Implementation Details
  • Resources for miRNA-target data:

    The miRNA to gene interaction data were collected from four well-annotated database miRTarBase v6.0, TarBase v6.0 and miRecords . The data for S.mansoni are predicted by miRanda by default parameters. The miRNA to molecule interaction data were collected from SM2miR and PharmacomiR. The miRNA to disease interaction data were collected from HMDD 2.0, and miR2Disease and PhenomiR 2.0 . The miRNA to epigenetic modifier interaction data were collected from EpimiR. The miRNA to lncRNA interaction data were collected from starBase v2.0. Also we optimize the data by removing the duplicated records and those miRNAs which proved to be wrong in miRBase.

  • The web application framework
    • Java Server Faces Technology using the PrimeFaces component library.
  • R packages used in statistical analysis:
    • edgeR: differential expression analysis for RNAseq data
    • limma: differential expression analysis for microarray or qPCR data;
    • HTqPCR: quantitative real-time PCR data analysis;
  • Network visualization and analysis
    • jquery for general purpose scripting;
    • sigma.js for network display and interactions;
    • igraph: network analysis and layout;
Server hardware

miRNet is currently hosted on a Google Cloud Computing Engine with 30G RAM and 8 CPU cores (n1-standard-8). The application server is Glassfish 4.0. Please note, the client-side data visualization requires a modern browser that supports HTML5 canvas and JavaScript. miRNet has been tested under Google Chrome (5.0+), Firefox (3.0+), and Internet Explorer (9.0+). The performance of data visualization depends on the user's computer. For best experience, we recommend using the latest version of Google Chrome on a computer with at least 4GB of physical RAM.

Contact & Support

The miRNet software is developed and maintained in the Xia Lab at McGill University, QC Canada. For bug reports, comments or suggestions, please email to Jeff Xia (jeff.xia at mcgill.ca).

Acknowledgement
McGill NSERC FRQNT
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