Meet the Trainer – Jonathan Manning

PHOTO: Jonathan Manning

The Introduction to RNA-seq and Functional Interpretation course (21 – 25 February 2022) is now open for applications and we thought we would introduce you to one of the course trainers, Jonathan Manning.

Jonathan is a Bioinformatician in the Gene Expression group. His role is to expand capacity for single-cell RNA-seq analysis, the Expression Atlas resource, in dialogue with the Human Cell Atlas project. Jon gives us his tips for when looking for scientific training and some inside information on what he would be if he wasn’t a Bioinformatician.

What is your research focus and why did you choose to become a scientist?

My answer here is going to be awkward, in that I don’t have a research focus! Much of my career has been as a ‘service’ Bioinformatician working in various bioscience institutes performing custom analysis for a variety of different experiment types in different biological fields. In my current role at EMBL-EBI I build and maintain RNA-seq pipelines we run the same way over a large number of experiments. In both cases, I use the outputs of other people’s research (tools as well as data) to produce the best results I can for the questions at hand.

I actually started out in Biochemistry due to a fascination with the molecular machinery of life. But I discovered early on that the lab was not for me, and I’ve been on the ‘dry’ side of things ever since.

Where do you see this field heading in the future?

In common with many other fields, machine learning and artificial intelligence will play progressively bigger roles in this field in the coming years, with ‘Big Tech’ companies such as Google having ever greater involvement. I’m sure this will be a double-edged sword, and people such as myself will have to run to keep up, but there’s no denying the potential of these techniques and I foresee some exciting results.

How has training influenced your career? 

I’d say my early Bioinformatics training (a Masters by Research and PhD after that) was pretty pivotal for me, setting me on a whole new path. After that my training was more incremental, for example, some introductory RNA-seq analysis similar to that offered at EMBL-EBI, followed up with a lot of self-teaching.

What is your number one tip for people looking for scientific training?

Be focused, choose courses that are related to your immediate objectives, and have clear goals about what you want to get out of the training. If you don’t have ways to immediately apply and expand what you’ve learned then the training quickly fades. I often find it more useful to do training only once I’ve tried to do something myself, so that I know which bits are tricky for me and what questions I need to get answers for.

If you weren’t a scientist, what would you be?

I’d really love to study historical linguistics, an interest I’ve picked a bit late in the day. I also learned to dance a bit over the last several years, maybe I’m a professional dancer in another universe where I started earlier!


Interested in this course? Apply by 12 November 2021

For more upcoming events on cancer research take a look at our event listing.

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Zooming into the PhD Symposium: “It’s about different scales of life, and not even just life on earth.”

Each year, a bunch of PhD students from EMBL join forces to organise a large symposium for their fellow PhD students across the globe. This year’s (virtual) PhD symposium is the 23rd of its kind. The Big Picture: Zooming into Life is taking place from 16 -17 December.

Around 30 first year PhD students are part of the organising committee for the symposium. Amandine and Dewi, both in Heidelberg, are two of the main organisers. Amandine is a joint PhD student at the University of Heidelberg (Kuner lab) and EMBL (Alexandrov lab)  on neuroinvasive cancer, and Dewi is working at EMBL in the Steinmetz lab, where she is working on developing a CRISPR/Cas9 screen in primary immune cells.

Dewi Moonen
Amandine Prats

How did the team come up with the theme of this symposium?

Amandine: “We wanted to have an interdisciplinary topic that is interesting for a lot of people. We all have such different research backgrounds, but it should be interesting for everyone. We tried to include more than just biology.”

Dewi: “I really like that this topic is about different scales of life, and not even just life on earth, we also have a talk about astrobiology.”

Amandine: “It is a very broad topic, but the talks themselves are not general. They are accessible, but they will be in-depth and connected to the bigger picture at the same time. We are hoping the talks will spark ideas and new collaborations.”

What are you personally excited about?

Dewi: “For the talks, amongst others, I am looking forward to Christoph Bock. His group performs interdisciplinary research at the interface of immunology, cancer and precision medicine, and develops new technologies to support this. This technology development is especially an interest of mine.”

Amandine: “We selected really great speakers for this symposium. Not just because of the research topics, but also because they are really good at giving talks. I am very enthusiastic about the astrobiologist Dr. Lynn Rothschild. It is not my field at all, and I never thought about it before, but I am very curious to find out more about bringing life to other planets.”

You are calling for abstracts for short talks and posters. What topics are you looking for?

Dewi: “This symposium is really made by and for PhD students, so we are giving PhD students the opportunity to share their research. We will have a virtual poster session and selected short talks, divided into different categories. It can be about any topic related to life science, but it would be great if you are able to place your research into the bigger picture.”

Can you tell us a little bit more about the programme elements?

Dewi: “We want the symposium to be interactive, so besides the talks, we are organising different workshops and social activities, like virtual lunches and coffee breaks. Because the organisers are all PhD students, the workshops reflect our interests. We have a career workshop and a scientific workshop on imaging. We also have a workshop on mental health that I am looking very much forward to.”

Amandine: “With regard to the workshop on mental health: it can be hard being a PhD-student, as we can be under a lot of stress. Not just due to the current pandemic, but also just in general. The pandemic just made it more visible.”

What was your experience with organising this virtual symposium?

Amandine: “In the beginning, we had to figure out a lot. Most of us have never met each other in real life due to the pandemic. We’ve never organised a large-scale event like this before. But it feels really good now that it is all coming together.”

Dewi: “I think working together in teams is going really well. We have eight different committees, but there is also overlap between them, so we stay connected and up to date.”

A group picture taken on Zoom, with the organisers of this years PhD Symposium. Around 20 people are on screen, with the visual of the symposium as their background.
The PhD Symposium Organising Committee

You have put a lot of effort and time into organising this symposium. When do you think it will be a success?

Dewi: “For me, it will be a success if the participants are actively engaged, and not just having their computers open and listening to the talks. We want to organise a truly interactive meeting.”  

Amandine: “I am hoping that people will talk to each other and make some longer-term connections, and maybe even collaborations.” 

The Big Picture – Zooming into Life takes place on 16 – 17 December 2021.
Submit your abstract by 10 October

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Meet the Trainer – Varsha Kale

PHOTO: Varsha Kale

Meet Varsha Kale, a Bioinformatician in the Finn team: Microbiome Informatics at EMBL-EBI and one of the trainers at the EMBL Course: Metagenomics Bioinformatics (08 – 12 November 2021).

We virtually sat down with Varsha and quizzed her on where she thinks the field of Metagenomics is heading in the future; and some inside information on what you can expect from the course.

What is your research focus and why did you choose to become a scientist?

Using metagenomics to characterise the chicken and salmon gut microbiome and its functions.

I enjoyed learning about bacteria and how they thrived in various environments. This opened a world of different microbes from symbiotic, commensal to pathogenic and highly resistant. It was exciting! When working in a lab, we would receive pre-analysed sequencing data from bioinformaticians. My mentors at the time were supportive to indulge my curiosity as to how the analysis was performed and hence I chose to study bioinformatics. At EMBL-EBI I have the opportunity to learn about new tools and analysis methods frequently.

Where do you see this field heading in the future?

The continued expansion of novel genomes and annotations deposited in public archives will give us more and deeper insight into some elusive environments. Additionally, as statistical modelling becomes more popular, many of the methods we use for annotation are adopting machine learning techniques. The challenges will be the integration of different data types, judging the optimal cutoffs for accurate annotation, and continuing to ensure that all of these new types are easily available through community-adopted public repositories.

How has training influenced your career?

I have been lucky to have opportunities to attend training courses which helped tremendously with understanding the basics of a new subject. Also, a field such as metagenomics is progressing so fast that training gives a great snapshot of the recent updates and methods that others are using for similar research.

What is your number one tip for people looking for scientific training?

Keep up to date with upcoming courses which are interesting to you. Twitter or LinkedIn can be useful for this, or even the webpages of some of your favourite institutions. However, I found that asking colleagues and peers about training courses they have attended is most informative.

If you weren’t a scientist, what would you be?

To be honest, I went home one day from school and startled my parents with the news that bacteria are the new “cool” – so I’m not sure that I would have done something else! I enjoy singing and it might have been fun and challenging to pursue that.

Which methods and new technologies will be addressed in the course?

There is currently a lot of interest in generating metagenome assembled genomes (MAGs) from microbiome data, so we will work through this process including potential tools you might use for the various steps, as well as things to consider in controlling the quality of your data. An introduction to MGnify will also highlight the specialised pipelines used to analyse different types of microbiome data: amplicon, WGS reads, and assemblies.

What are the highlights of the course?

The course will give an overview of metagenomic data analysis including, browsing public data, quality control, and assembly of sequenced metagenomes, tools, and methods to analyse metagenomic data and submission to public archives. There will be a mixture of live and recorded talks, practicals, and Q&A’s with lots of opportunities for discussion. A personal highlight is the chance to learn about the research projects of others attending the course!


Interested in this course? Apply by 03 September.

For more upcoming events on cancer research take a look at our event listing.

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EMBL is looking for scientists with artistic talent!

Are you a scientist who is interested in structural biology and bioinformatics and passionate about arts?

This is your chance to showcase your talent!

EMBL is looking for scientists with an artistic vein who can transform scientific theories into art.

What do you need to do?

Create an original piece of art representing scientific and/or societal concepts relating to a structure in the Protein Data Bank.

Need some inspiration? Look here: http://www.wwpdb.org/

If your artwork is selected, it will be hosted on www.artsteps.com, an innovative, web-based application targeted at the PDB research community.

“This art exhibition is part of the EMBL Conference: Bringing Molecular Structure to Life: 50 Years of the PDB run by our team, the Protein Data Bank in Europe. Through this project we aim to provide new interpretations of molecular structures through artwork. And this allows the introduction of complex scientific themes in a more accessible form to the general public,” explained David Armstrong, Scientific Database Curator from EMBL-EBI.

You can create your artwork using any technique or media.

And why should scientists submit their artwork?

“The exhibition will allow scientists to present their area of work or interest in a new context through the medium of art. This will also help them to think about how to communicate their work, particularly to people from a non-scientific background,” said David Armstrong.

Please bear in mind that we will need a high-resolution image of the artwork to be able to present it in the virtual exhibition.

Together with the artwork, the following data provided by you will be displayed:

  • Name of the submitter
  • Affiliation of the submitter
  • Research stage
  • Which protein the artwork is linked to
  • What technique/tools were used to create the final piece
  • Short description about the artwork.

The opening of the exhibition will take place on 13 October 2021, during the launch of the virtual conference platform for the EMBL Conference: Bringing Molecular Structure to Life: 50 Years of the PDB and will stay open for one year.

We are looking forward to getting to know the artist in you!

More information and submission details can be found on the conference website.

 

 

 

 

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From an online interview to running my first virtual course

Iva Gavran joined the EMBL Course and Conference Office in December 2020.

We asked Iva Gavran, who recently joined the team as a Course and Conference Officer, to give us her newcomer’s insights about the very first virtual course she organised (EMBO Practical Course: Drosophila Genetics and Genomics, 11 – 15 January 2021), held in the EMBL virtual learning platform – eCampus.

It was December 2020 and after a 5-day quarantine and a PCR test I had started working at EMBL. It was just one month before the EMBO Practical Course: Drosophila Genetics and Genomic was scheduled to take place. A virtual course, of course.

In fact, my job interview at EMBL was held virtually as well and I had seen the EMBL ATC building and the city itself only in pictures prior to relocating to Heidelberg (and oh, both are stunning).

A lot of things for the course were pretty much arranged by then, but I was still baffled about how one could organise a virtual practical course. The answer may well lie in the EMBL Advanced Training Centre building’s architecture that resembles the DNA’s double helix and reminds us that adaptation is the key. We have fully adapted the face-to-face training’s structure and interaction to a new, online format.

Virtual platform

What really helps is that there is a whole learning platform dedicated to our courses, called eCampus. A clean slate at first, it was soon populated with all kinds of learning materials, videos, articles and other input sent by the speakers and trainers.

The EMBL virtual learning management platform eCampus was launched in 2020 and is used as a collaboration and networking tool by the virtual course participants.

Course materials and programme

I would say there are three main pillars of eCampus: the pre-course materials, the interaction options and the daily programme. The pre-course materials are a proper little treasure trove of knowledge with pre-recorded videos, quizzes, articles and assignments. If you have any questions, just go straight to the Forum and ask away, or chat with another participant or trainer. The programme is always up-to-date with all the links you need and it also has a nice feature where you can adapt it to your time zone. If a live session has some pre-course materials that need to be watched or read, it will be hyperlinked in the programme or the material will be added below, which is pretty cool and very convenient.

Networking

Networking is a crucial part of every event, whether it’s a conference or a course, but it is hard to replicate in a virtual environment. I remember how it was for me to virtually meet my colleagues, and trust me, it’s definitely odd, but somehow at the same time it also felt normal. After all, we share the same work experience and it’s the same when attending a course. Well, not exactly the same if you are a work-from-home parent, but EMBL has amazing childcare grants to help you with that.

The Drosophila course started off on a Monday with an ice breaker event, where all participants shared a few slides to introduce themselves, their hobbies and their career path. It was a full display of lockdown life with cooking, baking and Netflix all over the slides (mine included). There were also networking activities like speed networking, student presentations, a discussion panel and a quiz which fostered interactions between participants and trainers and helped create a really nice group dynamic.

Course modules and learning process

The course was designed in a way that required some pre-course work.  The platform contained a lot of pre-course materials, papers and videos which the participants needed to go through before attending the full 5-day course with about 4-5 course hours per day.

I remember some participants were a bit unsure if they needed to watch them before the course. The idea (and I really liked this) was that participants watch the pre-recorded videos in advance, so that when the speakers and trainers joined live during the course, participants could ask as many questions as possible and thus learned even more from the discussion. This was actually the true benefit of the virtual course – a more thorough discussion and full understanding of the topic compared to the standard format of live lectures followed by 5 min of Q&As. And judging by the participants’ feedback, this format was quite a success.

Some of the interactive sessions of the course were designed in a similar way. For example, participants were assigned tasks that they had to complete before the course. During the course, they received feedback, could ask questions and go over the rest of the tasks with the trainers. To let this all sink in properly and to give them a chance to reflect on what they had learned, participants were able to access all the materials and live recordings for two weeks after the course. As some pointed out, this was amazing for a virtual event and I agree completely.

For me, the best part of the Drosophila course was watching the lively interactions and discussions between participants and trainers, and especially among participants during their presentations of their current research. I found it inspiring and rewarding to see their curiosity and ideas. There it was, 20 people sitting in their homes in different parts of the world, talking about one tiny fly with top experts in the field. How amazing is that!

Events Iva is organising or co-organising:

EMBL Course: Advanced Fluorescence Imaging Techniques, 23 – 27 August 2021

EMBL Course: Gene Expression at Spatial Resolution, 30 Aug – 2 Sep 2021.

EMBO | EMBL Symposium: Seeing is Believing – Imaging the Molecular Processes of Life, 5 – 8 Oct 2021.

EMBL Science and Society Conference: One Health: Integrating Human, Animal and Environmental Health, 3 Dec 2021.

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