Meet the trainer: Isidro Cortes Ciriano

We sat down with Isidro Cortes Ciriano to discuss his involvement with the upcoming EMBL-EBI Cancer genomics course, and find out what training means to him. 

Cancer genomics | 20 – 24 June 2022 | Hinxton, UK

Hi Isidro! Tell us a bit about yourself for those that don’t know you.

I joined EMBL-EBI in 2019 as a research group leader. My team focuses on the development of computational tools to understand the molecular alterations underpinning cancer, with a focus on the analysis of somatic mutations using sequencing data.

I am also one of the scientific organisers of this year’s EMBL-EBI Cancer genomics training course.

What is your research focus, and how long have you worked in your scientific field?

I obtained my PhD at the Pasteur Institute in 2015 before completing postdoctoral training at Harvard Medical School, under the supervision of Prof. Peter Park, and at the University of Cambridge, under the supervision of Prof. Andreas Bender.  My expertise includes biology, genomics and statistical modelling.

Tell us more about the Cancer genomics course you’re involved in. What advice would you give to anyone thinking of applying?

Do it! The course provides an exciting opportunity to learn about the latest approaches for cancer genome analysis, with relevance for both research and clinical applications.

That sounds great! How has training influenced or assisted your own career do you think?

Training at the MSc/PhD level is fundamental to cement basic knowledge in the field. This includes both reading literature and hands-on training to understand the particularities and limitations of the algorithms we use, all of which helps acquire the necessary expertise to drive research projects in a rigorous manner.

Thanks Isidro, we can’t wait to hear you talk at the course this June.

Join Isidro Cortes Ciriano at EMBL-EBI's Cancer genomics training course.
Join Isidro Cortes Ciriano at EMBL-EBI’s Cancer genomics training course.

Applications for Cancer genomics are now open until 11 March 2022.
View the full programme and apply now.

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Join EMBL-EBI training at our Wednesday Webinars!

If you’re looking for bite-sized learning opportunities delivered by EMBL-EBI experts, then our regular series of webinars might be just what you are looking for!

EMBL-EBI’s Training team has been running a series of webinars since 2013, featuring speakers from across EMBL and beyond. Over the years we have covered a wide range of subjects, but its roots are in the resources and databases made available by EMBL-EBI, as well as related biological topics. So far in 2021, we’ve heard from members of Ensembl, RNAcentral, EuropePMC, UniProt and the European Genome-Phenome Archive, with many more to come.

The webinars were started as a way to enable a much wider audience to access our training and interact with our experts. They provide attendees with an introduction to a topic and resource, along with the all important opportunity to ask questions directly to our trainers. If you want to know more about how to use a resource, or perhaps how to analyse or submit data, these are the people with the answers! 

Exploring our upcoming webinar listings provides an overview of subjects to be covered. For the majority of webinars the only thing required is an interest in the topic, though some may be aimed at a more specific audience.

The Training team’s Scientific Training Coordinator, Sarah Morgan, at the first webinar of 2021, introducing EMBL-EBI’s resources and the training available.

The series is currently organised by my colleague Ajay Mishra and I. One of us is on hand at every webinar, introducing the speakers and making sure everything runs smoothly. As well as ensuring questions are answered, we also provide an opportunity for all attendees to give feedback, so if you join us, please let us know what you think. You can also tell us if there’s a topic you are keen to see covered in the future. 

 

EMBL-EBI’s webinars are currently run by Anna Swan and Ajay Mishra.

Over the years we have run a number of focused webinar series, including programmatic access of EMBL-EBI resources and data management. From April this year, we will be running a new focused series, “A guide to…”, where we will introduce some concepts in bioinformatics and how they link to some of the EMBL-EBI resources. This series is aimed particularly at students and early-career researchers, but anyone with an interest will be welcome. We will be kicking off the series with topics such as “A guide to exploring genes and genomes with Ensembl” and “A guide to RNA families”. The first webinars in the series are available for registration now, but keep an eye out for future topics in this series, including drug discovery and pathway analysis. 

If you are ever unsure about joining a webinar, you can always contact the team at webinars@ebi.ac.uk and we’ll happily answer any questions you may have. We’re also always thinking about what to include next in the programme, so let us know if there’s something you would like to see.

Finally, if there is a webinar that has taken place in the past or there’s one you cannot attend, it is not a problem! We record them all and make them available, along with the slides, in the on-demand section of our website. We always include details on how to get in touch with the trainers and their teams so you can ask the experts a question anytime. We also encourage other trainers to use our recordings and materials in their own training – check out these details on re-use of our content for further information.

We look forward to seeing you at a webinar in the future.

 


Written by 
Anna Swan.

Anna Swan – Scientific Training Officer (e-learning) – EMBL-EBI Training

Anna joined the Training Team at EMBL-EBI in March 2019 as a Scientific Training Officer (e-learning). She has a PhD in Bioinformatics from the University of Nottingham, where she focused on the bioinformatic identification of biomarkers of osteoarthritis. Following her PhD, Anna worked as a medical writer, spanning many therapeutic areas and working both on promotional and educational content for clinicians. Returning to bioinformatics, Anna worked as a data wrangler for the International Mouse Phenotyping Consortium at the project’s data coordination centre based in the Medical Research Council’s Harwell Institute.

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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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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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CABANA – not just a shelter from the sun

You may have heard the name CABANA floating around the EMBL training programme, but you may not know exactly what it is. Here we present a handy guide to the project, its origins and where it stands now almost three years on from its launch.

PHOTO: CABANA logo
PHOTO: CABANA logo

CABANA is a capacity strengthening project for bioinformatics in Latin America. It aims to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme focusing on three challenge areas – communicable disease, sustainable food production and protection of biodiversity.

Want to know more about the project? Check out this video from the CABANA consortium.

With just over a year left of the project, funded by the Global Challenges Research Fund (GCRF) – part of the UK Aid Budget, the capacity building element of the project is ramping up. A big part of the project is running a series of training events for the Latin American audience, something that began with the centralised events team within EMBL-EBI, but is now increasingly being operated in Latin America by the partners themselves.

CABANA has virtualised its training programme for the rest of 2020 and has committed to a fully virtual 2021 programme too. Check out the latest events on offer, or visit the new virtual training portal for the e-learning options.

Follow the CABANA project on Twitter or Facebook for the latest news and updates.

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