Rebecca Nicholl – EMBL Events

Competency-based training in bioinformatics

This article was written by Victoria Hill, Chemistry PhD student at the University of Sheffield.

Recently, EMBL-EBI, in collaboration with a number of our EU project partners, launched the Competency Hub. This is a free platform where students and professionals can evaluate their abilities against the competencies of that framework.

Competency Hub hero image — Competency Hub: Supporting competency-based training and professional development.

What is a competency?

A competency is an observable and measurable ability of any professional, specific to those required in your field. They’re further broken down into the Knowledge, Skills, and Attitudes (KSAs).

The competencies are all mapped to career profiles ranging from PhD student to senior roles, both in industry and academia, and assigned a grade on a scale that measures the level the individual should be at in that competency depending on the profile. For a more in-depth analysis, the user can go into each graded competency and look at which KSAs are applicable at that career stage.

An example of a competency within the BioExcel framework graded at ‘Awareness’ and the associated KSAs mapped to the career profile ‘PhD Student in Biomolecular Simulations’.

What does the Competency Hub offer?

Evaluate your competencies against those of each framework by creating a profile and comparing them to the pre-defined career profiles.
Find training resources for each competency, and in some frameworks, more in-depth learning pathways for skills relevant to that field.
Develop courses as a trainer using the Competency Hub. Define your audience, plan your content, and write learning outcomes, as well as compare your resources to what is already available.
Assess whether, as a trainer, you are targeting the correct audience and use the competencies to provide an overview to stakeholders.
Evaluate your team and create job descriptions as a manager.

An example avatar

How did we do it?

After a pilot project with the BioExcel Knowledge Resource Centre, we decided to create a site where everybody can access all the information included in the competency framework.

The Competency Hub was developed by the EMBL-EBI Training and Web Development teams in dedicated two-week collaborative development sprints.

A goal was defined for each sprint; our most recent one focused on improving the career profile journeys. Previous sprints included making the site more user-friendly, adding learning pathway functionality, and adding career profiles, among other tasks to constantly improve the site.

What is next?

At the end of each sprint, we gain feedback from users to determine our next goals. The next sprint will focus on improving the connections between the competencies and the career profiles to the training resources.

Want to get involved with future development? Fill in our survey.

We’d love to hear what you think of this new feature! Tell us on Twitter using @EBItraining.

What’s new in EMBL-EBI on-demand training

What’s new for EMBL-EBI training: June 2022

At EMBL-EBI training we have a dedicated on-demand library of free to access training courses, materials, and recordings. Read on to see what each section of our 200+ strong catalogue entails.

Training materials

We’ve all had our fair share of training courses, zooms, conferences, and workshops in our careers – and can all relate to the sheer mass of materials generated in just one of these events.

EMBL-EBI Training is committed to creating FAIR and shareable data through our own courses and on-demand training. We welcome you to share these already created materials so that you don’t have to spend time recreating them for yourselves.

From EMBL-EBI resource tutorials to live course slide decks – our cohesive library of training materials is ready for you to use anytime, anywhere. All we ask is you credit us when presenting them!

Themed on-demand training sets

At EMBL-EBI training, we discovered a pattern of behaviour from our on-demand audience taking multiple courses within the same topic area.

So we’ve bought together four curated sets of learning to ease the journey for you. We have more ideas in the pipeline, but if you think of a curated set of learning you’d like to see, drop us a comment below!

Webinars – join in the next series

The bioinformatics topic du jour has to be AlphaFold. We’re planning a mini webinar series on the topic, beginning on 14 June 2022 with the ‘Scope and vision of AlphaFold’.

AlphaFold protein structure prediction showing detail of chemical elements.

Registration for the webinar series is free, but essential to secure your place. If you can’t make it live, the recordings will be made available via these same links shortly afterwards.

14 June 2022 | 13:30 – 15:00 BST | Scope and vision of AlphaFold
21 June 2022 | 13:30 – 15:00 BST | Impact of AlphaFold on teaching and training in life sciences
28 June 2022 | 13:30 – 15:00 BST | Impact of AlphaFold on research and development

To stay up to date with news from the EMBL-EBI training on-demand catalogue, create an account and opt-in to news from us.

EMBL-EBI Training website: one year on

Author: Anna Swan, Scientific Training Officer, e-learning at EMBL-EBI.

In February 2021, we launched the new EMBL-EBI Training website. Read more about that in our previous blog post.

Since then we’ve had over 600,000 visitors from around the world using the site to discover our live courses and learn from our on-demand training.

What does EMBL-EBI Training’s site offer?

Listings and registration pages for all of our live training, including face-to-face courses and webinars
Access to on-demand training, such as self-paced online tutorials and recorded webinars that are available anytime, anywhere
A simple search box on the homepage to help you search for training on a topic of interest
Support for trainers in using our materials and expanding their training skills

A screen shot of the EMBL-EBI training homepage — The homepage allows users to search and browse for training of interest.

What’s new since we launched in 2021?

After releasing the new site, we continued with further development. In line with EMBL’s mission to provide the world with #OpenData, we now provide sets of course materials from live courses, open to everyone, not just those that attended. You can find these in the on-demand section of the website.

Course materials can be in a variety of formats: lecture recordings, slides and practical instructions.

A screen shot of EMBL-EBI training, on-demand listings — Sets of course materials are now listed in our on-demand section – available for you to access anytime.

The materials are presented with overviews and learning objectives for each session of the course and are searchable to help you find the specific materials that are of use to you.

Not only that, all sets of course materials are labelled CC-BY, so you can use them for your own learning, or to train others. We encourage you to use our training far and wide.

As we continue to run live courses, the materials will be updated with the latest science and analysis methods to help you stay up to date.

A screenshot of the EMBL-EBI course website for bioinformatics for immunologists and its course materials — There are a range of topics covered by our course materials, including bioinformatics for immunologists.

What’s new for 2022?

With the site now a place many people come to find and complete learning, our next focus is on the community around bioinformatics training and learning.

If you are someone who teaches about EMBL-EBI resources, we’re keen to hear from you! Complete our short survey to join our community focus group.

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.

Meet the EMBL Events Team: Sophie

Meet the newest member of the EMBL-EBI training team, Sophie Spencer. She joined the team in October 2021 with a focus on the on-site and virtual training programme.

We sat down with Sophie to get to know her and find out about some of the other career paths she could have taken.

Welcome to the team, Sophie. Now that you have been able to visit the EMBL-EBI campus, what is your favourite place in the area?
The campus is absolutely amazing, and I have to say Hinxton Hall is a fantastic venue. I can’t wait to run an event there once restrictions allow.

As an experienced events organiser, what is the first thing you do before a course starts and the first thing you do after a course finishes?
Just before a course starts, I take a deep breath and visualise how the day will run. It might sound odd, but it helps me to work through my on-the-day checklist. The first thing I do after a course finishes is to take another deep breath and smile!

Changing tact, if you weren’t an events organiser what would you be?
I absolutely love working in events, but I do have a dream of running an alpaca farm with a cute little café when I retire. Of course, I will need to learn about how to care for alpacas first…

What is the funniest thing that has ever happened in an event?
That’s a tricky one! I’d have to go with this time I was running a virtual conference a year or so ago. During the event, we had some unforeseen technical issues which, unfortunately, disrupted the entire event. I managed to fix the issue and came on screen to explain to the audience what had happened and to apologise for the disruption. A little while later I was running a session with our keynote speaker who happened to be a polar explorer. He proceeded to invite me to join his next polar exploration because of how calm I am under pressure! Can’t see myself traversing the Antarctic any time soon but nice to know I’ve got options if my event organiser career doesn’t work out.

We think events organisers are already superheroes, but if you were a fictional superhero what power would you like to have?
It would be wonderful to be able to talk to animals, imagine if you could know what your pets are thinking!

And finally, tell us, what is your favourite book?
I’m going to cheat and give a series rather than a single book… I’ve just revisited “His Dark Materials” by Philip Pullman which I loved as a child, and still do today!

You can connect with Sophie on LinkedIn or join her at the following events she is currently working on:

Single-cell RNA-seq analysis using Galaxy – applications open until 7 January 2022.
Managing a bioinformatics core facility – register your interest.
Bioinformatics for T-cell immunology – register your interest.
Genome bioinformatics: resequencing and variant calling – register your interest.