Showing 331 open source projects for "void based linux"

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  • 1
    Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
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  • 2

    HomSI

    Homozygous Stretch Identifier from next-generation sequencing data

    In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation and several recessive disease genes have been discovered with the help of this technique in consanguineous families. The researchers typically use SNP arrays to determine the...
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  • 3
    OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability...
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  • 4
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    Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the...
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  • 5
    Luscinia is a program for archiving and analyzing field sound recordings (especially of animals). It incorporates an interface to a database, spectrogram measurement algorithms, sound comparison algorithms, and statistical analysis.
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  • 6
    GenoCAD
    GenoCAD is a CAD software for synthetic biology. 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: 3 This Week
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  • 7
    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. Publication: CIG-P: Cicular Interaction Graph for...
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  • 8
    The Investigation/Study/Assay (ISA) Infrastructure is the first pilot-stage freely available software suite that 1. assists in the reporting and local management of experimental metadata and facilitates submission to international public repositories.
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  • 9

    IQuant

    A pipeline for quantitative proteomics based upon isobaric tags

    IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system.
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  • 10
    Matchup

    Matchup

    Bioinformatics tool for universal primers and group-specific probes

    Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment.
    Downloads: 0 This Week
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  • 11

    SSWAP

    Simple Semantic Web Architecture and Protocol

    SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform that uses reasoning to semantically integrate disparate data and services on the web. Running live at http://sswap.info.
    Downloads: 0 This Week
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  • 12
    coalescent

    coalescent

    Software tool for Research in Computational Population Genetics

    Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration & recombination. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/COALESCENT
    Downloads: 0 This Week
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  • 13
    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
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  • 14
    The Diffraction Image Experiment Repository (DIMER) is an online archive for diffraction experiments, providing secure storage during analysis and publishing of experiments so they can be linked to, searched, and integrated into other databases.
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  • 15
    cy2fluxviz

    cy2fluxviz

    cy2fluxviz : Cytoscape 2 plugin for flux distribution visualization

    cy2fluxviz - Cytoscape 2 Plugin for the visualization of flux distributions in networks. Latest releases from https://github.com/matthiaskoenig/cy2fluxviz
    Downloads: 0 This Week
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  • 16
    AutoMATRIX is a tool to predict key transcription factors in microarray experiments.
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  • 17
    Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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  • 18
    Topiary Explorer
    TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.
    Downloads: 1 This Week
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  • 19

    Cylindrical BLAST Viewer

    Alignments in Rotating Cylinder / 3D

    3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App
    Downloads: 0 This Week
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  • 20
    SecStAnT

    SecStAnT

    Secondary Structure Analysis Tool for data selection and statistics

    SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only...
    Downloads: 0 This Week
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  • 21

    Systems Glycobiology

    Glycosylation Network Analysis Toolbox (GNAT)

    GNAT is an open source, platform-independent MATLAB based toolbox. It is written in MATLAB and Java. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms. The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]).
    Downloads: 0 This Week
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  • 22

    MendelScan

    Variant scoring and linkage mapping for family exome sequencing

    MendelScan is a tool for prioritizing candidate variants in family-based studies of inherited disease.
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  • 23

    locusvu

    Tool for genomics;automates data retrieval from db;enables workflows

    LocusVu is a novel Java based software tool that accepts a list of genomic loci (positions on the chromosome) as input and automates fetching of related information (cytogenetic band, gene name, OMIM data etc.) from public databases such as the UCSC genome browser database. It then enables multiple workflows on the retrieved results, like comparing multiple datasets (comparative genomics), viewing neighboring genes for a loci from within the tool itself, or graphically representing these...
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  • 24

    BioDare

    BioDare is Biological Data Repository focused on timeseries data

    BioDare (Biological Data Repository) was developed under the multi-site ROBuST project (http://hallidaylab.bio.ed.ac.uk/ROBuST.html) to support data exchange inside the project. It is a web application which allows data-sharing (including public dissemination), data-processing and analysis, with the main focus on time-series data produced in circadian experiments. The main features of BioDare are: - an online repository for experimental data accompanied by extensive...
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  • 25

    MatrixMaker

    Custom substitution matrix creator

    Create custom substitution matrices for BLAST protein search. Easy to use GUI based application.
    Downloads: 0 This Week
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