NGSchool — Summer School in Bioinformatics. The Beginning.

German Demidov
Sep 29, 2019 · 10 min read

“…Once upon a time, when druids were stitching ropes with the DNA in the forests of Britannia, when Frankonian wizards were boiling DNA and making healing potions from the decoctions and the Vikings were sequencing dinosaurs, deep in the mountains of Vysoké Tatry wiedźmini decided to reunite in a free society of sorcerers to share the wisdom of the bioinformatic magic with the most talented apprentices. They called it NGSchool…”
- ”Epics of Eastern, Central and Balkan Slavs”, IX century, Great Moravia

NGSchool 2017 edition (Warsaw) group photo

Hi there, community members,

we are the team of the #NGSchool — Summer School in Bioinformatics — and in this article, we would like to introduce our initiative to the community.

  • Why do we do this? First of all, we’d like to make a difference and provide excellent training in computational biology, especially for people that can’t afford to pay for it.
  • Why did we reach out to you? We want to spread the word about our school and find future students, mentors, supporters in general, and — maybe — recruit new members into our amazingly cool org team.
  • Why can it be useful for you? Because you can find links to handy materials in bioinformatics here, such as presentations and workshops, as well as the list of potential problems in organizing events similar to ours and our advice on how to solve them, and of course you may find that your ideas are in line with ours and join the network of bioinformatics scientists in Eastern and Central Europe in particular, and worldwide in general!

The next event we are organizing is #NGSchool2019, a school with an intensive program in machine learning for biomedicine, which will be held on 24–31 Oct 2019 in Poland. We encourage you to contact us with any questions or proposals you have — and in the meantime, we would like to describe to you how NGSchool was in 2016, 2017 and 2018.
For your convenience, we will divide the whole story into 2 parts: you’ll find here the introduction and the story about NGSchool2016. The story about the last 2 schools (’17 and ’18), some words about the current school ’19 and the feature plans will be published in the next post.

Moreover, the information about potential opportunities for collaboration will be published in the second part, so if you like the idea and wish to join our initiative for the next year (as a participant? as a speaker? as a hackathon mentor? as a team member?) — we’ll provide some info in the second post.

List of acronyms used:


HOW IT ALL STARTED

Leszek Pryszcz, NGSchool Society President, postdoc at CRG, Barcelona

“I was having a beer with Tomás and Broňa and they told me: ‘Hey why not organise a summer school…’”

As many great things in life, #NGSchool started from a hangout and discussion over a beer with a bunch of friendly and creative people. The idea was born over lunch in Bratislava, back in summer 2015. I was visiting a colleague at Comenius University and he invited a couple of his colleagues to have lunch together. During this lunch, I’ve mentioned that I’ve been organising trainings in bioinformatics in Warsaw and I’ve realised that there is a strong need to boost NGS-related expertise in our region. I was just worried that my approach at that time (hands-on training that lasted several hours) wasn’t working too well. That’s when Tomás and Broňa mentioned organising a summer school…
At first, the idea seemed totally insane. But when you really want something and dedicate enough effort, usually things are just going to work out :) So I’ve started from the most important things: money and time. Organisation of such a school would require substantial funding (€15k for 45 participants for 1 week) and time to organise it. First, I secured funding for myself and moved to Bratislava for my first sabbatical. Then I started working on securing the funding for the school. The idea for funding came from another colleague from Hungary — International Visegrad Fund mission matches our ideas perfectly! In parallel, the website was born (for several months it was hosted on my Raspberry Pi2). I started drafting the program, invited several speakers and advertised the course. But the idea only took off seriously when the funding was approved in May 2016. After announcing that week-long summer school will cost only 50€, people started to take it seriously and finally over 80 people from 15 countries registered!
Those initial months were really hard as everything was new and I didn’t have a clue how to do most of those things. At the same time it was also extremely exciting as I was learning a lot and getting to know great people. Support from Broňa and Tomás, direction and administration of IIMCB and numerous kind people was crucial. Without their help I wouldn’t ever try that!
The first school was a great thing. Organisation was far from perfect, quality-wise it was good and I knew it still could be improved. But I couldn’t do much better on my own… And this is when the big surprise happened. During the first school some participants expressed strong will to participate and help with organisation of the next events. This is how #NGSchool TEAM was born — purely bottom-up approach of a bunch of enthusiasts interested in learning together and sharing their expertise with others. And year after year, this group of enthusiasts is growing.
Now looking back, I’m extremely happy I decided to try it. #NGSchool allows me to develop both personally and professionally. Every school, although hard and exhausting in preparation, was truly an amazing experience. For me, the most exciting part of my research is when I can share it with others. And sharing it with early stage researchers is extremely rewarding. Besides, every year I’m having lots of `scientific` fun with other participants.
But most of all, over all those years I’ve made truly great friends!!!
Hopefully after reading a bit about why, how and what we are doing, you’ll be convinced that #NGSchool is far from typical educational initiative. #NGSchool is all about people and sharing. Building a Community of experts and enthusiasts of bioinformatics was with us from the very beginning. And everything that happened in the last few years is sort of a blend of ideas, expectations, desires and experiences of numerous wonderful people.
Now, we would like to invite You to get to know us and become the part of this Community. Enjoy the ride!


#NGSchool2016: NGS data analysis, Tatra Mountains and Slovak halušky

Roman is giving an Introduction to Lunix, Vysoké Tatry, Slovakia, 2016

German Demidov, #NGSchool team member from 2017, speaker in 2016, Akademischer Mitarbeiter at Institut für Medizinische Genetik und angewandte Genomik, Tuebingen:
”I applied as a participant. I became a professor. You can achieve the same. If you are as cool as me.”

The first NGSchool was a unique event. I applied as a participant initially, but then stars were aligned in a special order these days and I was invited to join the NGSchool team — one of the few events that actually made a change in my life. The thing was — the very initial NGSchool team recruited 30 participants, mainly from Eastern Europe and mainly people who just started their way into bioinformatics. And the team (1 person initially) wanted to provide a comprehensive review of all the methods used for NGS data analysis starting from introduction to Linux and basic data handling and ending with methylation NGS data analysis and GWAS methodology and RNA-seq, etc. and of course such bioinformatics bootcamp would not be full without a CNV detection workshop, and by chance this was the topic I was specialised in. The core team (1 person but why would smb care?) evaluated my application and then wrote to me and asked if I could do a workshop — and since I’ve already done several, I agreed.

The atmosphere at the workshops

Everything was new for everybody since it was the first school. Nevertheless it was great! We [participants, organisers and speakers] were staying at the same house in the mountains of High Tatry, Dolný Smokovec, Slovakia. So, basically, we had workshops and lectures during the day (together with breakfast and lunch — and it was the first time most of us tried Slovak cuisine such as halušky and local beer).

Happy Lunch Time!

And in the evening we had an opportunity to ask any questions from the speakers! I was more experienced than most of the participants — nevertheless I found it super useful and increased my knowledge. In my opinion we were able to achieve such a level of communication because of our social events when everybody — speakers and students — participated, such as barbecue nights and hiking session in the mountains.

…and happy Evening Time!

This first school showed us that the main point of our event should be not just high-quality workshops and lectures, but also creating a relaxed atmosphere that improves the level of scientific discussions and provides enough time for such discussions in the evenings.

Workshops were over for that day, but the scientific discussions were not

Social activities? Many of them. BBQ, movie night, guitar evenings, volleyball games…Honestly, we have no idea how did it fit into only 7 days of the school. And of course the unforgettable hiking in the High Tatry. Almost all the participants went there.

Maybe some of the NGSchool2016 members are here. Maybe not. But it was taken in 2016 in Tatry.

In summary, the first school showed us that we are on the right track and that we should continue working on this project. Lessons we’ve learned from NGSchool2016? almost none. It went without almost any problems. The smoothest 1-week educational event you could imagine. Which basically means that the most meaningful part of our story goes to the second part which will be published soon =)

You can find materials such as presentations and outlines with command-line instructions from the following topics:

  • general handling of NGS data,
  • genome and transcriptome assembly,
  • gene prediction,
  • detection of genomic variants (point mutations, indels, copy-number changes),
  • differential expression of RNA analysis,
  • epigenomics NGS data analysis,
  • GWAS methods
  • biomedical applications of the above-mentioned approaches

here.

Alina Frolova, #NGSchool team member from 2017, participant in 2016, Institute of Molecular Biology and Genetics, Kyiv, Ukraine

In 2016 I joined as a participant and the impression I got from NGSchool was so strong, that I couldn’t pass the opportunity to join the initiative and propagate NGSchool ideals further. I might have been affected by aroma of tatranský čaj, but I never regretted my decision and now I’m still here, organising upcoming editions of this roller coaster of science and fun. I might note that NGSchool really makes a difference for Ukraine as average Ukrainian student can hardly afford paying more than 100 EUR of registration fee and cover accommodation and travel. Another point is that NGSchool is heavily practical to the point that we stayed from 9AM till 23PM doing programming or begging German to give us an additional lecture on statistics. I’m glad that we were forced to go into the mountains for the whole day, otherwise we would have overworked ourselves. We are trying to improve the balance of mental and physical activities for the upcoming editions, but be prepared to suffer:)

Well, here I am sure that one of the NGSchool2016 members is depcited.

And of course it would not be fair if we just put opinions from the organisers, that’s why we asked (3 years later but still) the participants if they are willing to comment on that school, and we were not disappointed — the comments were matching our impressions.

Ádám Györkei, PhD Student at Biological Research Center Szeged, Hungary:

NGSchool2016 was a game changing introduction to genomics, transcriptomics and NGS data analysis for me. In a field where the learning curve is notoriously steep and most scientists struggle to find entry points, it provided a solid and practical introduction. From the most basics of shell programming, and data manipulation to visualization of end results we learned every important step of NGS data analysis. Detailed class materials and notes were provided, to which I sometimes return in my current projects, even after publishing in the field. Even though the teachers were experts in their own right, they succeeded to find common ground with us, students, creating a welcoming environment and a great learning experience. It has been the best of similarly themed practical schools I’ve attended so far.


How will our heroes survive NGSchool2017 and NGSchool2018? Who will win the heart of the beautiful Rosalind? How a camel can go through the eye of a needle? (actually, not a camel, its DNA, but through even a smaller hole) Can we decipher every single cell of our organisms with the power of science (and our computers)? And finally — how to make Eastern European bioinformatics great again?
Let’s see in the next episode…In the meanwhile, support our story with your reposts, if you find it interesting.

See ya next week ;-)

The main author: German
Read, edited, but not necessarily approved by
Alina, Gienio, Leszek, Maciej, Maja, Sam
Many thanks to all the people who supported us, took part in the organization of the school, was a speaker or a participant at one of the summer schools or satellite events, sponsored us.

This is our web site: https://ngschool.eu

And this is the contact form. Also, contact us if you have something to add to this story.

The last part of the story is here and the second is here.

More From Medium

Also tagged Biology

Top on Medium

Ed Yong
Mar 25 · 22 min read

20K

Welcome to a place where words matter. On Medium, smart voices and original ideas take center stage - with no ads in sight. Watch
Follow all the topics you care about, and we’ll deliver the best stories for you to your homepage and inbox. Explore
Get unlimited access to the best stories on Medium — and support writers while you’re at it. Just $5/month. Upgrade