Showing 86 open source projects for "php/java/fastcgi/fcgiinputstream"

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  • 1
    TreeBASE is a database and web front end that stores phylogenetic trees and the data matrices used to generate them. The current iteration comprises a complete rewrite of the schema and web layer, and will include a web services layer.
    Downloads: 0 This Week
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  • 2

    [DEPRECATED] Gene Ontology

    The DEPRECATED legacy location of the GO, see http://geneontology.org

    The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads.
    Downloads: 0 This Week
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  • 3

    MatrixMaker

    Custom substitution matrix creator

    Create custom substitution matrices for BLAST protein search. Easy to use GUI based application.
    Downloads: 1 This Week
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  • 4

    WHATCH'EM

    WHATCH’EM simulates mosquito container water temperature

    WHATCH’EM simulates the highly non-linear manner in which atmospheric conditions and container characteristics determine water temperature and height, leading to results that are not always intuitive and likely not simulated by simpler empirical models. WHATCH’EM has the capacity to be utilized for other mosquitoes and other container-inhabiting arthropods.
    Downloads: 0 This Week
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  • 5
    SeqWare has moved to GitHub, see https://github.com/SeqWare SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
    Downloads: 0 This Week
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  • 6
    An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.
    Downloads: 0 This Week
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  • 7
    Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.
    Downloads: 0 This Week
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  • 8
    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.
    Downloads: 0 This Week
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  • 9
    A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions
    Downloads: 3 This Week
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  • 10
    The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.
    Downloads: 0 This Week
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  • 11
    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/)
    Downloads: 0 This Week
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  • 12
    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.
    Downloads: 3 This Week
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  • 13
    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
    Downloads: 13 This Week
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  • 14
    Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
    Downloads: 0 This Week
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  • 15
    ProteoConnections
    ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications.
    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
    ProPHAnE: Proteomics result Pruning and Homology group Annotation Engine A perl script based workflow for annotation of protein data coming from the 'Mascot' (Matrix Science) and 'Scaffold' (Proteome Software) pipeline. Coming soon: Prophane 2, "a much improved and extended version of Prophane based on HTML5, PHP and MySQL. Most importantly, the pipeline includes now functional predictions on profile Hidden Markov models (HMMs), is fully-automated, and can be controlled via a highly intuitive and user-friendly interface." (Stephan Fuchs)
    Downloads: 0 This Week
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  • 18
    PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.
    Downloads: 1 This Week
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  • 19
    Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)
    Downloads: 5 This Week
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  • 20
    IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
    Downloads: 0 This Week
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  • 21
    CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
    Downloads: 0 This Week
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  • 22
    DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).
    Downloads: 3 This Week
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  • 23
    Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.
    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
    A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism
    Downloads: 0 This Week
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