ECCB18 at a glance

A few weeks ago I had the amazing opportunity to attend the European Conference of Computational Biology (ECCB) in Athens, Greece. As a proud greek, the moment I saw there was a bioinformatics conference in my home country I really wanted to go, but also it was an excellent opportunity for me to network, create new contacts and ideally find potential elective opportunities. Every trainee, depending on the trust, has a budget allocated by the school to cover the expenses of going to university. If you are not too frivolous when booking your university accommodation, you might end up with some leftover budget that can be used to attend conferences like this one. Don’t be afraid to ask! If you find an event or a conference that you think might be interesting, ask your TO if you can go. Obviously, don’t find the most expensive conference on the other side of the world cause there’s so much your budget can stretch to.

ECCB Overview

The European Conference of Computational Biology is one of the main computational events in Europe and it is organised every two years. This year’s conference was the 17th edition of the ECCB, organised by the Hellenic Society for Computational Biology and Bioinformatics in association with ELIXIR. It took place in the newly-built Stavros Niarchos Foundation Cultural Centre, an impressive facility in the heart of Athens. Each day started and ended with a keynote speech and the rest of the conference programme was split between three rooms that run simultaneously. There were seven themes that alternated between the rooms; Genes, Data, Applications, Genomes, Proteins, Systems and ELIXIR.

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ECCB Highlights

The opening keynote speech was given by Professor John Ioannidis on “Reproducibility with small and big data”. This was definitely one of the most comprehensive talks of the conference. Prof Ioannidis mentioned how 96% of papers claim significant results, however, there are discrepancies between fields on what “statistically significant” means, using a blanket p-value of 0.05 might not be appropriate for everything. Main messages from this talk: “sharing can go a long way in terms of achieving reproducibility” and “we need to redefine statistical significance”.

A fellow delegate @VeraMatser, tweeted her sketch notes and I think it is an excellent and very cool overview of this talk.

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On the same note, Raul Rodriguez-Esteban gave a talk on “Differential gene expression in disease: a comparison between high-throughput studies and the literature” where he mentioned that there are “subjective biases that affect the representation of expression data in literature”. Using the terms “high expression” or “highly expressed” might mean different things to different people.

Another interesting keynote was given by Dame Janet Thornton on “Integrating heterogeneous molecular data to repurpose drugs to improve human health during ageing’. She spoke about the how dietary restriction has shown to extend lifespan in animal studies and how mutations in single genes in the insulin/Igf pathway can extend lifespan in model organisms. Their hypothesis is that if we can treat ageing, we can treat ageing related diseases like cancer etc. It is an interesting approach.

MIT professor, Manolis Kellis, talked about how by understanding the role of epigenome and non-coding regions we can complement genomics and understand disease causing mechanisms.

There was a non-biology related talk that I found very fascinating. Professor Seiradakis from the University of Thessaloniki spoke about the Antikythera Mechanism, “the first analogue computer”. The Antikythera Mechanism has been estimated to date back to sometime between 70-200 BC and it was used to predict astronomical positions and eclipses in advance. It is quite cool that such technology existed so early in history.

During this conference, I attended a lot of the ELIXIR track talks. ELIXIR is an organisation that attempts to bring together scientists and resources across Europe. They strive to create a single infrastructure to coordinate bioinformatics research by sharing data, sharing tools and training scientists on areas of bioinformatics. At the moment, ELIXIR has 22 country members, with Greece being their newest member. During ECCB, there were presentations on a few of the ELIXIR resources:

  • TeSS, ELIXIR’s training platform, aggregating all available ELIXIR courses around Europe in one place.
  • EGA , European Genome-phenome Archive a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.
  • GA4GH Beacon an open sharing platform that allows any genomic data centre in the world to make its data discoverable.
  • Biocontainers, an open source framework that allows sharing of bioinformatics-specific containers.

 

My poster got accepted.

When I asked our lab manager if I could go to that conference, they suggested I try and submit an abstract for a poster. My training officer and I decided to submit an abstract about a small django project I had started and to be honest, I really didn’t think it would be accepted for the conference. But it did. I was over the moon and terrified at the same time as I had never presented any of my work at such a big event. In the end, it wasn’t that bad. I proudly stood by my poster for two hours, and I had some really interesting and insightful conversations with a variety of people from different bioinformatics disciplines. My poster described a tool that could be used by clinical scientists to analyse and store cancer signatures without the need for any specialist bioinformatics knowledge. The majority of people who came to talk to me didn’t really know what a cancer signature is since it is a fairly new concept only known amongst people working in cancer biology or cancer genomics. My first task was to explain to them what a cancer signature is followed by how it could potentially influence patient treatment in the future. Sometimes it is difficult to explain how signatures work and what they mean. A range of people from different backgrounds came to talk to me, some were lecturers at universities, some just MSc or PhD students, some working in the industry. There were also people that were very familiar with the signature concept and started asking specific questions on the analysis, that I was unable to answer. Some people didn’t know that genetics is offered routinely in the UK, they were pleasantly surprised. Overall, it was an interesting experience, and gave me a lot to think about in terms of improving the tool, and how to explain complex terms in the future.

 

 

Take home messages

Although Jes has already written an excellent guide on how to make the most of a conference, here’s my take home messages from this event.

  • If you don’t ask, you don’t get. If you find something interesting ask your training officer if you can go.
  • Pick and choose presentations carefully, as not all might be relevant to you.
    Sometimes, conference presentations are way too specialised. It is ok to not understand everything. Try and note down the major concept and go back and have a look at your own time.
  • Submit an abstract. If you have a piece of work you want to present, submit an abstract for a poster. Worse case scenario it doesn’t get accepted, but at least you would have gone through the process and can improve it next time.
  • Network!!!! I know it might sound daunting, but try and meet some people. If you go to a conference alone, try and find a conference buddy. Try and meet people and discuss what you do, who knows, someone might be doing something interesting and looking for collaborations.
  • Tweet,tweet,tweet. It helps you go back and check what you really found interesting, and helps interact with other conference delegates.

I am so glad I had the chance to attend this conference. I  learned new things, got to present my work, made some new friends and spend a few days in one of my favourite cities. Seize the opportunity while on the training programme to attend conferences as it is slightly more difficult when the deparment is actually paying for it in the future.

Thank you for taking the time to read this.

Author: Adriana

I am a trainee Clinical Bioinformatician based at Addenbrooke's Hospital in Cambridge. I am all for increasing genomics awareness in and out of healthcare and interested in bioinformatics and cancer genomics.

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