Search Results for "java-gnome" - Page 16
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Showing 826 open source projects for "java-gnome"
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Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)
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3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
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Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.
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A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
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OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
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CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
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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
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Contemplate is a bioinformatics tool for finding cis-regulatory modules (CRMs) in noncoding genomic regions using comparative sequence data.
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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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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).
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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).
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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.
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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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NeuroBees
Multi-agent algorithm
Software tool (NEURON, Python, C++) based on the multi-agent Bee algorithm and aiming at multi-parametric optimization. 2 versions : - Link with NEURON (need download and install NEURON and NEURON-python) - Autonomous, with two types of neurones (Izhikevich and hodgkin huxley) -
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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.
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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.
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PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
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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.
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Volumetric file viewer for the human brain. Easy, powerful and flexible fMRI/MRI brain research and clinical neuro-surgery tool. Using state of the art open VTK 3D library, the proven Qt GUI toolkit, coded in Python.
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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.
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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.