Spring Equinox Updates

What is new at the Big Data Biology Lab. Spring 2021

This is the first edition of our Quarterly Updates. In the meanwhile, we also semi-regularly post on our Blog and on Twitter, but these newsletters will come out four times a year (not more, not less), so you can subscribe to them to get low-traffic updates.

Everyone is an expert and everyone is a novice

For 2021, our lab motto will be everyone is an expert and everyone is a novice. This reflects the fact that our group is a multi-disciplinary group where we attempt to learn from each other.

Spring Focus: remote internships

This programme started in the Summer 2020 as part of NSURP, but we kept going afterwards. The main idea is to exploit the fact that we are partially remote already to enable students to get some research experience (develop skill of their interest while being part of a research team) that would be typically hard for them to access locally (either because the pandemic has closed labs, or because they somewhere where these opportunities are scarcer, or because they are in a different field, or whatever the reason may be).

We are now looking for a new remote intern.  Thus, this edition, we hear from our past interns:

Who are you?

Fernanda Ordoñez Jiménez. I am a senior majoring in biomedical physics at UNAM. I am interested in the intersection between biology and informatics, with hopes to transform the interface between the ever growing genome sequence acquired data and clinical decision making.

Tobi Olanipekun. I am currently a final year veterinary medical student with much enthusiasm for Genomics and Biological Big Data analysis for the aim of improving global health.

Tristan Gallent. I am a recent BSc graduate in mathematics from Monash University, Australia curious about connections between computer science, mathematics and biology. I am also interested in the engineering side of scientific research.

Why did you apply to the program? When did the fact that it’s remote work well (and less well)?

Tobi Olanipekun. I applied for the program majorly in search of experiences in the lines of genomic analysis, but this was boosted by the pandemic complications which put a stop to most school activities at the time.

Tristan Gallent. Being mainly interested in pure maths at university, I thought it was a great opportunity to get some experience in a more applied field while working out what I wanted to do next. I really enjoyed working with people from all around the world through remote work too. Weekly random coffee chats lead to interesting discussions about both work and non-work related aspects of culture and science.

What did you do? What did you learn (scientifically and otherwise)?

Fernanda Ordoñez Jiménez. I improved GMGC-mapper a command line tool that allows users to query the Global Microbial Gene Catalog v1.0 by adding graphic visualization for the output of the tool in four categories, and at the same time provides the user with basic analysis of their data. My time at the lab also taught me the importance of time management, collaboration and ways to overcome language barriers.
Summary blogpost of the work

Tobi Olanipekun. I applied web-based bioinformatics tools and in silico tests for Microbial Genome analysis and protein modelling, I also learnt from other aspects of research going on in the lab via the regular lab meeting groups that are held.
Summary blogpost of the work

Tristan Gallent. I learnt about both engineering and scientific problems in computational biological research as well as working collaboratively on github/remotely in a professional research environment.
Summary blogpost of the work

Anything else you want to add?

Fernanda Ordoñez Jiménez. Before this experience I had a hard time trying to categorize myself into a particular field, having the opportunity to perform interdisciplinary research and cross between fields freely was enthralling.

Tobi Olanipekun. I will like to add that it was a very wonderful experience for me, I was able to carry out a whole project with my mentor virtually and that means a lot to me since i was feeling bad the pandemic had stopped other activities. The big data biology lab was very welcoming to me.

Tristan Gallent. BDB Fudan is a great opportunity for anyone trying to explore bioinformatics/computational biology. With such a welcoming team and a broad range of projects, you get a real opportunity to explore your interests in the area.

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Big Data Biology Updates

Shaojun Pan has been working on a new binning tool, called S³N²Bin. We explain the reasoning behind it in a blogpost, but the summary is that we get more high-quality genomes by exploiting reference genomes while still allowing for the discovery of completely new species. The tool still needs user-experience work and robustness testing, but the basic functionality should be available at https://github.com/BigDataBiology/S3N2Bin.

Célio Dias Santos-Júnior released the first version of AMPSphere on Zenodo, our survey of antimicrobial peptides from the global microbiome. This was done using macrel. Again, we have a couple of blogposts with more details: initial release and the update with AMP families.

We are also happy to have played a supporting role in developing GUNC, a tool for detecting chimeric genomes. The preprint is up at bioRxiv, the tool is available at http://gunc.embl.de/ and we have a blogpost explaining some of the inner workings.

We updated two of our long-maintained tool NGLess to version 1.3.0 as well as Jug 2.1.

Yiqian Duan and Célio Dias Santos-Júnior presented their work at the Virtual Conference on Prokaryotic Small Proteins (January 12-14, 2021).

Looking Forward

April 28. EMBARK webinar series. Gerry Wright Approaches to measure and monitor AMR in various environments & Luis Pedro Coelho/Svetlana Ugarčina Perović Quantifying AMR at very large scales

June 20-24. We submitted several abstracts to the World Microbe Forum

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