The small RNA Workbench Version 3.1

The small RNA Workbench Version 3.1: Released: 25/01/2014

Some changes to existing tools and general software updates. All details can be found below:

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General

The sRNA Workbench has now become dependant on Java version 1.7 and above for all supported operating systems. Users using an earlier version of Java should update their install before attempting to run the latest sRNA Workbench code.

User Participation

  1. We have added a user participation option through google analytics (very similar to the type of tracking that is on most websites). There is a wide variety of reasons as to why it has become necessary to include such an option into the workbench. Chief of which is to help us improve the most widely used areas of the software. You can opt out of this during your first run of the software but please consider allowing the collection of anonymous data as it greatly helps this project succeed. For a complete rundown of what we want to achieve and what type of information we record please visit the following page: http://srna-workbench.cmp.uea.ac.uk/user-participation/

History Browser

  1. Although the time was stored internally, to improve the visual aspect of sorting file access the “Date Accessed” column format has changed from month/year to
    dd-MM-yyyy HH:mm:ss

miRProf

  1. A bug that prevented the reading of files with normalised abundances has been fixed
  2. The GUI output table now includes a combined count  (raw and normalised) for all IsomiRs and a total for genome matches if the genome data is supplied
  3. A bug causing miRBase to attempt a download each time miRProf was executed has been fixed
  4. A bug in the output of csv files from miRProf when running in graphical mode causing a misalignment of columns and rows has been fixed
  5. A bug that prevented the complete output of CSV information when running miRProf from the command line has been fixed

CoLIde

  1. Fixed a bug that was putting the right click menu in a strange place
  2. Fixed the titles not displaying correctly on the size class distribution window
  3. Fixed a bug that could generate an error if replicate mode was selected and a way of calculating confidence intervals was not. The software now selects min/max mode as a default
  4. Fixed a problem that would not allow a locus to be displayed when calculated over data that contains replicate files
  5. Fixed a problem that was showing too many sequences when displaying standard arrow renders over multiple samples

VisSR

  1. Fixed a problem with the aggregate view not being able to display abundances lower than 1
  2. Changed the behaviour of displaying normalised abundances from rounding to two decimal places to rounding to two significant figures to prevent very low abundance values from being displayed. This also affects the aggregate render mode

miRCat

  1. A bug that left the terminating thread pool window open on the miRCat parameter browser after the tool closed down has been fixed
  2. A bug that triggered a null pointer exception if closing miRCat without running any data has been fixed
  3. A bug causing miRBase to attempt a download each time miRCat was executed has been fixed
  4. A bug that prevent in place filtering of files has been fixed
  5. The back end code that controls loading, filtering and stripping adapters from raw sequence data that has been added to miRCat has been improved

SiLoCo

  1. Fixed a bug that was putting the right click menu in a strange place

Filter

  1. Added option to output redundant and/or non-redundant reads. Users can select either check boxes or both to output their data, the non-redundant file will remain with the same naming convention as before (_filter.fa tagged onto the original filename). The redundant data if requested will have _filter_R.fa tagged onto the end of the original filename
  2. Users can now view size class distribution plots for each stage of Filtering. Please see the updated tutorials for an example

Adapter Removal

  1. The adapter removal can now process data produced using the HD adapter protocol. Please see the following paper for more information on preparation of HD libraries:
    K. Sorefan, H. Pais, A. E. Hall, A. Kozomara, S. Griffiths-Jones, V. Moulton, and T. Dalmay, “Reducing ligation bias of small RNAs in libraries for next generation sequencing.,” Silence, vol. 3, no. 1, p. 4, Jan. 2012.
  2. The ability to view abundance plots for processed data has been modified to generate one plot per stage of adapter removal including the new HD protocol. This can be used to indicate various problems in the data (such as large scale adapter-adapter ligation)

TASI

  1. P_Values are now rounded to 4 Significant Figures (scientific notation remains however)

Abundance Distribution Viewer

  1. The truncation of longer values along the x axis has been removed and will now show the complete number
  • Tibor Nagy

    Error at initial setup (Linux version, Ubuntu 13.10, 64bit):

    Caused by: java.lang.UnsatisfiedLinkError: Can’t load library: /home/nagytibi/Documents/srna-workbenchV3.1_Linux/lib/amd64/libglass.so
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1854)
    at java.lang.Runtime.load0(Runtime.java:795)
    at java.lang.System.load(System.java:1062)
    at com.sun.glass.utils.NativeLibLoader.loadLibraryFullPath(NativeLibLoader.java:200)
    at com.sun.glass.utils.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:88)
    at com.sun.glass.utils.NativeLibLoader.loadLibrary(NativeLibLoader.java:31)
    at com.sun.glass.ui.Application.loadNativeLibrary(Application.java:74)
    at com.sun.glass.ui.Application.loadNativeLibrary(Application.java:81)
    at com.sun.glass.ui.gtk.GtkPlatformFactory$1.run(GtkPlatformFactory.java:28)
    at com.sun.glass.ui.gtk.GtkPlatformFactory$1.run(GtkPlatformFactory.java:25)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.glass.ui.gtk.GtkPlatformFactory.(GtkPlatformFactory.java:25)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:190)
    at com.sun.glass.ui.PlatformFactory.getPlatformFactory(PlatformFactory.java:20)
    at com.sun.glass.ui.Application.Run(Application.java:104)
    at com.sun.javafx.tk.quantum.QuantumToolkit.startup(QuantumToolkit.java:274)

    • The sRNA Workbench

      Hi Tibor,

      I believe this issue is due to missing libraries in your Ubuntu install. I will investigate which packages you should download in order to resolve and get back to you.

      Cheers,
      Matt

      • Tibor Nagy

        Hi Matt,

        I have figured out. libglass.so is part of the Oracle JVM, so OpenJDK is not supported.

        • The sRNA Workbench

          Hi Tibor,

          Yea the workbench has never worked with the OpenJDK. Thanks for letting me know.

          Cheers,
          Matt

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