All posts by M.B.Stocks

The small RNA Workbench Version 4.4

The small RNA Workbench Version 4.4 ALPHA: Released: 07/04/2017

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle.

We highly recommend using the latest version of Java to run this build. Anything past update release 111 of the JDK/JRE is well advised due to fixes made to the javascript portion of JavaFX

This release is only available as an ON DISK mode build.

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Filter 2

A new version of the filter tool is now available as part of a preconfigured workflow (currently the workflow is on its own, new workflows will be available soon with the filter tool included).

The Filter 2 program retains all of the functionality of the original tool with the added ability to update the RFAM database files. The original Filter program used an old version of the t/rRNA database taken from the original srna tools programs. The updated database is likely to be much larger and therefore will add to the processing time.

The small RNA Workbench Version 4.3.1

The small RNA Workbench Version 4.3.1 ALPHA: Released: 03/02/2017

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle.

We highly recommend using the latest version of Java to run this build. Anything past update release 111 of the JDK/JRE is well advised due to fixes made to the javascript portion of JavaFX

This release is only available as an ON DISK mode build.

Download

General

Differential Expression

  1. Annotation errors have been resolved, the software should now always report the correct annotation
  2. The annotation table has new column headings

Offset Review

  1. An error that could place the software in an unrecoverable window state has been resolved

Quality Checking

  1. MA plots now have labels on the X and Y axes
  2. Fold Change box plots should now always be sorted by size class

The small RNA Workbench Version 4.3

The small RNA Workbench Version 4.3 ALPHA: Released: 16/12/2016

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle.

We highly recommend using the latest version of Java to run this build. Anything past update release 111 of the JDK/JRE is well advised due to fixes made to the javascript portion of JavaFX

This release contains the Alpha build for our newest workflow tool miRCat2

This release is only available as an ON DISK mode build.

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miRCat2

  1. A new tool added to the sRNA Workbench suite for the prediction of novel miRNA sequences from HTS data. More information on this tool can be found here

General

  1. Minor performance improvements to database construction phase of workflows
  2. Minor graphics improvements

The small RNA Workbench Version 4.2.3 ALPHA

The small RNA Workbench Version 4.2.3 ALPHA: Released: 09/11/2016

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle.

This release is only available as an ON DISK mode build.

Download

General HotFix

  1. Fixed an issue found in the latest JRE garbage collection that was removing all javascript bridges preventing workflow windows from displaying

The small RNA Workbench Version 4.2.2 ALPHA

The small RNA Workbench Version 4.2.2 ALPHA: Released: 08/11/2016

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle.

This release is only available as an ON DISK mode build.

Download

General HotFix

  1. Fixed an issue that stopped menus from showing in the latest update to the JRE

General

  1. Workflow menus now have arrows showing direction of work
  2. Bug fixes to plot visualisations
  3. Bug fixes for legacy Version 3.2 code
  4. Bug fixes for command line access
  5. New shorter workflows added
  6. Performance improvements

Good things come in small packages…

We used the small RNA Workbench among other bioinformatics tools to conduct a “miRNA Workshop 2016” at the Earlham institute. The goal was to train early-career bioinformaticians from across the globe how to analyse small RNA data generated by next generation sequencing for both animal and plant research.

Read more at the following link:

http://www.earlham.ac.uk/good-things-come-small-packages-microrna

The small RNA Workbench Version 4.2.1 ALPHA

The small RNA Workbench Version 4.2.1 ALPHA: Released: 23/06/2016

This release is the next Alpha test for the latest version of the workbench, Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle

Download

General HotFix

  1. Added the 64bit binary for GhostScript LINUX build

The small RNA Workbench Version 4.2 ALPHA

The small RNA Workbench Version 4.2 ALPHA: Released: 20/06/2016

This release is the next Alpha test for the latest version of the workbench,
Version 4.0 (check the frequently encountered problems for a list of known issues).

This version is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle

Download

General

  1. All linux binaries are now compiled as 64bit removing the need to install the 32bit libraries prior to running the software
  2. Bug fixes and stability improvements

miRCat 1 (Version 3.2)

  1. Fixed the show genome browser view

RNA Annotation

  1. Fixed the issues with hairpin sequences not rendering

VisSR

  1. Fixed the issues with the VisSR tool not having required resources included within the most recent build

Database

  1. Chromosome headers can now be much longer than in previous versions (very long chromosome headers such as those found in scaffolded files caused the software to crash)

 

The small RNA Workbench Version 4.1 ALPHA

The small RNA Workbench Version 4.1 ALPHA: Released: 22/02/2016

This release is an Alpha test for the latest version of the workbench,
Version 4.0 (check the frequently encountered problems for a list of known issues).
It includes brand new tools for quality checking, normalisation
and differential expression analysis of small RNA data.

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Main fixes relating to the preconfigured pipeline for Quality Checking, Normalisation and Differential Expression

The tutorial video for this pipeline is now available and can be found here

Workflow View

  1. Interface updated to show more information about which nodes are running, correctly configured, completed and those that are waiting user input (key displayed on the interface)

File Hierarchy Wizard

  1. Replicate files now index from 1 instead of 0
  2. Multiple files can be selected when adding replicates to samples
  3. Options added for outputting aligned sequence files
  4. Bug fixes including:
    1. File removal works correctly for all file types
    2. Performance and UI improvements

Database

Major performance improvements

File Review

  1. Users can now choose to remove ranges of size classes from the dataset using the sliders placed at the top of the interface or individual size classes using the input text box found in the options menu
  2. Bug fixes for removal of files so that it now works as expected

Report modules

  1. Performance improved greatly
  2. Export options improved
  3. Some fixes to CSS JavaFX validation problems still causing black marks to appear. Issue still remains in some plots, if unusable use the export menu to view the file in a web browser.
  4. Fixes for menu disable functionality when certain graphs are not available
  5. Jaccard Index table no longer produced for second report. Producing the data for this plot is extremely time consuming and does not add much information to the plot produced in the second report.

Normalisation

  1. Performance improvements
  2. Normalisation now waits for the user to press continue before running, this is to give time to select desired normalisations before the module begins

Offset Review

  1. KL divergence graph now renders more clearly
  2. If only one normalisation is selected in the previous stage the node automatically selects it
  3. Users can now control the window length (default 4000nt)

Differential Expression

  1. Fixes for some of the issues with annotation display
  2. Performance improvements
  3. Several new options for plots
    1. Fold Change cross plots
    2. MA plots
    3. Differential Expression plots

The small RNA Workbench Version 4.0 ALPHA

The small RNA Workbench Version 4.0 ALPHA: Released: 04/09/2015

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This release is an Alpha test for the newest version of the workbench (check the frequently encountered problems for a list of known issues). This version comes with an early release of a new tool that will be included in the final 4.0 Workbench Release and a new look to the interface.

The workbench will slowly be completely migrating to the new interface over the coming months.

The new interface discards the old style of single tool multi document interface from Version 2 onwards to this point in favour of a workflow style. Users currently have the option to use only one preconfigured workflow, however more preconfigured options will be coming soon along with the ability to completely customise a workflow for a user’s own needs.

In addition to the new workflow a completely new backend to the program has been included, this removes all of the previous IO based in memory calculations in favour of a database module that should help to counteract some of the problems faced with memory requirements for the software. More details will be given out in a post on the workbench diaries section similar to that of the Adapter Removal low memory post.

Also some new functionality for sequence alignment has been included

General

  1. A new front end in the form of a Workflow model has been included. Users can still view the old style from the new interface by clicking the version 3.2 button and using the program as before.
  2. Bowtie can now be used from the wizard to align sequences, however, currently only pre-indexed genome files should be used in this mode. Pre indexed genomes can be found at the bowtie website: http://bowtie-bio.sourceforge.net/index.shtml

Quality Checking and Normalisation

A brand new tool for quality checking and normalisation of small RNA data. This tool works as a flow from setup through review and completion. Users can setup the software to reflect exactly how their experiment was formed, check the initial quality of the data, deselect problematic files and then normalise the results.

users can then export the data as CSV format for use in GEO uploading or as normalised FASTA files. Users can also export all of the graphs shown in the quality checking stage of the workflow. Further details can be found here

Differential Expression

A second workflow containing all of the previous normalisation and QC analysis nodes but with the addition of a differential expression node is also included. Further details can be found here

Changes to the Version 3 build…

As previously mentioned, the version 3.2 release can still be accessed from this build by clicking the “Show version 3.2” and the Version 4.0 alpha can be returned to from the tools menu.

The version 3 tools will continue to be updated until a time that they move to the new interface or are completely replaced. As such, some tools from the previous version have received improvements. Details below:

Adapter Removal

  1. Low memory version has received some back end improvements to speed of processing
  2. Low memory version has corrected errors produced when processing HD adapter samples

miRCat

  1. Users can now specify the output directory for miRCat results when running from the command line. The extra flag

    -output_directory followed by the desired location can be added to the miRCat instruction.