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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Bioinformatics for Biobusiness: make biodata work for you

This year EMBL’s European Bioinformatics Institute (EMBL-EBI) is teaming up with Medicines Discovery Catapult (MDC) on 22nd April to deliver an exciting new SME forum: Bioinformatics for Biobusiness (B4BB). This virtual event will promote the power of bioinformatics in driving success across the life science business sectors.

We’re welcoming all businesses engaged in using biodata to take a deep-dive into how to use bioinformatics to grow your business. The agenda has been developed in an open forum style, with a full line-up of expert speakers, including John Overington, Chief Informatics Officer at MDC, Jason Swedlow, Professor of Quantitative Cell Biology at the University of Dundee and Neil Hall, Joint Head of ELIXIR-UK). There is also an opportunity to book a 1:1 meeting with Marc Daigneault, Head of Research Funding at Medicines Discovery Catapult.

Meet in small groups with expert bioinformaticians, and like-minded SMEs using informatics to advance their businesses Explore software tools and services enabling access and analyses in various biomolecular domains Discover available support, and the diverse range of open biological data resources Hear updates on the latest developments in genomics, proteins, chemical biology and imaging Discover available support, and the diverse range of open biological data resources

The half day interactive forum will bring together a raft of information from EMBL-EBI’s bioinformatics resources that are made public and freely available to the global R&D community, and a chance to discover the support available from MDC and their work to reshape the medicines discovery community by championing innovative life science technology in the UK. 

There has been a fantastic response since the event opened for registration, and there are still places available. Visit the website for the full event information including the agenda, register your place and for a chance to view a series of preview videos presented by the experts showcasing resources at B4BB. 

For any other questions contact Effie Mutasa-Gottgens, Senior Scientific Officer or Lucie Smith, Event Organiser, in the EMBL-EBI Industry partnerships team.

       

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The smarter way to find bioinformatics training

The EMBL-EBI Training website is the first port of call for many life scientists, bioinformaticians and computational specialists looking to further their knowledge of the field. We’re proud to offer world-leading bioinformatics training to users across the globe, with over 600,000 visitors to our online courses alone each year.

Now more than ever before, we see the need to make our training easily accessible, visible and findable so that anyone, regardless of location, career stage or experience of training with us can find the resources they need.

We’re therefore very pleased to be able to introduce to you the brighter, smarter way to find bioinformatics training from EMBL-EBI.


What’s new?

  • Find relevant training more easily, in the format that works best for you 
  • Flexible free-text search based on EMBL-EBI’s own search engine 
  • Combine search and filters to quickly identify the course you need 
  • A modern, clean look and feel with simple navigation 

Site tour searching our virtual courses

Site tour searching our recorded webinars

How did we do it?

This project officially began in April 2019, when we discussed the brief and set things in motion for the next 12-18 months. Little did we imagine that an idea sketched out on a plane journey from London to Amsterdam in early 2019 would lead to such a large scale project. We constantly review our engagement with users and potential trainees, enabling us to think about how we can better provide the content and course information they will be searching for. This in turn enables us to remain world-class leaders in what we do. From the start we were led by user feedback and web analytics in order to define where improvements were needed.

The main purpose of this project has always been to enable and encourage you (our users) to engage with all our content and put the training into your (virtual!) hands.

We needed a new interface that works for a diverse user base, regardless of research needs, scientific interests or career stage. Given that we offer a mix of live training and on-demand content (freely accessible, anytime), this was always going to be a task requiring a lot of man-power from across the organisation to make it the best it could possibly be. 

Team creation and adoption of agile methodology

Our ongoing collaboration with the EMBL-EBI Web Development team has been crucial to getting us from concept to a final product. They have not only provided us with several talented developers who make our ideas come to life on the web, but also user experience (UX) experts, who have helped us explore what our users really need. 

We began the project with a plan to implement agile scrum methodology as our guiding framework, which was new to many members of the project team. As such we worked in two-week ‘sprints’ where the team would focus exclusively on the project, maximising efficiency and creating a potentially releasable product at the end of each sprint. 

First steps

Our first task was to redesign the courses in our Train Online catalogue, our freely-available library of online tutorials. We took one of our most popular courses, called Bioinformatics for the terrified, and soon released a live BETA version for our users to try out and provide feedback to guide us as we worked on other course types and pages.

If you have used our website regularly, this image will look pretty familiar to you. This is what the team started with at the beginning of the project.

We then moved to this updated design which you can see looks very different from our old course pages. This is where the design really took off and we used this as a base to make other minor changes which took us to our final design which you can see below.

Here it is, our final design. The layout and functionality remained largely the same from the first design based on user feedback, but we updated the graphics which you can see in the page header. Read more about the background behind the graphic changes below.

Design 

The users and the EMBL-EBI training team gave very positive feedback on the layout and functionality of the new online course pages. However we quickly realised that we required some design expertise and our colleagues at EMBL Design were brought on board to assist with providing beautiful new graphics for the page headers. We also utilised the EMBL visual framework to create a look that was coherent and consistent with other pages in the wider EMBL brand. The EMBL visual framework is what provides the building blocks of this new look and feel.

New event pages

We followed up the creation of the online courses by implementing similar design and layout changes to our live courses. We gradually began to make the switchover with both upcoming live events and our extensive back catalogue of on-demand materials.

What’s next for the project?

Two years on, the whole of the EMBL-EBI Training site has been redesigned and deployed following an iterative and user-centered approach. We are thrilled to be able to release this to you – our users – so you can benefit from the new look and functionality.

Our hard work doesn’t stop now. Next up, we will be looking to enhance your experience even further by enabling you to track your personal progress, and enhancing the way you access past content to help you continue your learning journey with us.

Acknowledgements

We’d like to thank all those that have been involved in this project from across the EMBL and EMBL-EBI teams, as well as you (our users) that have feedback across the journey. 

Special thanks go to Adam Broadbent, Ajay Mishra, Anna Swan and Sarah Morgan from the EMBL-EBI Training team, to Nikiforos Karamanis and Prakash Singh from EMBL-EBI Web Development team, and to past team members Melissa Burke and Joseph Rossetto – without you, this project wouldn’t be the success it is today.

Photos from the project

Here are a few snaps from the project along the way.

One of the first sketches of the cover page of the online tutorials.
A wireframe with notes after a feedback session.
One of our many higher fidelity mockup with feedback from a usability test: Green sticky notes report positive feedback (but there are some remaining issues).
Here we have Jonathan Hickford (previous Head of Web Development) and Sarah Morgan (Scientific Training Coordinator in the Training team) writing user stories.
When we got to the end of a sprint there was only one way to celebrate…cake.

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EMBL-EBI Industry Partnerships: Work with us to solve your data challenges

Partnering with industry has been a core part of EMBL-EBI’s mission right from the very beginning and a significant number of our users come from this sector. As we celebrate an incredible 25 years of industry collaboration next year, let’s hear from Andrew Leach, the new Head of Industry Partnerships at EMBL-EBI to find out a bit more.

Image: Dr Andrew Leach, joined EMBL-EBI in August 2016 following a 20 year career at GSK Research and Development. He took on the role as Head of Industry Partnerships in the summer this year, and will also continue as Head of Chemical Biology.

Industry Partnerships: What does this mean at EMBL-EBI?

Industry Partnerships at EMBL-EBI is about helping to connect public and industry science. We aim to foster and facilitate collaboration, knowledge exchange and networking between scientists and technologists at EMBL-EBI and their counterparts working in industry. We work across multiple sectors and with organisations from very large multinationals to very small start-ups.

Tell us more about the opportunities for scientists in industry to interact with EMBL-EBI.

EMBL-EBI’s Industry Programme is a subscription-based programme for global companies who are using EMBL-EBI’s data and resources as part of their research and development. Representatives from the member companies meet regularly in a forum where we share details of the latest innovations in EMBL-EBI’s services and research. The programme also organises a series of knowledge exchange workshops that explore new emerging areas for R&D. These events are open to any employee of the member companies. The programme also provides a great opportunity for scientists to meet their peers in a pre-competitive, science-oriented environment to discuss the latest developments.

We are always keen to hear of opportunities to explore new strategic partnerships with industry. Open Targets is an excellent example; this ground-breaking public-private consortium was established in 2014 with the overall goal of improving how we identify and prioritise drug targets. Open Targets currently involves six partners: EMBL-EBI, the Wellcome Sanger Institute, GlaxoSmithKline, Bristol Myers Squibb, Takeda and Sanofi.

We also have a proud history of research collaborations that bring together expertise from academia and industry to work on a common research problem or to address a particular data or technology challenge. One particular advantage of collaborating with EMBL-EBI is that we have tremendous flexibility in the way that collaborations can be set up, from small projects lasting a few months, to much larger projects. Key to success is active participation and commitment from everyone involved.

What about smaller companies? 

Every company has to start somewhere and we are committed to engage with small and medium-sized enterprises (SMEs) and start-up enterprises. These are very often the drivers of innovation, and we find that such organisations make extensive use of the resources available at EMBL-EBI. We actively work with organisations such as OneNucleus, the UK Trade and Investment agency (UKTI), the InnovateUK Bioinformatics knowledge-transfer network and the ELIXIR SME and Innovation Forum to showcase the opportunities at EMBL-EBI. Of course, we are also very keen to hear from any smaller company interested in collaborating more directly with us on a particular problem.

What can be achieved by connecting with industry?

Having worked in industry myself (for many years at GSK), I know that industry science is often just as cutting-edge as in traditional academic circles – but historically it has been much less visible due in part to commercial sensitivities together with the fact that publication was not seen as a key goal in industry. These attitudes are changing now; there is a real drive within industry to collaborate externally and especially with leading academic groups and institutions. Industry can bring “real world” applications of the resources and research that we do at the EMBL-EBI; it can be very rewarding to see how the work we do can translate into practical applications. Plus, it can be a way for students and post-docs to get some insights into what a career in industry looks like, and potentially for industry to identify potential recruits for the future!

What would you like to see in the future for Industry Partnerships at EMBL-EBI?

I would like to see our connections with industry continue to grow and strengthen. We have historically had very strong connections with the Pharma and biotech sectors and it would be good to see us strengthen our relationships in other areas of bioscience and also with relevant data science and technology sectors. Of course, we are always keen to create new large-scale strategic partnerships such as Open Targets but we also recognise that a smaller-scale, one-on-one collaboration for example between an SME and an EMBL-EBI Principle Investigator can be equally fruitful. We also want to make further steps to encourage entrepreneurs; this includes working with Jo Mills (Entrepreneurship and Innovation Centre Manager) who with her team is creating a new Startup School for genomics and biodata. This will support early-stage ideas and provide knowledge and confidence to develop them into future products or services.

We always welcome opportunities to explore new partnerships and ventures.

Find out moreGet in touch

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In Focus: EMBL-EBI Training

In 2019 EMBL-EBI celebrated their 25th anniversary. To commemorate this milestone, a series of videos – In Focus – were filmed, including one with our very own Cath Brooksbank, Head of Training at EMBL-EBI.

In the video, Cath discusses the role of technology in bioinformatics training from past to present and through to the future.

Traditionally bioinformatics training has been face-to-face, but EMBL-EBI also have a large online training offering through our Train Online programme.  Train Online can be remotely accessed around the globe, at anytime, allowing our training to reach a much larger global audience at a time that suits the user.

Train Online is currently undergoing a makeover – check out the new look at bit.ly/betaBix

At EMBL-EBI we also want to breakdown the isolation faced by solo bioinformaticians in institutes, and bring them together with peers through our training offering – whether in person or online via collaborative tools such as Google Docs.

And of course there will be times where face to face will not be possible. Whether due to ill health, parental leave or visa issues we understand that sometimes people cannot physically reach our on-site training courses. For those times, we have our robot avatar to enable remote access to our events. Read more about our robot.

EMBL-EBI Robot Avatar facilitates remote learning

Check out our range of online courses; access anywhere, at any time.

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