People

This site and the tools it contains were developed by the RNA Computational Biology group at the University of East Anglia (UEA):

Group Leaders
Professor Vincent Moulton
Professor Tamas Dalmay

Current Developers
Dr Leighton Folkes
Dr Irina Mohorianu

Previous Developers
Dr Matthew B. Stocks (Aviva)
Dr Christopher S. Applegate (Aviva)
Dr Daniel Mapleson (Earlham Institute, NRP)
Dr Hugh Woolfenden (John Innes Centre, NRP)
Dr Frank Schwach (Sanger Institute, Cambridge)
Dr Simon Moxon (School of Biological Sciences, UEA)

Contributors of new tools
Joshua Thody
Salma Alzahrani
Dr Matthew L. Beckers
Dr Claudia Paicu

Other contributors
Prof D Baulcombe (University of Cambridge)
Dr Dan MacLean (The Sainsbury Laboratory, NRP)
Dr David Studholme (University of Exeter)
Dr Helio Pais

IT support
Russell Smith (School of Computing Sciences, UEA)

  • Jay

    Hi, I would like to annotate mouse small RNAs to my sample. However, I have tested several version of .gff3 and .fa file from UCSC or ensembl but none of them worked. Could you please give me some hints about what kind of primary genome file and GFF file does this software supported? I use version 4.3.1a to annotate my sample. BTW, the test data works fine.

  • Aftab Ahmad

    Hi, I am using mac os sierra. I downloaded the sRNA workbench and also installed the java but when I double click It led me to an initial setup page, where I clicked Academic user, and then clicked Next. However, the program just froze there. I have also used command prompt to open but the results are same.

  • Sharvari

    Hello,

    I came across your tool looking for miRNA differential expression analysis for mouse genome for a research project . I did download the .dmg file on MAC, but nothing comes up when I click on srna-workbenchV3.2..

    Could you please help.

    Thanks
    Sharvari

    • The sRNA Workbench

      Hi Sharvari,

      Thanks for your message. Could you let me know which version of OSX and java you are using? Type java -version into the console and use the “about this mac” option from the drop down.

      Best wishes,
      Matt

  • Andrew

    Hi, I was wondering if there are command line tools available for each tool?

    Thanks

    • The sRNA Workbench

      Hi Andrew,

      Yes all of the tools can be accessed from the CLI. Have a look through this page:

      http://srna-workbench.cmp.uea.ac.uk/quick-start/

      and let me know if you have any further issues

      Best wishes,
      Matt

      • Andrew

        Thanks for the reply…

        I’m using the adaptor trimming and can’t seem to find any details or examples about the structure of the -params parameter … Do you have any examples available? Thanks

        • The sRNA Workbench

          Hi,

          There are examples of parameter files for each tool found in the data/default_params folder in your workbench directory.

          Let me know if you need any other help getting the tools to run 🙂

          Best wishes,
          Matt

  • Jun

    Hi, I am trying to run the small RNA workbench on my win7 laptop, but without success.
    I downloaded the v3.1 file, unpacked it, and tried to run the Workbench.jar file by double clicking on it. It led me to an initial setup page, where I clicked Academic user, and then clicked Next. However, the program just froze there.
    I also tried to run the sRNAWorkbenchStartup.jar, but after a logo with messages of loading some programs, the logo disappears and nothing happens.
    I really hope to get this to work. I am running Java build 1.7.0_25-b17 (version 7 update 25).
    Thanks much for help.

    • The sRNA Workbench

      Hi Jun,

      Sorry for the delay on reply for some reason I was not informed of this comment by email…

      Can I ask, could you attempt to launch the program from the windows command prompt? Let me know if you are unfamiliar with this procedure.

      If you could reply with any messages that are placed into the command window that would be helpful!

      Cheers,
      Matt

      • Aftab Ahmad

        It remains frozen after opening it from command prompt.

  • Jacques van der Hofstede

    Dear sirs,
    I am interested in using your software for sRNA.
    What are the conditions for commersial use of the sRNA package?
    Kindly, Jacques

    • Hi Jacques,

      Currently we have no restriction on commercial use of the sRNA Workbench. Just that companies cannot re-package (or deconstruct) the software for profit.

      We are looking into an update on the licence agreement at the moment but if you wish to use the software within a company for research that is fine, all we ask is that you cite our paper(s) in any publications you make.

      Please feel free to contact me if this does not answer your question or you require further info.

      Thanks,
      Matthew

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