Showing 382 open source projects for "java swing application"

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  • 1
    Seqshell

    Seqshell

    A JAVA GUI for performing the function of Tophat and Cuffdiff

    Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email...
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  • 2
    Based on HL7 v.2.3.1 Orders & Results Reference Information Model (RIM)s, The project is NOT a CPOE per-se. Instead, the project provides "applications" that allow EHR's to perform Outpatient Orders and Results via HIE, and collect these into their EHRs to feed the EHR "CPOE module / section" (ex. with prescribed drugs, ordered labs and results, ....) The first module in the project was the "ePrescribing application"; certified by RxHub and SureScripts back in 2007. New...
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  • 3
    Onco-STS

    Onco-STS

    A web-based Laboratory Information Management System

    Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations,...
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  • 4
    BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
    Downloads: 1 This Week
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  • 5
    GeneNetWeaver
    GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.
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  • 6
    CloudAligner
    A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
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  • 7
    AgED

    AgED

    AgED - Analysis given Experimental Data

    AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments. Elliptic Fourier Descriptors have been applied in a large range of applications in...
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  • 8

    VSMOExp

    Ontologies, which are made up by standardized and defined controlled

    Ontologies, which are made up by standardized and defined controlled vocabulary terms and their inter-relationships, are comprehensive and readily searchable repositories for knowledge in a given domain
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  • 9
    Timina is a Java web-based application for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences.
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  • 10
    Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.
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  • 11
    TreeLiker

    TreeLiker

    TreeLiker is a collection of fast algorithms for working with complex

    TreeLiker is a collection of fast algorithms for working with complex structured data in relational form. The data can, for example, describe large organic molecules such as proteins or groups of individuals such as social networks or predator-prey networks etc. The algorithms included in TreeLiker are unique in that, in principle, they are able to search given sets of relational patterns exhaustively, thus guaranteeing that if some good pattern capturing an important feature of the problem...
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  • 12
    BioGenie

    BioGenie

    BioGenie is presented as a complete package for Biological solutions.

    Bioinformatics as an emerging research area spreads out many challenges to both the Bioinformaticists and the Bioinformaticians. BioGenie is presented as a complete package for tackling these challenges. Accommodating all three platforms, that is, a desktop application, a web application and a mobile (android-based) application, BioGenie outperforms all existing softwares engineered to assist heavy and complex computations. The GUI is very well-designed guiding the user technically with ease.
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  • 13
    NMR Spectroscopy tools. See http://connjur.uchc.edu
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  • 14
    Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files
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  • 15
    Ferox

    Ferox

    Ferox - Sequence Alignment with Fuzzy K-mers

    Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file.
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  • 16
    Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.
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  • 17
    CUO

    CUO

    Codon Usage Optimizer

    CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during...
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  • 18
    sigTOOL
    sigTOOL provides a user-extendable signal analysis environment for processing electrophysiological data within MATLAB. Neuron spike-train, + spectral and time-domain analyses are built in. See http://dx.doi.org/10.1016/j.jneumeth.2008.11.004
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  • 19
    The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.
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  • 20

    Face Detect (JavaCV)

    Face Detection and Facial Feature Extraction using JavaCV

    A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition.
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  • 21
    FastMap is Java based software that performs quantitative trait locus mapping for gene expression data (eQTL Mapping).
    Downloads: 1 This Week
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  • 22
    Screening Assistant 2
    ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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  • 23

    JGBA

    This project is a genome browser and annotation tool in java.

    This project is a genome browser and annotation tool in java.
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  • 24
    (AB)² Simulation

    (AB)² Simulation

    Simulation for Physics / Bilogics Systems

    Supports flow Simulation for Physics and Meso-Compartimental Simulations for Biological Systems. Uses a Container-Flow based System.
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  • 25

    iPiG

    Integrating PSMs into Genome browser visualisations

    iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please...
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