating-system-independent command line tool for this purpose that can be integrated easily into complex as well as existing environments, and can be used to present the theoretical spectrum to the user in either graphical or tabular format by third party products. AVAILABILITY: The code is available via the website http://www.protein-ms.de.

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