Getting to know us: Uma from EnsemblProtists

This month we’re getting to know Uma Maheswari who works in the Protist branch of Ensembl Genomes.

What is your job in Ensembl?

I am a Bioinformatican in the Ensembl Genomes team. As the team motto goes “Extending Ensembl across the taxonomic space”, my role is to extend Ensembl to the very diverse branches of unicellular Eukaryotes in Ensembl Protists.

What do you enjoy about your job?

Photo credit: Venkat Muthukrishnan 

In my current role, I get to interact with software developers who are involved in creating the backbone of Ensembl, and biologists, who both provide us with the data and also  use Ensembl themselves. This interaction and constant learning from the two extremely different worlds to work towards a common goal of analysing and distributing genomic data makes my role very interesting.

Consequently, there is a lot of variety in my routine – one day I learn about bug fixing in the pipelines and solving conflicts in Git merging and the next day we debate about sharing green, red and brown algae genomes through the Ensembl Plants or Ensembl Protists portal.  

What are you currently working on?

I am currently working on annotating an Arctic coral genome and also validating the performance of a new Ensembl comparative analysis pipeline for the diverse protists group.

What is your typical day?

A typical day varies depending on Ensembl genomes release cycle. If we are in the middle of the production cycle, the priority will be to check the status of pipelines. The comparative analysis pipeline for example, can run for over couple of weeks also needs lots of love and care to produce beautiful trees for the genomes browser.  I also meet the developers weekly to get an update about the changes they are planning to introduce and to discuss bugs, which have made reaching the release deadline challenging. Some days I spend few hours in conference calls with the collaborators about the data that they want to add in Ensembl.

How did you end up here?

After completing my Masters in Biology, a computer diploma and bioinformatics training in India, I moved to Paris for my PhD in comparative and functional genomics of a very interesting brown algae – diatoms.  During my PhD, I was working very closely with a molecular biologist who produced lot of expression data in diatoms under various environmental conditions to explore how these tiny organisms are resilient to changing environment and can adapt to survive on ice and thermal springs. I enjoyed writing Perl scripts to analyse these data and to store/retrieve them by creating databases.  At the end of my PhD I got this wonderful opportunity to expand my experience  from working with two genomes to thousands of genomes in Ensembl.

What surprised you most about Ensembl when you started working here?

I was fascinated with the infrastructure to handle a huge amount of growing data and the people with diverse backgrounds and expertise coming together to work towards a common goal. Ensembl started as a human genome browser but has evolved to handle thousands of genomes and continues to expand to handle the ever-growing genomics data.

What is the coolest tool or data type in Ensembl that you think everybody should know about?

Ensembl Protists: One ‘virtual’ division with representatives from all the major Eukaryotic taxonomical divisions. This resource includes genomes from photosynthetic, parasitic and pathogenic organisms that are the ancestors of plants, animals and all the multicellular organisms.

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