Blog / COG Train

19 Nov 2022

“It was a great way to share my knowledge to something that could contribute to a better world”: speaking with COG-Train course’s Organisers

COG-Train delivered the Viral Genomics and Bioinformatics Virtual Course for scientists based in Asia, between 22-26 August 2022, in collaboration with the MRC-University of Glasgow Centre for Virus Research, Savitribai Phule Pune University and Oxford University Clinical Research Unit. The course taught participants fundamental viral bioinformatic techniques including the analysis of viral genome sequences and interpreting genomic data, with an emphasis on SARS-CoV-2 genomics.

We spoke to two members of the training and organising team and to the course lead who explained the process of developing the course, why they wanted to be involved, the challenges they faced, and their key learnings:

  • Dr Sreenu Vattipally, Senior Bioinformatics Researcher at the MRC-University of Glasgow Centre for Virus Research (course organiser and trainer)
  • Dr Urmila Kulkarni Kale, Information Scientist at the Bioinformatics Centre at the Savitribai Phule Pune University (course organiser and trainer)
  • Jorge Batista da Rocha, Education Developer at COG-Train (course organiser and developer)

Initially, the focus was on collating a representative pool of facilitators who could provide a steer on the course content and recommend other experts to partner with. Experts based in Asia provided insights into the regional landscape of viral genomics, training needs and interests. Jorge says, “It’s essential to bring regional representatives into the fold so they can weave in their unique experiences.”

The team needed to establish their target audience and assess the current needs and requirements of this group. “It’s important to recognise the diverse backgrounds of the participants and tailor the course content to ensure it is accessible to everyone,” notes Urmila.

Developing a training course of this scale for researchers spread across a whole continent naturally comes with challenges and learning opportunities. For example, Jorge recalls how challenging it was “to coordinate people from around the world who are operating on different time zones, which had an impact on our communications with each other.” To overcome this, the team used a variety of communication channels including Slack. Internet connectivity and reliability is a significant challenge across the world, particularly as this course required a large download of software and data which is packaged as a virtual machine. To ensure that learners could download this effectively the team used Globus, a data transfer system which automatically resumes broken downloads and checks file integrity.

Despite the ease of communication via new technology, Sreenu notes that virtual training sessions do not allow for ideal interactions with other researchers, which are critical for forming long-term collaborations. “This is a common problem across the board with any course taught online,” highlights Sreenu. Jorge echoes a similar sentiment “It would be good if virtual training could be followed up with events that integrate learners and instructors together in practical applications of their skills”. He hopes that learners can make use of GitHub, the platform used to share course content with learners, to create a space where both learners and trainers work together and share their outputs with the world.

There were many positives from the course. Sreenu and Urmila commented that they were very pleased to have been part of the experience. “We really enjoyed being able to share knowledge with so many people and support them with their research from the bioinformatics skills they have learnt,” says Sreenu.

Looking back, Sreenu reflects on the impact of such courses: “A student who was new to bioinformatics who attended a similar course we ran in the past became a collaborator following the training, and has since started her own company in India.” Urmila commented that “For me, it felt like a win-win situation – we impart knowledge as facilitators and gain so much more through the participants and other facilitators on the course. One of my main highlights was being able to watch participants run through the exercises that we set, and generate and interpret their outputs as we envisaged when we put the course together.”

Sreenu, Urmila, and Jorge agree that virtual courses will have a big impact in the future and that the content can be applied to other infectious diseases. “COG-Train has a very significant impact in terms of creating resources for capacity building in the field of viral bioinformatics,” Urmila highlights, “the pandemic has demonstrated a need for skilled manpower for viral bioinformatics, and COG-Train caters to that need.”

“I applaud COG-Train and Wellcome Connecting Science for the wonderful and orchestrated efforts in developing such training programmes as they are tailored to the needs and requirements of the field. The courses are a fantastic contribution to human resource development and to science.” Urmila concludes.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.