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The ultimate goal of this project is to create a Java based DNA viewer that is both flexible and extendable. The initial phase will involve the design and implementation of a framework that can be used either with this project or other similar projects.
A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk
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/
http://www.princeton.edu:80/pr/pwb/01/0326/1b.shtml
http://www.cs.princeton.edu/immsim/
Immsim is an immune system simulation used by Immunology students and researchers. Currently it is being used at Princeton University.
Cooperative effort to develop a Java-XML API and architecture to manage and share health concepts and processes eficiently. Includes a framework to develop healthcare applications (from PDA reminders to hospital information systems) quickly and easily.
The Open Genome Analysis Platform (OGAP) provides an effectual analysis and visualization toolset for a variety of genome, proteomics, and associated data.
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...It converts messages from your hospital information system (HIS) into an easily accessible database for further processing. helese is free open-source software written in Java.
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
The GeneDB project is aiming to develop and maintain a curated database resource for multiple pathogen organisms, both partially and completely sequenced.
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.
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).
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.