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GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features
The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
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This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.
A wrapper for Apache UIMA (http://incubator.apache.org/uima/) that connects to the Open Biomedical Annotator (OBA) rest service from the National Center for Biomedical Ontology (http://www.bioontology.org/wiki/index.php/Annotator_User_Guide).
RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).
Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME data mining platform, providing additional nodes for reading, processing and visualizing sequence information.
Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
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Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.
PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
GenoGUARD is a DNA sequence screening software that implements the best match method recommended by the federal government to detect the presence of biosecurity threats in synthetic DNA orders.
HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.
GEAX is a Java application used to visualize and analyze cross-species gene expression microarray data.The program allows comparisons based on fold-change, p-value, quantile matching, or a combination of criteria.
TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
VI Compute Server (VICS) is a collection of grid-enabled bioinformatics tools with HTTP (browser) and Web Services (scriptable) interfaces. JCVI VICS is licensed under the Perl Foundation Artistic License 2.0.
Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.