Paving the way for future sheep genome studies
Creating and analysing reference datasets on immune gene expression
Researchers in the Wendy Bickmore research group have a lot of information on a particular gene and its regulatory elements on either side. They were looking for a way to organise it, manipulate it, visualise it, and share it in a user-friendly way. With the help of Eleanor, they developed a web-based application to do this.
The gene in question is called PAX6 and has been studied for four decades. It is the ‘master regulator’ of eye development and also plays important roles in the formation of various tissues and organs during embryonic development (e.g. brain and pancreas).
The regulatory elements around the gene – the bits of DNA which (amongst other things) decide whether a gene is “on” or “off” – are long and complex. Shipra Bhatia, Research Fellow, explains that this caused difficulties for new joiners. “Every time a new person joined the group, they had to start from scratch a build a whole reference framework”.
The web-based application, built with Eleanor, offered a solution to this problem. Eleanor is the University of Edinburgh cloud computing service. It allows users to create virtual machines configures to exact requirements.
More about Eleanor View PAX6 browser
The PAX6 application compiles all the information in one place in a systematic way. For instance, it includes the start and end points of different regulatory elements, what species they are conserved in, what tissues they are expressed in and hyperlinks to relevant bibliography. Moreover, the PAX6 applications links up with a public genome browser (the UCSC browser), which a lot of people use to display a sequence of a genome at any scale.
Web-app interface with annotations, as seen here
All in all, it took about six to seven months to build the application. The researchers received support from Alison Meynert and Murray Wham, both bioinformaticians, and together established a workflow for adding new information to the tool in a straightforward way.
Alison explains: “We chose Eleanor as a host for the web application. It gives us more control over the virtual machine and the resizing, stopping, deleting, recreating, etc. Moreover, you only pay for what you use, rather than a flat rate. Setting up the hostname was easy, and involved opening an IS ticket giving an IP address of the Eleanor instance.”
Overall, Murray found the documentation on Eleanor helpful. However, some experience with OpenStack and cloud computing is required. The team used the university GitLab version control system to keep track of the web code scripts.
More about GitLab
The PAX6 browser has proven very useful for collaborating with researchers worldwide. For instance, Shipra is working with a research group in New York and is now able to share information with them in a systematic way.
The next steps for the browser involve conducting user testing sessions, consulting experts in the field and then writing a paper. Once the tool has been verified in this way, it will go into the public domain – currently the PAX6 browser is hidden behind VPN.
“I did not know the browser would work, but it worked perfectly”, explains Shipra. “And it did not take that long”. Now that the research group has a prototype, they might expand the browser project to other genes that are studied at the MRC Human Genetics Unit.
Picture of Wendy Bickmore research group
This case study was written by Dr Sarah Janac, Research Facilitator for the College of Medicine and Veterinary Medicine. Thank you to Dr Shipra Bhatia and Dr Alison Meynert for their input and contributions.