Welcome: Alexey Sokolov
EMBL-EBI’s new Genomics Technology Infrastructure Team Leader discusses how the Ensembl platform is keeping pace with the genomic data deluge
It took scientists 13 years and about £2.5 billion to attempt to sequence the first human genome as part of the Human Genome Project. In the decades since, advances in next-generation sequencing have made genome sequencing possible at a fraction of the cost and time. This is leading to a surge in the amount of genomic data available to researchers.
Access to centralised, well-curated resources such as Ensembl enables scientists to glean biological insights from such immense volumes of data. As a leading platform for genome data, Ensembl provides researchers with freely accessible data and tools to explore, analyse, and compare the genomes of thousands of species across the tree of life.
To support even more data, the platform recently rolled out a new, more scalable version of its website. As the new Genomics Technology Infrastructure Team Leader, Alexey Sokolov has taken the helm of this new release. Here he discusses the importance of openly available genomic data and the role Ensembl plays in enabling impactful scientific discoveries.
Can you tell me a little bit about your background?
My background is fairly broad: I have a specialist degree in biology from Yaroslavl Demidov State University in Russia, an undergraduate degree in computer science from University of the People, and a master’s degree in data science from University of Colorado Boulder, USA. It’s an ideal combination for what I do now, as I get to draw on all these different areas of expertise.
I joined EMBL-EBI as a bioinformatician in 2018, but I’ve been working in bioinformatics for the past twenty years or so. Working at EMBL-EBI has felt like a natural fit for me; aside from the fact that it’s well-renowned for its bioinformatics expertise, it gave me the opportunity to be involved in the services that I’d relied on for so many years.
What is Ensembl and why is it important?
Ensembl is a freely available online platform that helps scientists make sense of the information stored in DNA. It draws on publicly available genomes and transcriptomes from the European Nucleotide Archive, cross-species data, and AI-based approaches, to identify genes and interpret genomes.
Scientists from all over the world can then use these data to find out where genes are located in the genome and what they do in different species. They can also compare genes between species, or track and predict the effects of genetic mutations, among other applications.
You now lead the Genomics Technology Infrastructure team. In simple terms, what does your team do?
My team is responsible for building and maintaining the Ensembl platform. We make sure that Ensembl’s underlying technical infrastructure can effectively store and process genomic data. Without it, users wouldn’t be able to access the data they need for their scientific research.
We also build user interfaces, which are the visual elements that people see and interact with when they are searching or analysing data.
What exciting projects have you been working on so far in your new role?
We just released a new version of the Ensembl website, so it’s been quite a critical period for the team. Data generation nowadays is incredibly cheap, thanks to advances in next-generation sequencing. As a result, Ensembl receives tens of terabytes of data every month. With this new platform, we’ll be able to scale much more seamlessly.
We’ve also changed the core programming language to Python to make it easier to add new features in the future. The previous version of Ensembl was written in Perl, which was the standard programming language of bioinformatics when the platform was launched almost thirty years ago.
Why is it important that genomic data is openly and freely available to the scientific community?
Science is such a collaborative effort; if data weren’t freely available, scientific discovery would be greatly impeded. Open data means that anyone, anywhere in the world, can access the same research and data irrespective of resources.
What’s the best part of your work?
I like to find creative ways to simplify complex systems. Ensembl allows me to do that on a whole other level. There are lots of moving parts in my work, which makes it challenging but also really exciting.
There’s also a unique opportunity to innovate. The scale of genomic data available today allows us to make an impact in ways that would have been impossible in the past. It’s rewarding to know that the work we do plays a part in enabling so many impactful scientific discoveries.
