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sRNA Workbench Changelog

What's new in sRNA Workbench 4.4 Alpha

Apr 8, 2017
  • 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.

New in sRNA Workbench 4.3.1 Alpha (Mar 5, 2017)

  • Differential Expression:
  • Annotation errors have been resolved, the software should now always report the correct annotation
  • The annotation table has new column headings
  • Offset Review:
  • An error that could place the software in an unrecoverable window state has been resolved
  • Quality Checking:
  • MA plots now have labels on the X and Y axes
  • Fold Change box plots should now always be sorted by size class

New in sRNA Workbench 4.2 Alpha (Jun 20, 2016)

  • General:
  • Bug fixes and stability improvements
  • miRCat 1 (Version 3.2):
  • Fixed the show genome browser view
  • RNA Annotation:
  • Fixed the issues with hairpin sequences not rendering
  • VisSR:
  • Fixed the issues with the VisSR tool not having required resources included within the most recent build
  • Database:
  • 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)

New in sRNA Workbench 4.1 Alpha (Feb 26, 2016)

  • Workflow View:
  • 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:
  • Replicate files now index from 1 instead of 0
  • Multiple files can be selected when adding replicates to samples
  • Options added for outputting aligned sequence files
  • Bug fixes including: File removal works correctly for all file types; Performance and UI improvements
  • Database:
  • Major performance improvements
  • File Review:
  • 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
  • Bug fixes for removal of files so that it now works as expected
  • Report modules:
  • Performance improved greatly
  • Export options improved
  • 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.
  • Fixes for menu disable functionality when certain graphs are not available
  • 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:
  • Performance improvements
  • 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:
  • KL divergence graph now renders more clearly
  • If only one normalisation is selected in the previous stage the node automatically selects it
  • Users can now control the window length (default 4000nt)
  • Differential Expression:
  • Fixes for some of the issues with annotation display
  • Performance improvements
  • Several new options for plots
  • Fold Change cross plots
  • MA plots
  • Differential Expression plots

New in sRNA Workbench 4.0 Alpha (Sep 5, 2015)

  • 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:
  • 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.
  • 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.
  • Adapter Removal:
  • Low memory version has received some back end improvements to speed of processing
  • Low memory version has corrected errors produced when processing HD adapter samples
  • miRCat:
  • 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.

New in sRNA Workbench 3.2 (May 20, 2014)

  • General:
  • A more informative message is now given to the user and written to the log if the input file has bad formatting or invalid lines that will cause the software to crash
  • A fix for GA tracking data initialization occasional crashes from the command line
  • Adapter Removal LM (Low Memory):
  • The first in a set of major changes to the underlying data structure of the sRNA Workbench. Memory was becoming a major issue so our focus switched toward strategies for counteracting the large volumes of data our users wanted to process using the workbench. The new Adapter Removal tool (currently shown as Adapter Removal LM beta) can be used in exactly the same way as the old tool with one change, the users will notice a redundant version of the direct FASTQ to FASTA conversion in their output directory.
  • Adapter Removal (All Versions):
  • The GUI no longer outputs HD stats if the HD adaptor trimming option was not selected
  • VisSR:
  • Users now have the option to change the background colours and colours of the glyphs used to represent; GFF annotations, Aligned small RNA files (including the aggregated mode) and the backgrounds of all tiers to suit their usage. Users should use the help->settings menu on the VisSR panel to change the colours they are interested in.
  • RNA annotation:
  • A new version of Ghost Script has been included that no longer requires an X11 build to be present on OSX computers (as support for X11 was removed in Mountain Lion)
  • CoLIde:
  • A bug that left a hardcoded value in place for the offset absolute differential expression value has been fixed
  • Rounded P values that read 0 have now been replaced with a more informative message. Remaining P values have been rounded to two significant figures
  • miRProf:
  • The CLI output now matches the updated output style created for the GUI mode
  • Fixed an issue in GUI mode where genome matches were not being summed up correctly
  • Fixed an issue where normalised counts were being summed over rows incorrectly

New in sRNA Workbench 3.0 (Jul 8, 2013)

  • GENERAL BEHAVIOR CHANGES:
  • .dmg OSX Style package for MAC users!
  • Users of LINUX and other operating systems must run the software in the old way until a solution to wrapping the code up presents itself…
  • Users will now notice there are downloads per Operating System now. This is unfortunately unavoidable if we are to provide specific wrappers for the program. However, sourceforge should recognise your OS and automatically point you to the correct version to download
  • Added code to set the locale at run time. This is to fix any problems found by people running on a machine that is using ‘,’ for decimal points
  • Help Files:
  • The help files have all been updated to reflect the changes made in recent versions (long overdue!) All packaged HTML files relating to tools within the Workbench should now be up to date with new screenshots of the latest interface
  • STARTUP PROCEDURE:
  • Some improvements to this see a time out added to the splash screen animation for people using the workbench through X window style forwarding. The screen should now run for no more than 5 seconds then proceded to fire the workbench up
  • HISTORY BROWSER:
  • The history browser has been modified to update records of file usage rather than adding a new record for each file that has been added. If you access the same file from the same tool only the date and time is updated. If you update the same file from a new tool, the tool name and date and time is updated. This is to prevent multiple entries of the same file path appearing in your history
  • The date and time format has been updated to use the local date and time for the machine that is running the workbench (previously it was locked to GMT)
  • Added a double click to the history browser table for single file quick selection
  • Improved the time date format stamp
  • History can now be sorted, sorts on columns one and two are lexicographical (file name and tool name) and column three is date sorted (I expect most people will use this column for sorting mainly)
  • ADAPTER REMOVAL:
  • Files that are processed using the Adapter Removal have their file names auto generated. These files are now all added to the history log after processing has completed
  • Added a new option to view the size class distribution as a bar chart post processing (see the Adapter Removal pages for further information)
  • A new check box has been added to force overwriting of files that are found in the output directory that have the same auto generated name. If the check box is not selected any files that would result in an overwrite of existing data will be ignored, a message is shown to the user and the file names are added to the general workbench log
  • Some layout modifications to fix strangeness with the max length text box
  • Fixed a bug that was showing all length distributions as 0
  • Fixed a bug that would add duplicate tabs if identical files were processed more than once prior to a reset
  • FILTER:
  • Files that are processed using the Filter have their file names auto generated. These files are now all added to the history log after processing has completed
  • A new check box has been added to force overwriting of files that are found in the output directory that have the same auto generated name. If the check box is not selected any files that would result in an overwrite of existing data will be ignored, a message is shown to the user and the file names are added to the general workbench log
  • COLIDE:
  • The CoLIde program now conducts the significance test on the top 4 most abundant size classes in the putative locus (previously it was always using sizes 21-24)
  • The CoLIde program now allows users to control the amount of offset added during the calculation of the offset Chi-Square test on the size class distribution of a locus
  • improved the layout of the result table when maximised
  • TASI:
  • added new parameter to change the phasing register prior to run time. A user must modify the value in the box to view phased sequences of the defined length and phase
  • Fixed the help when running the tool from the command line. Previously it did not mention the need for a genome (you would have received an error if the file was not found though)
  • SiLoCo:
  • A bug in the Export to CSV functionality has been fixed. Previously the file was always opened in “append” mode meaning that if a user selected a file for overwriting the new data would in fact be appended to the file. Now the file is blanked before new writing takes place
  • Show locus in Genome View: A bug that was causing abundances of sequences that appeared in multiple samples to be summed rather than having individual values displayed has been fixed
  • SiLoCo now features the same context functionality as CoLIde. This include: the standard arrow view genome render, the aggregated view genome render, the output each entire selected locus to FASTA, the output all individual sequence each selected locus to FASTA.
  • miRProf:
  • The issues affecting miRProfs CSV export functionality when certain grouping options were selected have been resolved.
  • Save parameters now also includes the miRBase version and category details in the resulting .cfg file
  • miRCat:
  • A hopeful solution to the hanging thread problem has been included! With any luck the zombie error that many people have been experiencing after premature ends to miRCat runs will no longer be experienced
  • Added a proper logger to the miRCat program. Activate using the check box on the parameters window. The Logger should be completely thread safe and will track all sequences examined by miRCat and tell you why they were not classified as a miRNA (or complete details if they were). File can be found in the log directory “miRCat_Info.log”
  • miRCat show genome view now adds a tier to display the entire miRNA locus in the VisSR visualisation
  • VisSR:
  • Normalized abundances generated from SiLoCo and CoLIde are now displayed properly in the tooltips
  • VisSR can now generate the aggregated view added for CoLIde directly from aligned data files produced in the sequence alignment tool
  • VisSR now shows the complete percentage of abundances for the 100nt windows generated for the aggregate view. Percentages are formatted to 2 s.f as are all normalised abundance values
  • The tooltips should properly reflect those abundances that are being shown as normalized or raw counts