Tag Archives: featured

The Small RNA Workbench Version 4.5

The small RNA Workbench Version 4.5 ALPHA: Released: 02/05/2018

This release is the next Alpha release of the latest version of the UEA sRNA Workbench, Version 4. Please check out the frequently encountered problems for a list of known issues.

This version has two Java binaries. The first, ‘Workbench.jar’, is the standard binary for running the Workbench using the graphical user interface or through the command line. The second, ‘ServerWorkbench.jar’, is a version that can only run through the command line but does not require any JavaFX dependencies. This second version should hopefully resolve many problems regarding servers and machines that do not have the required libraries for JavaFX.

We highly recommend using the latest version of the Java 8.

This release contains the Alpha build for our latest workflow tool PAREsnip2, a much faster version of miRCat2, and a new version of FiRePat.

CLICK HERE TO DOWNLOAD

PAREsnip2

A new degradome analysis tool has been released in this version of the workbench. More information about this tool can be found here. PAREsnip2 is able to efficiently predict small RNA targets evidenced through degradome sequencing on a genome-wide scale using a configurable set of targeting rules. More information can be found here.

miRCat2 changes

As of version 4.5 of the Small RNA Workbench, we have included a much faster version of miRCat2 known as the ‘standalone’ version. This was developed as some users experienced long waits to obtain results due to the low memory database feature. Therefore, if you have the memory (RAM) available and you are running miRCat2 from the command-line, we recommend using the standalone version.

miRCat2 standalone version does exactly the same as the standard miRCat2 workflow, i.e. same input, output, and algorithm. The only difference in this version is that it does not use the Workbench database, it relies on the personal machine memory. It only works through the command-line, and to use it add the flag “-standalone” to the command-line parameters.

You can run miRCat2 standalone through the command-line using the following command:

java -jar Workbench.jar -tool mircat2 -config configFile.json [-standalone]

FiRePat

In this version we have included an updated FiRePat workflow. FiRePat (Finding Regulatory Patterns) is an unsupervised data mining tool for detecting sRNA-gene pairs with correlated expression levels. FiRePat is suitable for both animal and plant data. More information can be found here.

 

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.

Download

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

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 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 4.0 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.