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A straight-forward Java implementation of a mixture model with pluggable mixture functions, e.g. a mixture of Gaussian functions. The number and dimensionality of the mixture functions is not limited. All critical calculations are performed in log-space.
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
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.
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A software framework to support distributed evolutionary software development. It dynamically creates a network of nodes that can run a pre-distributed source code (e.g. artificial lifeforms). The results of the calculation will be sent back to the maste
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).
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.
GraphSpider is a pattern matcher which searches parsed text in phrase-structure tree or dependency graph format for syntactic structures matching a set of patterns in MPL, a regexp-like pattern language. Applications: information extraction, text mining.
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.
Decision support tool that assesses breast cancer risk and identifies risk-reducing interventions. Includes web service implementations of established models -- BRCAPRO, Gail, Claus, BCSC Density -- for calculating breast cancer risk.
** 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 OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.
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.