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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Looking back on a year of organising virtual events

Exactly one year ago, the Covid-19 pandemic hit Europe. All on-site events had to be cancelled and we had to rethink our entire program. Our Course and Conference Officers worked really hard to create a virtual equivalent of EMBL’s on-site training offering.  We successfully launched our first virtual conference and many more followed. 

The learning curve was steep and so was the stress level. But when the going gets tough, the tough get going. Two of our Conference Officers, Nathalie and Diah, share with us their experience from being in the eye of the storm, the lessons they have learned and some tips for organising a virtual meeting.

Conference Officers Nathalie and Diah
Conference Officers Nathalie (left) and Diah

How does organising a virtual event compare to organising an on-site event?

Diah: “It is a different world, but equally fun! Organising a virtual event is harder than people think and often more challenging. Not getting to see anyone in person and mastering all sorts of virtual platforms can be quite tough.”

Nathalie: “Some of the milestones we have are the same, for example: preparing the website, programme, opening registration, emails with participants and invited speakers, abstract review and selection… But a huge bulk of the work is totally different: instead of booking buses and ordering catering, we are setting up Zoom webinars and populating the virtual platform.

The massive change has been adapting to the new tasks we have to do and how we should do them consistently for all our events. In our team we have numerous working groups looking at areas of event organisation and creating guidelines, procedures and templates that will help us all. It really is a whole team effort!”

Read: Why do we charge fees for virtual events?

What kind of feedback do you get from participants, speakers and organisers?

Nathalie: “The feedback I have received from speakers and participants has been great: they are so happy we converted our event to virtual instead of cancelling/postponing it. Initially a few speakers were disappointed for the event to turn virtual but the same people commented afterwards that they were impressed with how well it went. What is wonderful is that it is still so beneficial for them in their continued research.”

Diah: “Very humbling! Many agree that onsite face-to-face events are somehow irreplaceable but at the same time they are amazed at the number of benefits virtual events offer too! They give you more flexibility: you don’t have to travel across the world. Also, some people feel more comfortable asking questions in the virtual format. ”

What is the most important lesson you have learned about organising virtual events?

Nathalie: “It’s been necessary for us to turn to virtual events but the lessons we have learned are that virtual events are effective, valuable and have many advantages! We’ve noticed that participants feel more comfortable asking questions during Q&A, that virtual talks have had a wonderful response, that virtual networking works well and you can meet different people from all over the world just at your desk!

On a bigger scale, virtual events mean less travel and a lower carbon footprint and they are more inclusive as they allow some people to participate who couldn’t have done so before. This is hugely important and is a very positive outcome of this difficult situation and it will have an impact on how events are organised in the future.”

What do you miss most about on-site events?

Diah: “The buzz when everyone arrives and the ATC is full of people is very exciting – after all the planning, everyone is there! And my favourite moment is the end of the conference: everyone is smiling and happy and you wave goodbye to the buses that leave EMBL. That sense of relief and accomplishment at the same time. I miss that!”

Nathalie: “Parties! One of the best things about the onsite events is meeting the speakers and participants you’ve been in touch with for months and when it comes to the conference party, it is really fun to see everyone let their hair down and enjoy themselves! And taking silly pictures at the Photobooth with people is something I loved and a really cute memento of the conference. That is a small thing I miss too!”

What in your opinion makes virtual events better than on-site events?

Nathalie: “The inclusiveness: more participants can take part as there is not the same financial barrier (travel, accommodation) and people can join from anywhere in the world.”

Diah: “Virtual events are resilient. There is no need to cancel an event because of the weather or a disaster. Participants can attend the event from anywhere!”

Conference Officer Diah wearing a face mask in an empty auditorium during a virtual event
Conference Officer Diah working a shift in an empty Auditorium

A common criticism is that networking doesn’t work well in the virtual world. What is your experience with virtual social events?

Nathalie: “I think it is great to see how Zoom breakout rooms allow people to mix in small groups or 1-to-1. Particularly the speed networking translates very well.”

Diah: “It’s my favorite part of the programme and I am amazed at how well it has been accepted and running so far. We have had live-streamed concerts and participants love it. At one conference some of the scientific organisers even stayed for the whole duration of the social session and wanted to continue mingling even after it had finished.”

Read our blog on virtual speednetworking.

Top tips to keep in mind while organising a virtual event?

Nathalie: “First of all – be open-minded. There are so many new technologies out there and different things you can try!

Have clear guidelines and templates: you use so many different apps and systems that saving time when setting things up can be a lifesaver!”

Diah: “I would also say: Test, test and test. Glitches are always likely to happen, so be prepared and stay calm.”

Read our blog for more tips on how to organise a virtual event

How do you see the future of EMBL Events?

Nathalie: “I hope we will embrace this new world of virtual events and have effective hybrid events in the future: allowing for face-to-face interaction for those who want to come on-site, but also giving the opportunity for those who prefer to join virtually and get the benefit of being part of the event without having to leave their home!”

Diah: “I think hybrid events will take a central place in the format of EMBL Events in the future. But whatever the format will be, we will keep improving and finding the best way to support the scientific community.”

Looking back in general, what are your thoughts?

Diah and Nathalie: “It has been very rewarding during the last year to see how we at EMBL have been able to adapt to the situation we have found ourselves in and been able to ensure that we can still provide a platform for scientific exchange. The aim of EICAT is to provide excellent training to scientists, and, despite the challenges, this is being achieved virtually for the first time! We are really proud of being able to provide opportunities for this exchange of knowledge and research.

Personally, this time has also been one of continuous learning for all of us on the team. We have developed our skills and experience in a number of ways and massively increased our knowledge of online platforms and tools! It has truly been a time of teamwork as we have adapted into the virtual event world and we are grateful to everyone involved: our marketing team, our Photolab technicians, designers and scientific organisers. It has been a challenging but very valuable learning experience!”

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Meet the Trainers – Tobias Rausch and Alexey Larionov

On the occasion of World Cancer Day (4 February), we meet two of the trainers of the virtual EMBL Course: Cancer Genomics  (17 – 21 May 2021) – Tobias Rausch and Alexey Larionov.

PHOTO: EMBL Photolab

Tobias Rausch (TR) received his PhD in “Computational Biology and Scientific Computing” at the International Max Planck Research School in 2009. He then started to work at the European Molecular Biology Laboratory (EMBL) as a bioinformatician. His primary research interests are population and cancer genomics, structural variant discovery and omics computational methods development. (https://github.com/tobiasrausch).

 

PHOTO: Alexey Larionov

Initially educated as a clinical oncologist in Russia, Alexey Larionov (AL) switched to  experimental oncology upon completion of his PhD. Initially he worked as a postdoctoral researcher in Edinburgh University studying transcriptomics of breast cancer, with a focus on markers and mechanisms of endocrine response and resistance.  Working with data-rich methods (qPCR, micro-arrays, NGS) he became interested in data analysis and switched to bioinformatics. Since completing his MSc in Applied Bioinformatics, Alexey has worked as a bioinformatician at Cambridge University, focusing on NGS data analysis and heritable predisposition to cancer. See http://larionov.co.uk for more details.

What is your research focus?

TR: Computational genomics.

ALHeritable predisposition to cancer

Why did you choose to become a scientist?

TR: When I started at EMBL I saw myself as a software engineer who loves to design, develop and implement algorithms to solve data analysis problems. With the advent of high-throughput sequencing, this engineering background gave me a competitive edge as a data scientist, and that’s how it happened!

ALIt was interesting…

Where do you see this field heading in the future?

TR: Nowadays cancer genomics is a data-driven team science, but it is a long way from obtaining data to obtaining insight. In the age of analytics we all have to wrap our heads around multi-domain data with spatio-temporal resolution, ideally in real-time.

AL: I assume that the question is about translational cancer research in general.  I expect that in the near future the field needs better integration of different types of biological data and better collection of relevant clinical data. 

How has training influenced your career?

TR: I think training is essential to get you started. Training is like a kind person who takes your hand and guides you through unknown territory. It goes along with mentorship and I was lucky enough to have good training and good mentorship already as a student.

ALSince my initial clinical and bioinformatics degrees, cancer research has changed so much that I would not be able to even understand current papers if I hadn’t taken regular in-depth training in different aspects of computing and bioinformatics. 

How has cancer research changed over the years?

TR: I hope I am still too young to answer that :-). I leave that question for Bert Vogelstein or Robert A. Weinberg.

ALCancer research has become much more complex and powerful because of the development of new methods; specifically significant progress in bioinformatics, sequencing and human genomics.

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

TR: We try to give an overview of how high-throughput sequencing can be applied in cancer genomics. We cover a range of technologies (short-read and long-read sequencing), data types (RNA-Seq, DNA-Seq and ATAC-Seq) and data modalities (bulk and single-cell sequencing), and last but not least – we take a deep dive into cancer genomics data analysis.

ALIn my sections of the course, I will discuss established methods for the analysis of bulk RNA sequencing, focusing on differential gene expression.  Then I will touch on the new methods being developed for the analysis of long-read RNA sequencing.  

What learning outcomes should participants expect to take home after the course?

TR: To come back to my previous answer: I hope after the course, cancer genomics won’t be an unknown territory anymore for the participants. I hope we pave the way and then it’s up to the students to make something out of it.

ALIn my section of the course, participants will learn:

1) Bioinformatics algorithms and tools for QC, alignment, and gene expression measurement in bulk short-read RNA-sequencing data

2) Current approaches to analysis of long-read RNA-seq data, comparing the Oxford Nanopore and PacBio sequencing technologies.


Interested in this course? Apply by 26 February.

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

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Meet the Trainer – María del Mar Vivanco

PHOTO: María del Mar Vivanco

Meet María del Mar Vivanco, Team Leader at CIC bioGUNE in Bilbao, Spain. Maria is one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020).

What is your research focus?

I am interested in cancer heterogeneity, why some cells respond to therapy while others do not, thus contributing to development of resistance and metastasis. In particular, I am intrigued about the complex effects of transcription factors, which are required for normal physiology of the mammary gland and are also implicated in tumorigenesis and development of resistance to therapy in breast cancer.

Why did you choose to become a scientist?

When I was young I had a variety of interests – psychology, physics, art, biology… However, I was intrigued by science and anything related to DNA and its regulation. Then I did my PhD at EMBL Heidelberg (Gene Expression Programme) and discovered the opportunities in research for identifying problems, looking for solutions and the thrill of finding some of the answers…and I was hooked!

Where do you see this field heading in the future?

Despite significant progress in cancer research and clinical advances, breast cancer still is the most commonly diagnosed cancer – one in eight women will develop this disease during their lifetime – and it claims the lives of more women than any other cancer, plus men can also get breast cancer. This highlights the unmet clinical need for improved strategies for prevention, early detection and more efficient and specific treatments in order to accelerate progress and help more patients survive the disease.

One of the features that characterises breast cancer is its heterogeneity, both among patients and within each patient tumor. This heterogeneity is found at molecular, phenotypic and functional levels, complicating diagnosis and challenging approaches to therapy. Currently, huge efforts are dedicated to understanding this heterogeneity at all levels, including at single-cell resolution, which is anticipated to open new possibilities for more efficient and specific anti-cancer therapies.

How has training influenced your career? 

Doing my PhD at EMBL marked the way I envision science, and this vision was reinforced and developed further at UCSF. Science can – and SHOULD – be fun. Later on, funding struggles and the current publishing madness have somehow taken a toll on the fun element, so I just have to remind myself sometimes that science is still exciting!

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

An artist.

You are one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

Some of the techniques practiced at this course are specific for the mammary gland and thus it provides a solid base for researchers starting in this field. In addition, there is a significant emphasis on imaging and comparison of mouse and human studies, the two major systems for looking at normal physiology and cancer research that, when combined, offer great insights into this heterogeneous disease. In addition, having the opportunity to work alongside other trainees contributes to the establishment of a network that may be helpful in the future. Cancer is a very complex problem, and having collaborators with different views and expertise will be very useful in your career.

Interested in this course? Submit your application by 8 December!

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10 ways to get your scientific course application accepted

 

Rejection.

We have all experienced it in one way or another. Scientists perhaps more than others – rejected papers, job applications, fellowships, grants or training applications. But what can we do when it happens again and again and again?

In the EMBL Course and Conference Office we see it all – our scientific courses are way oversubscribed, and competition is tough! We’ve taken a look at the most common mistakes that will lead to your application being rejected. These 10 tips will help you to be among the minority of successful course applicants, and while we can’t promise that every application you submit will be accepted, following these tips will ensure that you stay towards the top of the pile!

  1. Apply on time!

It sounds simple, but we have so many requests from late applicants to submit after the deadline. Newsflash – you won’t be considered! The application deadlines are part of a well-planned process, and we stick to it. So plan in advance and don’t leave things until the last minute!

  1. Complete ALL questions directly and clearly

Again – sounds simple, right? It’s amazing how many applicants think some questions are optional. Organisers have to select participants from a highly qualified pool of applicants, and if they have no comparison, you will be put straight on the “no” pile.

  1. Submit all requested documentation

Take the time to collate all requested documentation before submitting your application. If you make it past the first round, these will be vital in securing your spot in the final selection.

  1. Read the guidelines…and follow them!

Generally course guidelines will be provided. Take the time to read through them and make sure you follow them – they are there for a reason!

  1. Be sure that it is the right course for you

Make sure the course WILL actually be of benefit to you. Check that you have the required pre-requisites, and that the learning outcomes are the same as your learning desires.

  1. The motivation LETTER – not the motivation THESIS

Most likely you will be provided with a word limit. Stick to it. If you don’t have a word limit, don’t take this to mean you can write a thesis. The scientific organisers have a lot of applications to go through and limited time to do it. Yours needs to catch their eye from the onset, so make sure the important stuff stands out! 

  1. The motivation letter – the important stuff!

This is perhaps the most important part of your course application, so take it seriously! There is a lot of competition, so show that you have put some effort into it. Things that you should definitely include:

  • Why would you like to attend?
  • What do you expect to learn?
  • How will you benefit from what you learn?
  • How and when will you use the skills learned on the course?
  • A brief description of your current research and future plans
  • Any relevant skills, experience and qualifications
  • Your scientific career and training
  • Relevance in the lab – is the knowledge lacking and can you pass it on?
  1. Show academic curiosity

Make it clear that you have done your research and are actually interested in the topic. If it is clear that you are only applying for the course because your PI told you to, chances that you’ll be considered are slim.

  1. Make sure you can spare the time and, if necessary, get a visa on time

If you have other commitments or think it won’t be possible to get a visa on time to enter the country where the course is taking place, please reconsider and apply for a course taking place at a later date. Otherwise you will take the spot of someone else who would be able to attend.

  1. Show your application to your supervisor

Ask your supervisor to check over your application before submitting. They will have much more experience in submitting successful applications and can give you advice on what to change and adapt to increase your chances of getting accepted.

 

So it’s over to you now! And if you’re not sure where to start looking for your next scientific training course, take a look at our upcoming events under www.embl.org/events.

Check out our video for some more tips on successfully applying for practical courses!

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