University of Dundee

COVID Stories: Scientific innovations by Dundee scientists to tackle COVID-19 (Part 4)

23 Sep 2020

In the final part of our COVID Stories series, we look at the impact of the coronavirus pandemic upon scientists that do not work in a “wet” laboratory, namely members of our Division of Computational Biology, plus learn about recently funded COVID-19 research now underway in the School.

Part 4: Computational Biology and Immunology Research

The coronavirus pandemic has resulted in new research projects to tackle SARS-CoV-2 and new ways of working for our world-leading life sciences experts in the School of Life Sciences.

The majority of our scientists in the School of Life Sciences at the University of Dundee work within a ‘wet-lab’ environment where they work in a laboratory equipped with chemicals and other liquid substances that allow hands-on experimentation to take place. When lockdown happened, the majority of those working in these environments had to cease their work. On the other hand, members of the School that work in a ‘dry-lab’ could continue their research. A ‘dry-lab’ is a laboratory where computer simulations or data analysis takes place, usually using computers. This did not mean that there were not challenges for this community, most of whom are part of our Division of Computational Biology, to move to the working from home model.

Moving your lab to your home

Professor Geoff Barton, Head of Computational Biology explained, “We are 100% computational, so certainly had an easier time to shift to home working than groups that are ‘wet-lab’. However, it is certainly not like being in the lab/office for us.  Some members have school-age children and were home-schooling. People were working in their kitchens, in corridors, in bed, a lucky few like me, have a dedicated office at home.”

There were also technical challenges with monitors, connectivity to core, firewalled facilities and so on needing to be addressed. “Thanks to a great support team in the University IT Team we are now able to do most things as if we are in the office. Though there are still challenges depending on the number of people using the VPN, for example. This can slow work down,” continued Geoff.

As the wet-labs started to open at the end of June and those based there, started to return to work, mainly on shift basis, the dry-lab scientists generally remained at home. Other than not going into the office, not much has changed! A laptop can be used anywhere,” said Simon Li, a systems and software engineer in the Open Microscopy Environment (OME). For other members of the OME team, they always had always worked remotely. Frances Wong, Curator for the Image Data Resource (IDR), lives and works in Edinburgh while other team members are based across Europe and the United States. This did not mean that there have not been changes for these individuals, some worked in shared workspaces or have had to adapt to having their children at home full time during the immediate lockdown. “I was working 2 days a week from home and 3 days a week at the University of Edinburgh as a visitor.  I enjoyed this balance of working from home and working in an open-plan office with scientific colleagues.  So, working from home every day now has been a slight adjustment to my weekly working pattern,” commented Frances. 

Isolation

Isolation has been a universal issue. Geoff explained, “For my own group, we encourage everyone to say “good morning” on MS Teams to say they have arrived.  It has become a bit of a competition for some to see who is first in the morning…. The point of the daily check in is just to make contact and be sure everyone is OK.  We try to look out for each other. Some are living alone, others have family, others, flatmates.  All are having to deal with a very different way of living.”

More widely, the Division of Computational Biology have established daily “coffee” at 11:00 on Zoom. “Anyone can drop in for a chat. This is not about work but about maintaining social networking. Some do, some don’t but it is there…” This does not compensate for seeing people in person on a daily basis or the casual conversations that play an important part in science, a recurring comment made by many the Schools’ community.

COVID and Computational Biology in Dundee

One impact of Covid-19 has been the increased usage and demand for the computational packages created in Dundee. Jalview, a free program for multiple sequence alignment editing, visualisation and analysis, has seen a substantial and sustained increase in people accessing the program. Since April, usage has trebled in the number accessing it at the same point in 2019. This activity was mirrored with OMERO (the client-server software created by OME) usage, "People needed remote access to their data.  Our biggest two months ever for starts of OMERO applications were June and July.  A big part of that is people loading data into their OMERO systems," commented Professor Jason Swedlow, Director of Open Microscopy Environment (OME).

New research and partnerships

The coronavirus pandemic has instigated a huge shift in focus for many within the worldwide scientific community to understand and try to combat the SARS-CoV-2 virus. Within Dundee, many new projects and partnerships have been born since the start of the year due to Covid-19 as covered in parts 1 with the MRC-PPU and 3 with the Drug Discovery Unit of this stories series. This work is not isolated to these two areas of our School. Within Computational Biology, OME have provided their platform to share some of the largest and highest resolution images yet recorded of the SARS-CoV-2 virus. These images are freely available to scientists and the public to scrutinise and study. Geoff Barton’s lab have new covid-19 analysis that builds on their sequence, genetics and structure analysis experience. This work is now being corroborated in ‘wet-lab’ experiments in a new partnership with a research group in Oxford.

A cross-School and University project, funded in the fast response call from the Chief Scientist Office, is now underway. This work involving the labs of Profs Doreen Cantrell and Angus Lamond in the School and Prof James Chalmers in the School of Medicine aims to help identify patients experiencing symptoms of Covid-19 whose condition could significantly worsen. The logistics for this project have been complicated and we’ve had to think carefully about how to design experiments to get the most out of these precious samples,” said Andy Howden, a postdoctoral researcher working on the project.

The impact of this coronavirus pandemic in terms of scientific research will be continued and long-lasting. The work underway in the School of Life Sciences is the start of a longer journey with Covid-19 and future coronaviruses.

Staff Q&As

Simon Li, Jason Swedlow, Frances Wong and Andy Howden are working on projects with connections to Covid-19. Click on the links to read their full COVID stories:

“Other than not going into the office, not much has changed! A laptop can be used anywhere.”

Simon Li, Systems and Software Engineer, OME.

“We’re publishing the key data for some of the most important studies on how the virus works and what treatments do.”

Jason Swedlow, Professor of Quantitative Cell Biology and Director of Open Microscopy Environment.

“The Image Data Resource published these images of the SARS-CoV-2 virus, the cause of Covid-19 with additional annotations, for use by the global scientific community.”

Frances Wong, Image Data Resource Curator, OME.

“Life is now very different to before. Every minute is very valuable as we only have a limited amount of time in the lab. Like many people I’m juggling science and family.” 

Andy Howden, Postdoctoral Researcher in Doreen Cantrell's lab.

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