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Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.
GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
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Unlike spreadsheets or clunky PSAs, Float offers a clear, centralized view to schedule teams, plan capacity, estimate work, and track margins in real-time so that you can keep your people and profits on track.
For interactive clustering and visualization, Cluster and TreeView by Mike Eisen are great. XCluster by Gavin Sherlock solves the problem of clustering large numbers of files. Now slcview allows you to script generation of cluster and tree images.
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OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.
BioQuery is a bioinformatics tool that acts as a query builder for genetic, protein, publication, and other biomedical databases. BioQuery is also an update service that periodically resubmits saved searches and sends you new data as it is found.
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Cytoscape is a software platform for computational biology and
bioinformatics, useful for integrating data, and for visualizing and
performing calculations on molecular interaction networks
A python library for handling and analyzing biological sequence annotations as described in GFF files (General Feature Format). The library is intended to be a complete framework for this file format.
SPedit is a new curation environment for the Swiss-Prot and TrEMBL databases. For more information about these databases see http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
Shred is a fast and scalable faceted data browser. The application allows users to navigate the data in an intuitive way and by any path they wish to take. Immediate intuitive information regarding the data is apparent.
BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.
Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells
** IMPORTANT NOTICE ** 10 Feb 2006 Code is being moved to the SMI subversion repository (http://smi-protege.stanford.edu/svn/owl/trunk/) Project will continue to be open source. ProtegeOWL info at: http://protege.stanford.edu/overview/protege-owl.html
The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.
Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies.
It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements.
Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).
The Helmholtz Open Bioinformatics Technology (HOBIT) aims to improve the interconnection of bioinformatic resources based on Web Services and community standards for data representation to facilitate open exchange of biological information.
The Open Genome Analysis Platform (OGAP) provides an effectual analysis and visualization toolset for a variety of genome, proteomics, and associated data.
PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format