FAQs

  1. What are the main features of OmicsNet?
  2. What are the new features of OmicsNet version 2?
  3. What are the data formats accepted by OmicsNet?
  4. Which browsers are supported by OmicsNet?
  5. What if WebGL is supported but disabled on my browser?
  1. What are the main features of OmicsNet?

    OmicsNet has been developed to allow researchers for creation and visualization of relationships among genes, proteins, miRNAs, transcription factors, and metabolites in a three-dimensional (3D) space and conventional 2D visualization. In particular:

    1. From a list (or multiple lists) of molecules of interest (genes, transcription factor, miRNA, microbial taxa, metabolites or even MS peaks) to molecular interaction networks using build-in comprehensive knowledgebase.
    2. Visual exploratory analysis of the network in our innovative 3D network visualization system with rich features for layout, coloring, highlighting, functional and topological analysis.

    Some example visualization results can be seen from our Overview page.

  2. What are the new features of OmicsNet version 2?

    OmicsNet version 2 has been updated to enable researchers to integrate less well established omics data including untargeted MS peaks, microbial taxa and SNP with other omics data. In details,

    1. Users could upload a list of MS peaks (in csv or txt format). The predicted potential metabolites and their corresponding chemical artifacts (e.g. adducts, isotopes) will be annotated and predicted directly.
    2. Microbiome data (from different taxonomic layers) are also supported to integrate with other omics data by through microbial taxa-metabolites interactions. Override software rendering list
    3. Single nucleus polymorphism (SNP) data can be uploaded and mapped to closest or corresponding gene depending on its position on the chromosome. The positional mapping has been generated using Ensembl Variant Effect Predictor (VEP).
  3. What are the data formats accepted by OmicsNet?

    1. Molecular Lists: OmicsNet accepts one or multiple lists of genes, transcription factors, miRNA, metabolites or microbes. The format is such that the first column takes the input type and the second column takes the expression value or any other quantitative measurement. Multiple ID types are supported for different organisms.
      • List of 691 DE genes from helminth infection signature (download)
      • Data from multi-omics (transcriptomics, metabolomics) study to identify biomarker of intrahepatic cholangiocarcinoma cancer (ICC)
    2. MS Peak List: OmicsNet accepts MS peaks from LC-MS based untargeted metabolomics studies (formatted as csv or txt). The data list consists of four columns (m/z, RT, intensity and P value, sequentially). The first three columns are mandatory, while P values column is optional. If no p value provided, all annotated compounds will be included for network construction.
    3. Network Files: three different formats are supported including .sif, .txt and .graphml format. Please click on the following links to see example files supported:
  4. Which browsers are supported by OmicsNet?

    The 3D visualization system was developed based on the Web Graphics Library or WebGL technology. WebGL is the standard 3D graphics API for the web. It allows developers to harness the full power of the computer’s 3D rendering hardware from within the browser using JavaScript. Before WebGL, developers had to rely on plugins or native applications and ask their users to download and install custom software in order to deliver a hardware-accelerated 3D experience.

    WebGL is supported by most major modern browsers that support HTML5. We have tested OmicsNet in several major browsers (see below). Our empirical testings have shown that Google Chrome usually gives the best performance for the same computer:

    Name Version Note
    Google Chrome 50+ ★★★★★
    Mozilla Firefox 47+ ★★★★☆
    Apple Safari 10.1+ ★★★☆☆
    Microsoft Edge 12+ ★★★☆☆

  5. What if WebGL is supported but disabled on my browser?

    Chrome

    First, enable hardware acceleration:

    • Go to chrome://settings
    • Click the + Show advanced settings button
    • In the System section, ensure the Use hardware acceleration when available checkbox is checked (you'll need to relaunch Chrome for any changes to take effect)

    Then enable WebGL:

    • Type chrome://flags in the browser and press Enter
    • Ensure that Disable WebGL is not activated (you will need to relaunch Chrome for any changes to take effect)
    • Here you will have to change Default to Enabled in the drop down.

    • [Try this if above doesn't work] Enable - Override software rendering list

    For more information, see: Chrome Help: WebGL and 3D graphics.

    Firefox

    First, enable WebGL:

    • Type about:config in the browser address bar and press enter
    • Search for webgl.disabled
    • Ensure that its value is false (any changes take effect immediately without relaunching Firefox)

    Then inspect the status of WebGL:

    • Go to about:support
    • Inspect the WebGL Renderer row in the Graphics table:

    If your graphics card/drivers are blacklisted, you can override the blacklist. Warning: this is not recommended! (see blacklists note below). To override the blacklist:

    • Go to about:config
    • Search for webgl.force-enabled
    • Set it to true

    Safari

    • Go to Safari's Preferences
    • Select the Security tab
    • Make sure to check theAllow WebGL checkbox
    Source: https://superuser.com/questions/836832/how-can-i-enable-webgl-in-my-browser
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