Version 4.0 Workflows

Workflows

The Workbench Version 4.0 has moved to a new style of interface from the old MDI (Multi Document Interface) to a Workflow model that more accurately describes how a complete bioinformatics analysis is performed.

An image showing a complete workflow. Each node can be double clicked on to configure or view its results
An image showing a complete workflow. Each node can be double clicked on to configure or view its results

 

In addition to the Workflow interface an entirely new back end has been designed for the software. More information can be found here

  • Shobhana Rajasenan

    Hello, when I run version 4.4 I don’t see any of the workflow options in the GUI. I was however able to successfully run miRProf. Is there something else I need to install?

  • mohammad reza Bakhtiarizadeh

    Hi
    I downloaded the latest version (4.3.1) and ran with below code:

    java -Xms5g -Xmx5g -jar sRNAWorkbenchStartup.jar

    after this, I see a window with “The UEA sRNA Workbench” and then, the window disappears, and this error message
    appears :
    Splash took too long
    memory: 3091.6367

    my java version is:
    java version “1.8.0_121”
    Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
    Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

    Also i tried different versions of java (JDK)). my operating system is windows 10. Also i saw already some users could ran this software on this operating system.

    Any idea to help ?
    Thanks,

  • Ethan Roos

    Hi,
    I’ve been doing the version 4 differential expression tutorial, but I can’t get it past the database module. I’ve tried on both os 10.12 and windows 7 computers, with the latest version of JDK, but both stop at the “Calculating alignment totals” stage. I’ve also tried using version 4.2.3 of the workbench, but it stops at the same place. I’ve given the program 20 minutes to an hour to run, but still no progress. Any ideas?

    Cheers,
    Ethan

    • The sRNA Workbench

      Hi Ethan,

      The program can take a long time to run at the moment. This first set of releases is simply there to get the program out and I am now working on improving its performance.

      Probably it will finish if it hasn’t crashed but it may take several hours to get through. How large is the dataset?

      Cheers,
      Matt

      • Ethan Roos

        Hi Matt,
        I’m trying to follow the version 4 tutorial, so I’m using that data. After giving it an afternoon it got to the offset review, but crashed there. A common crash for me seems to be when I’m trying to get back to the home menu from a module menu.

        Do you have recommendations regarding the minimum system requirements for what I should be using to run this?

        Cheers,
        Ethan

        • The sRNA Workbench

          Hi Ethan,

          Yes I found that crash too. I have fixed it in the latest release hopefully…

          Have you been using 4.3.1?

          As for system requirements, the idea is that is scales to what you have, the more RAM you can give it theoretically the faster it should run but it should always work even within small environments.

          Cheers,
          Matt

          • Ethan Roos

            Hi Matt,
            I’m using 4.3.1 now. Getting back to home seems to work most of the time, however, I can’t get the workflow to continue once it stops for user input. Is there a command I can try instead of using the GUI?
            Cheers,
            Ethan

  • Thulile Nhlapo

    Hello 🙂

    I recently downloaded the sRNA workbench v.4.2.1, I’m able to successfully load my data, reference genome and gff files, but I get an error message when I start running the pre-configured differential expression workflow (please see image attached). I’ve tried the workbench on windows and mac machines. Am I doing something wrong? Please help.

    Kind regard
    Thulile

    • The sRNA Workbench

      Hi there,

      I am unable to see the image you mention, could you email it to me instead?

      Cheers,
      Matt

      • Thulile Nhlapo

        Hi Matt

        Thanks for your response, please share your email address?

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A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices