Showing 891 open source projects for "sandbox:/mnt/data/project_plan.pod"

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  • 1
    OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.
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  • 2
    Hyperballs
    We present an improved ball and stick representation called HyperBalls. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of non covalent bonds and takes advantage of GPU capabilities. HyperBalls are now fully integrated into the UnityMol software and are actively developed in that context. You will find the most up-to-date versions of the shaders in the http://unitymol.sourceforge.net project.
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  • 3
    The project would include the development of XUL, CSS and Javascript components to assist biologists in sequence manipulations, data mining, data analysis, etc.).
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  • 4
    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. The method details are explained in the following paper: Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. ...
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  • 5

    SVGMap

    Open source web tool to help you in the data visualisation

    SVGMap is an open source web tool to help you in the visualisation of experimental data associated to some graphical representation. More at : 1. Project website http://bg.upf.edu/svgmap 2. Reference : Xavier Rafael-Palou, Michael P. Schroeder, and Nuria Lopez-Bigas SVGMap: configurable image browser for experimental data Bioinformatics 2011 : btr581v1-btr581.
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  • 6
    PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.
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  • 7
    Shrec is a bioinformatics tool for error correction of HTS read data.
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  • 8
    Diversity Maps
    Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals.
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  • 9
    The Parenthesis Classifier takes the contents of a set of parentheses and classifies it into one of several categories. It includes a parenthesized-data extractor and the classifier.
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  • 10
    RepMiner takes a graph theory approach to the classification and assembly of the repetitive fraction of genomic sequence data. Sequence lengths analyzed by RepMiner can range from full length transposable elements to low coverage sample sequence data.
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  • 11
    This is a c-library that provides tools for advanced analysis of electrophysiological data. It features denoising, unsupervised classification, time-frequency analysis, phase-space analysis, neural networks, time-warping and more.
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  • 12
    GLIEP
    A plugin for the VANTED system, called Glyph-based Link Exploration of Pathways (GLIEP). It helps to guide the navigation and exploration process of interconnected pathway visualization as well as insight into the overall interconnectivity.
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  • 13
    ESMERALDA is a development environment for statistical recognizers operating on sequential data (speech, handwriting, biological sequences). It supports continuous density Hidden Markov models, Markov chain (N-gramm) models, and Gaussian mixture models.
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  • 14
    Populating Research Data Australia (RDA) with collection descriptions of Australian-related biomolecular data held in the European Bioinformatics Institute (EBI) databanks. This project is ANDS-funded through the DIISR Education Infrastructure Fund.
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  • 15
    Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.
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  • 16
    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.
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  • 17
    The TIMTAM (Target Information Management Tracking And More) system implements a secure knowledgebase supporting the management, tracking, and analysis of experimental data associated with structural biology projects.
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  • 18
    Databases to aid Metabolomics projects providing storage functionality for raw and preprocessed data, and integration with existing data analysis environments.
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  • 19
    SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk
    Downloads: 0 This Week
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  • 20
    IMPACT

    IMPACT

    Integrated Multiprogram Platform for Analyses in ConTest

    Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003
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  • 21
    PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
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  • 22
    Katsura: Metabolic Pathway Analysis Tool
    The Katsura tool overlays microarray gene expression data, proteomics, and similar biological data onto metabolic pathways. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]
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  • 23
    ODD is a tool for optimal domain decomposition of atomic structure guided by the given molecular dynamics data.
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  • 24
    TaxPub is an extension of the NLM/NCBI Journal Archiving DTD for markup of taxonomic treatments. Maintenance of TaxPub has moved to: https://github.com/plazi/TaxPub
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  • 25
    Flow Investigation using N-Dimensions
    Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.
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