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This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
The MML Framework is a temporal-spatial biological model representation language. The MML Project provides the application tool set which facilitates the goals of representing biological models using the MML specifications.
Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.
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XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.
The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers
The goal of this project is to make a biologic pathway simulation / emulation application. The ultimate goal is to feed different file types to the application and configure a pathway and its behaviour.
SeEvolution is the first application that lets you see the effects of mutation events on 3D models of chromosomes. It takes you on a journey through time, showing you the changes that are necessary to go from the genome of an organism to another.
Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.
SCAMPI is designed to rapidly detect molecular markers in silico through sequence comparison. For this purpose it creates a unique workflow integrating third party tools like NCBI Blast or Primer3.
Data and animal management software for large-scale phenotype screening Used by GNF for mouse ENU mutagenesis project. Data visualization & analysis, animal husbandry management, & automated QTL mapping. Usable as stand alone animal husbandry system.
A simple Javaapplication for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.
Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.
OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing complex queries against the Gene Ontology Database.
EZMWeb is an open source web-based bioinformation integration and search system. Users can search the integrated enzyme information.It implements the analysis of correlation between different enzymes,gives its visualized results through java applet.
Re-searcher is the system for recurrent psiblast searches. It enables timely detection of new proteins on the protein sequence databases. Searches can be done on a local server or at NCBI. It has a user-friendly web interface.
The TandemSearcher is a Java based application for searching for tandem repeats in the DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).
Referent Tracking (RT) is a novel approach to store data in electronic (health) records by referring to real world entities by means of a unique ID. The RT System is a back-end that uses RDF as a representation, but adds to it a referential semantics.
The Systems Biology Research Tool (SBRT) is both an application and an application programming interface (API) intended to facilitate the computational aspects of systems biology.