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HeliconiusDB is a project to develop a database schema and web-based software tools for the study of Heliconius butterflies (and other organisms) in evolutionary biology.
Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.
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SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.
Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.
IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
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PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery.
Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996
Author's thesis - http://openwetware.org/wiki/Kalidas_Y
JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.
It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.
A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.
Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .
An open source MAGE-TAB database and import/export tools to read and write MAGE-TAB formatted data. MOLGENIS is being used to autogenerate it. Import/export tools creation is in progress.
BiVeS - Biochemical Model Versioning System BiVeS is a tool based on the XMLDiff algorithm. You can think of it as a kind of SVN for models with biological or chemical background encoded in XML.
Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
DIVAT (Diagnostic Immunohistochemistry Visualization and Analysis Tool) is designed to graphically analyse comprehensive data sets of immunohistochemical results as those used in clinical diagnostic pathology.