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COB editor is a collaborative editor for biological ontology (e.g., Gene Ontology) building. Building on the idea of modular ontology from KR research, it supports multiple people to work on the same ontology.
The CHIP Cluster Generator attempts to create spatio-temporal cluster data in an automated fashion to help evaluate epidemic detection software. The spatio-temporal data will then be used to determine robustness of spatial detection algorithms.
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Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
PHLIP is a MATLAB centric academic software application for quantification of biofilm structure from confocal laser scanning microscopy (CLSM) data, intended for automated processing and statistical analysis of large data sets produced by CLSM.
BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.
BioGraphNet is a 'sandbox' within BioMOBY, comprising a common standard and collection of services for sharing distributed protein-interaction network information. We now serve several network data types, and encourage others to participate.
The program consgen takes multiple protein structures in PDB format and aligns them using a modified Procrustes method that aims to maximize residue similarity. The principal result is a consensus structure showing residue conservation.
Xipe-Totec is a companion program to the paper
"An application of statistics to comparative metagenomics"
by Beltran Rodriguez-Brito, Forest Rohwer and Robert Edwards
BMC Bioinformatics 2006, 7:162
doi:10.1186/1471-2105-7-162
BioPostgres is a collection of modules that extend PostgreSQL for applications in Computational Biology. These modules implement new datatypes with query operators and other tools for large-scale query and analysis.
Cleaver is a program for comparing restriction endonuclease digests of orthologous DNA sequences from different taxa. It performs virtual restriction digests and searches for endonucleases that cleave DNA fragments from given taxa but not others.
StatGen uses information from a genetic distance matrix or a newick tree to summarize the sequence variation within or between groups of sequences with summary statistics and produce graphical reports of those statistics.
Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program.
It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user
written MAEPlugins, documentation, tutorials, demo data.
The BioSchemas project develops XML schemas for the exchange of biological data e.g. through SOAP-based web services. It is a collaborative and open project intended to increase the interoperability between bioinformatics applications.
UMD Overlapper takes a set of reads and quality data and determines which read pairs plausibly overlap; that is, it determines the pairs of reads containing subsequences that are similar enough that they may have come from overlapping parts of the genome.
In silico experiments. Express Taverna's workflows using XQuery. Integrates with Taverna, provides automated XQuery generation from SCUFL. A standard Taverna processor that runs XQuery. Easy XML transformations inside Taverna workflows.