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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
ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
RmscopII is a Tcl/Tk script responsible to redirect protein structure files (PDB files) or RasMol scripts to multiple RasMol sessions. It can be used as a web browser helper application or as a standalone program.
BASE is a database server to manage (locally) the massive amounts of data generated by microarray analysis. It handles biomaterials, raw data and images, and provides integrated and plug-in-able normalization, data viewing and analysis tools.
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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.
...BioSap selects unique oligos for microarrays by detecting user-defined parameters and running parallel instances of Featurama and Blast on compute engines, producing xml output files.
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/
The goal of the GeneJock Project is to produce an Open Source DNA sequence editor that is cross-platform, full featured and extensible. A second goal (which may become more important), is the development of a C++ library for biological data manipulation.
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Biological research groups need to store and analyze large amounts of diverse data. LISA (LabInfoSystem:) stores this information in an easily accessible customizable web-based database. LISA requires PHP4 and MySQL. Keywords: Structural Biology, Genomics
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.
eagle-i is an ontology-driven, RDF-based distributed platform for creating, storing and searching semantically rich data. eagle-i is built around semantic web technologies and adheres to linked open data principles.
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.
A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies.
Website:
http://bioinformatics.ubc.ca/atlas
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