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  • Portah
    Member
    • Jan 2012
    • 14

    Wardrobe Web-based Experiment Management System

    Hi,
    Almost a year ago I have started to develop a system to simplify a growing routine work with NGS data. The lab (to which I belong) works on epigenetics and all connected experiments RNA-Seq (single/pair, spikeins, dUTP) DNA-Seq (single/pair, ChIP, Transcription binding sites). There are a lot of biological parameters like histone modifications (H3K4Me3,H3K4me1,H3K27ac, H2AZ, etc.), fragmentation (Sonication, MNase, etc.), etc., as well as technical for an each experiment.

    At some point I have realized, that I did not make new analysis. I only did the same work over and over again (even with prepared pipelines). Thats why I designed a web interface, which does not scare professors or technicians, because adding a record is simple as in Excel. Then for combinations of parameters I programmed a corresponded pipeline which runs automatically in the background. All output is represented as charts and tables in the interface. I don't need to send it by email or bring a flash or something like that anymore. Preliminary analysis is fully automated mapping (bowtie/tophat), QC, quantification (enriched islands, RPKMs), island distribution, all data is deposited as a track to a local UCSC genome browser for the best visualization and annotation. And it is worked, they indirectly did whole routine work.

    In addition to that I have added a project designer and now biologists with no extensive experience in informatics can run DESeq, MANorm, AVTD and so on.

    I think, that the System is somehow different from existed Galaxy, Illumina basespace, Genespring server.
    Last edited by Portah; 08-17-2015, 10:02 AM.
  • Portah
    Member
    • Jan 2012
    • 14

    #2
    BioWardrobe

    Finally, version 1.0 is released and we have been published
    High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps. BioWardrobe can be found at http://biowardrobe.com .

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