Showing 802 open source projects for "java open source"

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  • 1
    Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates...
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  • 2
    SBMLforge is a tool that enables the user to convert and merge KEGG metabolic and signaling pathways (KGML format) to create a single SBML pathway model.
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  • 3
    OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.
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  • 4
    Annotare is a tool for annotating Microarray and Gene Expression data. It will help a bench biologist construct a MIAME-compliant MAGE-TAB file.
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    AI-First Supply Chain Management

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  • 5
    Extension of the DAS server MyDAS to support writeback capabilities.
    Downloads: 0 This Week
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  • 6
    JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).
    Downloads: 0 This Week
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  • 7
    DEPRECATED PROJECT! SolexaTools is becoming the SeqWare project (http://seqware.sourceforge.net) to better reflect its expanded sequencer support. Please go to this project page for code and documentation.
    Downloads: 0 This Week
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  • 8
    ZAE is a Zoomable multiple sequence Alignment Editor
    Downloads: 0 This Week
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  • 9
    Quantitative Evalution of Blush: a program to assess myocardial reperfusion on coronary angiograms. This program calculates a value that can be used for risk classification of STEMI patients or as a surrogate endpoint in clinical trials.
    Downloads: 0 This Week
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  • 10
    LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal. !!!!!! PROJECT MOVED TO GITHUB !!!!!! Please check out http://raphaelbauer.github.io/lajolla/
    Downloads: 0 This Week
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  • 11
    This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
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  • 12
    A sorting tool for Bioinformatics, Biochemistry and/or Molecular biology. This sorts nucleotide sequences aligned using "ClustalW". There may be a way to do this w/ original app, but someone I know couldn't figure out how - thus this project was born
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  • 13
    This project contains a set of files (Perl, Java, and an R package) used to perform analysis of oligonucleotide signatures in metagenomes and genomes.
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  • 14
    Multimedia, Medicine Computing and BioInformatics --- This Project is a collection of several subprojects for Solutions in Multimedia, Medicine Computing and BioInformatics focus on video-,EEG- & Multichanels-signals developped in Web 20, J2EE.
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  • 15
    JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.
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  • 16
    The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.
    Downloads: 3 This Week
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  • 17
    A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.
    Downloads: 0 This Week
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  • 18
    J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).
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  • 19
    Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them
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  • 20
    CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.
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  • 21
    This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
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  • 22
    ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.
    Downloads: 0 This Week
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  • 23
    Testing tools source code of the Integrating the Healthcare Enterprise (IHE) Cross-Enterprise Document Sharing for Images (XDS-I) Integration Profile
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  • 24
    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.
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  • 25
    RepeatMap is a collection of time/memory efficient algorithms and data structures to enable rapid counting & querying of kmers (sequences of length k) counts in large sequences. E.g. a query could be "how many times is 'ACGTCATGGTAC' found in a genome."
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