Showing 68 open source projects for "git:/git.code.sf.net/p/docfetcher/code"

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  • 1
    CellCompiler
    The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
    Downloads: 0 This Week
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  • 2

    TUIT

    Taxonomic Unit Identification Tool

    For the installation instructions please see Wiki page: https://sourceforge.net/p/tuit/wiki/ IMPORTANT: since version 1.0.4.0 TUIT allows to select RDP-like formatted output to improve out of the box compatability with tools, that assume RDP-formatted input. A new field has been added to the properties.xml, please make sure to update it to contain <OutputFormat format="tuit"/> or <OutputFormat format="rdp"/> in the <BLASTNParameters> section.
    Downloads: 0 This Week
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  • 3
    CIG-P

    CIG-P

    CIG-P is a simple yet flexible data visualization tool

    CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset.
    Downloads: 0 This Week
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  • 4
    GenoCAD
    ...This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
    Downloads: 1 This Week
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  • Unrivaled Embedded Payments Solutions | NMI Icon
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  • 5

    IQuant

    A pipeline for quantitative proteomics based upon isobaric tags

    ...This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".
    Downloads: 0 This Week
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  • 6

    NIKS

    NIKS (Needle in a K-stack) - detection of mutations in NGS data

    To get access to the code, please check it out with svn as described in the code section.
    Downloads: 0 This Week
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  • 7
    This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
    Downloads: 7 This Week
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  • 8
    Seqshell

    Seqshell

    A JAVA GUI for performing the function of Tophat and Cuffdiff

    ...This program will save the output into separate folders. An alert email will be sent to your email address when the job is done. (You will need to modify the source code to change the content to meet your special needs) Run-time information will be displayed in a JAVA output window.
    Downloads: 0 This Week
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  • 9
    The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. !!!! Important Announcement !!!! We have moved the curation and development of Systems Biology Ontology (SBO) to a git-hub repository https://github.com/EBI-BioModels/SBO. Hence, this SourceForge SBO project has also been retired. Please use the Git-Hub issue tracker https://github.com/EBI-BioModels/SBO/issues to request the addition of new terms.
    Downloads: 0 This Week
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  • Network Performance Monitoring | Statseeker Icon
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  • 10
    Javamony

    Javamony

    A Student's Approach to the Phylogenetic Problem

    ...Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve fundamental problems in phylogenetics. Therefore, for my own educational benefit, all code is original. Of course, there are probably a good deal of mistakes as well. I distribute Javamony, as I did Pysimony, hoping that it will be of educational value to someone else or at least vaguely amusing. Upcoming features will be: - Support for Amino Acid sequences - Support for additional file formats (e.g. Nexus) - Multithreading - Additional scoring methods (e.g. maximum likelihood)
    Downloads: 0 This Week
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  • 11

    samsn

    A tool to handle multi-stage mass spectrometry data

    The source code for SAMSN can be found in github at https://github.com/miquelrojascherto/samsn
    Downloads: 0 This Week
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  • 12
    This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted.
    Downloads: 0 This Week
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  • 13
    A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions
    Downloads: 1 This Week
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  • 14
    CALBC
    The code here is a parser for CALBC corpus into Java object.
    Downloads: 0 This Week
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  • 15

    clinicalStudyTracker

    Clinical study tracker tracks case study members through activities.

    Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.
    Downloads: 0 This Week
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  • 16
    Scanner based Bioparsers
    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.
    Downloads: 0 This Week
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  • 17
    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.
    Downloads: 0 This Week
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  • 18
    FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.
    Downloads: 0 This Week
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  • 19
    The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
    Downloads: 0 This Week
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  • 20

    ChiBE

    Chisio BioPAX Editor

    ...ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes. !!! For latest version, please see !!! http://code.google.com/p/chibe
    Downloads: 0 This Week
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  • 21
    This project has moved to http://code.google.com/p/synthetic/
    Downloads: 0 This Week
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  • 22
    MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
    Downloads: 0 This Week
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  • 23
    Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.
    Downloads: 0 This Week
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  • 24
    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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  • 25
    Testing tools source code of the Integrating the Healthcare Enterprise (IHE) Cross-Enterprise Document Sharing for Images (XDS-I) Integration Profile
    Downloads: 0 This Week
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