Category Archives: Software Downloads

The UEA sRNA Workbench has been tested on various platforms including:

Mac OSX (Version 10.5 Leopard; 10.6 Snow Leopard)
Linux (Ubuntu Version 10,11; CentOS Version 5, 6)
Windows 7

sRNA Workbench Version 2.2

sRNA Workbench Version 2.2: Released: 21/02/12

Includes improvements and bug fixes relating to several tools for all operating systems:

  • The hairpin annotation tool was colouring an extra nt for each short sequence highlighted on the secondary structure plot. This has now been addressed and fixed
  • miRCat “show in VisSR” now targets and zooms to the exact region on the chromosome
  • The search function was not performing correctly in the miRCat output table, it should now check all columns. Users are now also warned when the value searched for was not found
  • miRCat parameters have undergone a slight tweak for the plant default values (note, animal defaults have not changed for this version):
  1. Minimum hairpin length has changed from 150 to 60 after it was discovered that 150 would cause miRCat to miss many hairpins found in miRBase.
  2. Sequence Flank Extension length has been reduced to 100 as this proved to be a more effective default value.
  • SiLoCo is now available from the command line using the “–tool siloco” instruction. More information on executing Workbench tools from the command line can be found in the Quick-Start pages
  • MiRProf is now available from the command line using the “–tool mirprof” instruction. More information on executing Workbench tools from the command line can be found in the Quick-Start pages
  • Logging information is now output from all server threads and the main program giving users a record of any jobs they have ran through the workbench and information on why a job may have failed. Logs can be found in the user/logs directory

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sRNA Workbench Version 2.01

sRNA Workbench Version 2.01: Released: 15/02/12

Includes bug fixes for all operating systems:

  • Addressed an issue with flickering GUIs on the miRCat parameter browser window when populating the thread queue
  • Addressed major issue with the hairpin annotation tool shutting the server-side program down after execution not allowing any further hairpin images to be generated.
  • Above issue also affected miRCat “render all hairpins” option which now appears to be fixed
  • Layout fix to the miRCat params GUI where the p-val option was only barely visible and users could not access the check box for allowing complex loops (only appeared to affect those running MAC OSX)

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sRNA Workbench Version 2.0

sRNA Workbench Version 2.0: Released: 10/02/12

Includes many performance and functional improvements to Version 1 with support for multi-threading hardware, and several new tools, including:

  • SiLoCo: short Interfering Locus Comparison – a tool for comparing sRNA Expression levels across multiple samples
  • miRProf: miRNA Profiler – a tool for determining normalised expression levels of known miRNAs across multiple samples
  • ta-siRNA: trans acting short interfering RNA detection – a tool for prediction of phased ta-siRNAs in plant sRNA datasets

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sRNA Workbench Version 1.01

sRNA Workbench Version 1.01: Released: 16/09/11

No longer available.

Includes several bug fixes for the Linux and Mac OS operating system:

  • Hairpin Annotation tool now works correctly on Linux!
  • Executable program permissions modification now works on Linux!
  • Saving all hairpin files for Mac OS and Linux now allows for missing directories to be created at save!