CyVerse UK Workshop 2017

This meeting is focused on researchers who are either toward the beginning of their studies or have moved onto a new subject area. We will provide a hands-on sessions that will describe the use of software tools that can interrogate RNAseq, imaging, gene expression or GWAS data. Previous CyVerse users will provide real-life examples of how the software has been successfully used. This is the Learner Track

In addition we will host a concurrent track for more experienced bioinformaticians who wish to learn how to use CyVerse to host their own programs. This is the Intermediate Track. The concurrent tracks will run in separate rooms.

These software tools have been developed as part of the CyVerseUK grant. We will also highlight the opportunities that exist for the sharing of big data in a meaningful manner. This workshop is organised by GARNet with Professor Katherine Denby at the University of York.

Day 1: Monday March 20th

10.30am: Registration Opens

11.30am: Introduction to CyVerse and CyVerseUK

1.00pm: Lunch

2.00pm: Data Sharing, Management and Reuse

3.30pm: Break

Learner Track

4.00pm: CyVerseUK Tools: Earlham Institute: Tuxedo pipeline for RNAseq Analysis - Descriptive hands-on Workshop - User example

Intermediate Track

4.00pm: Working with Docker

6.00pm: Session End

7.00pm: Workshop Dinner at Walmgate Ale House

Day 2: Tuesday March 21st

Learner Track

9.00am: CyVerseUK Tools: University of Nottingham: Image Analysis - Hands on workshop - Introducing BISQUE - Image-Based Phenotyping - Introducing RootNav and RooTrace - Successful Use Example

11.00am: Break

11.30am: CyVerseUK Tools: University of Warwick: Transcriptomic Data Mining - Descriptive hands-on Workshop - User example

Intermediate Track

9.00am: Introducing the Agave API - What Agave is - What Agave isn’t - How you can use it to empower your code with CyVerse hardware

11.00am: Break

11.30am: Working with the Agave API - “Bring your own scripts” - BASH/shell scripting on basic VM hardware

1.30pm: Lunch

Learner Track

2.30pm: CyVerseUK Tools: Earlham Institute: GWAS Analysis Pipeline - Descriptive hands-on Workshop - User example

Intermediate Track

2.30pm: Bringing Agave and Docker together - Building programmatic interfaces - Submitting user-space jobs through CyVerse UK scheduling systems - Building user interfaces

Whole Group Finale

4.00pm: The Future of CyVerse and CyVerseUK

4.30pm: Meeting End

Other Information


There is accomodation available on a first come-first serve basis at the University of York bed & breakfast facility, Franklin House. - This is bookable online through the URL - Select the Accommodation tab, click 'Bed and Breakfast' and then onto 'Book'. Dietary Requirements If you have any dietary requirements then please can you email Geraint at with those details. We will send out information about the workshop dinner closer to the time.

Computer requirements

  1. Please bring a laptop to the workshop for the hands-on portions of the sessions. Closer to the time we will send out the data that we will analyse at the meeting.
  2. Please sign up for a CyVerse account. You can register at and we recommend that you take a brief look at the website before you attend the meeting.
  3. Please ensure your computer is registered with the EduRoam network. If this is not possible we will provide some Guest Logins for the duration of the workshop.


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