Category Archives: General Information

A list of general information related to the sRNA Workbench project and website

Updated Video Tutorials

New tutorial files relating to Version 3.1 of the sRNA Workbench are now available!

Visit the tutorials page for further information or alternatively, follow the links below to view a tutorial page for the tool you are interested in.

Helper Tools

Adapter Removal Tutorial

Sequence Alignment Tutorial

Filter Tutorial

Analysis Tools

miRCat Tutorial

miRProf Tutorial

TA-SI Prediction Tutorial

SiLoCo Tutorial

CoLIde Tutorial

PAREsnip Tutorial (Coming soon)

Visualisation Tools

RNA Annotation Tutorial

VisSR Tutorial

The new UEA small RNA Licence changes in a nutshell

Our original licence was constructed to allow all users free access to the software at all times.

However, it was brought to our attention that it was rather unclear exactly who this means and what they are able to do. Our only stipulation was that the software could not be repackaged and sold for profit. This meant anyone including non-academic institutions could download as many copies as they like and install it anywhere for use in their own research provided they agree that the software was sold “as is” and we cannot be held responsible for any issues.

So why change it?

Well, it was a cause of major confusion in some instances, more to the point we wanted to add more freedom to the software. Blogs such as Mick Watsons Opinionomics  http://biomickwatson.wordpress.com/2013/01/28/gatk-why-it-matters/ illustrates some of the great things that bioinformatics software can offer but some of the challenges that can be added by restricting use of the software in any way.

So what did we decide on?

Well, in essence not a great deal has changed from our old version of the licence. Anyone is free to download and use the software. However, now, private non-academic companies are free to do with the software as they please, we just ask one thing. That if they enjoy using the software and find it useful for their purposes that they write a short letter to us (email, comment system on the website) letting us know that they support the software and would like to see improvements. This is also a great opportunity for them to request features they would like to have added. It serves two major purposes for us, it allows us to keep a loose track on how the software is utilised in the commercial environment and helps us provide a case for support when considering application for further funding in creating new free to use tools.

It’s Alive! The UEA sRNA Tools is back online

The UEA small RNA toolkit, the predecessor to the UEA small RNA Workbench lives on.

http://srna-tools.cmp.uea.ac.uk

Migration to UEA’s GRACE cluster has completed and testing is now underway, I have run a few jobs on each tool and hopefully others will do the same. All the original limitations remain (i.e. the 200mb file size limit is still in place) some jobs may run a little faster because of the new hardware.

It is unclear how long I can keep the service running and the system still remains largely unsupported as most of my efforts are put into the workbench. However, for those short on system resources it can now be used again, at least until any new solutions are available from UEA.

Thank you for your patience

Known Issues

Hi all,

I am aware of two major issues affecting the workbench at the moment, one being that miRCat cannot currently use the pipeline mode. For now please use the adapter removal and filter tools by themselves and use your output data directly within miRCat through the history browser or standard file browser. Please email me or leave a comment if you require further instructions on this.

The second issue is related to the recent release of miRBase 19 and changes to their file structure and internal file information causing our auto update procedure to fail. If you have miRBase 18 installed from previous use of the workbench then do not update your miRBase files and the tool will work fine. If you have tried to update please remove any files related to miRBase 19 from your install directory (data/miRBase) and continue for now with miRBase 18. I can also supply miRBase files for anyone who did not manage to download that version.

The only tool that relies on miRBase to function is miRProf, miRCat will still work without this data. I am working on a fix to the miRBase issue and will release a new version of the software as soon as it is available and add a post to the feed to inform all of our users. This issue will not affect any other tools in the workbench

Thanks,

Matthew Stocks

Some information on changes to our website

We have made some updates to the website, some related to recent issues delivering feeds and some in preparation for the next software release along with a new set of tutorials pages!

RSS Feed information

You will notice that there is a new feed option on the main website page. You can now choose to subscribe to: our entire feed (to get all the details in one place), our publications feed (to only receive news on publications) and our software downloads feed (to only receive news on software downloads). Most feed readers will allow you to filter categories of information as you desire so for most people, the main feed will be fine. For anyone subscribed already you will not need to change anything but you will notice the publications have begun to appear in the feed once more!

Some new pages on the website

I have begun work on a complete set of tutorials for the sRNA Workbench. Each tool has its own tutorials page with a short video showing basic usage with some test data provided on the source forge downloads. You can just watch the videos to get an idea of the tool or download the data and follow the video yourself. For further information please visit the main tutorials pages found at:

http://srna-workbench.cmp.uea.ac.uk/tutorialsmain/

Some information on changes to our feed

Just a quick post to inform subscribers that our publications feed has now been separated from the main sRNA Workbench feed.

This means that users currently subscribed to our main feed will no longer receive posts about related publications to the sRNA Workbench project and instead will only receive information on software updates and comments. This decision was made to ensure important software information does not get lost as our citation list grows.

However if you still wish to recieve notifications on related publications to our work a new feed has been created for this purpose. The URL for the new feed is:

http://feeds.feedburner.com/TheUeaSrnaWorkbenchPublications

Alternatively you can access the feed from the main page of the website as before or view the feed archive directly on our webpage by visiting the publications category