NGSchool — Summer School in Bioinformatics. Becoming.

German Demidov
Oct 21, 2019 · 11 min read

This is a series of blog posts about the NGSchool, previous posts may be found here and here.

#NGSchool2018: viewing Lublin through a NanoPore

Medieval Lublin

And again in 2018 we have decided to teach (and learn!) about the cutting edge technology — long read sequencing that only recently became available at the market. The second topic of the school was more established, but nevertheless very important — applications of bioinformatics for healthcare analysis. We invited top-level scientists from the best scientific centers to give workshops, but it was amazing how well all of them fit into the community and were eager to discuss their discoveries and giving advice to our participants!
The lectures and workshops covered during the school:

  • Bioinformatics 101
  • Wet-lab 101
  • Juggling
  • De novo genome assembly
  • Precision Oncology. Applications of tumor genome and transcriptome sequencing. Liquid biopsy
  • Algorithms for nucleic sequence alignment
  • Pushing state-of-the art in transcriptomics and metagenomics on the road to personalized medicine
  • Next generation sequencing in clinical diagnosis — what do we need to improve analysis.
  • Variants calling based on long reads.
  • Graph data structures for personalized genomics
  • Magnusiomyces/Saprochaete genome project
  • Molecular biology methods in forensics
  • MinION explained: principles, running and hacking
  • Long reads and Mendelian diseases
  • Construction of a logical model for interpreting the multifactorial risk of disease
  • Block-chain use in science and medicine
  • Insights into the rare and the small: genome sequencing of non-model organisms
  • Genome sequencing reveals how DNA repair is organized in human cells

The materials from the school may be found here.

The lecture in long reads usage for the deciphering of complex SVs

The laboratories were kindly provided by the medical faculty of the University of Lublin.

The venue

The first day we had a juggling workshop. It was cool. Seriously, guys. I could have never imagined 40+ young scientists in the same room, juggling and being fully immersed in the process. You should try it too.

We started with these scarves and then switched to the proper balls for juggling. Tons of laugh.

The new idea for us were hackathons (only in 3rd generation sequencing, not in personalised medicine — we did not have a licence to do medical practice in Poland). We organised 4 groups that started to work since the first days of the school and continued until the end, with presentations of the projects at the end of the school’s week.
The topics of hackathons were:

  • sequencing and de novo genome assembly
  • metagenomics of oral microbiomes
  • direct RNA-seq & de novo transcriptome assembly
  • human genomics

How was it? Well, tough. Almost all the hackathons had a large wet-lab (experimental) part and there were quite a few failures (which are common for biology in general).

Even though we had access to the University’s labs, we still had to bring a lot of equipment for DNA preparation with us. We had to borrow it from other labs from different corners of Poland — which meant many cars and many additional expenses.

A small piece of the equipment that we had to bring to the school

Also, the hackathons were led by invited mentors and we had to fully rely on their organisational skills. And each hackathon’s team was led not only by a supervisor but by a team of people: technicians, assistants, bioinformatics support… We were extremely tired at the end. Was it worth it? Can we recommend doing this to others?

Some of us had experience with pipetting. Some — not. But it was really interesting.

Yes and no. Many people learned new things and many people found their scientific projects. And even some of the speakers from the personalised medicine field decided to adapt single-molecule sequencing in their further medical routines. So, for most of the participants — the effect was tremendous. But on the other hand, we put in so much effort and — let’s be honest — we managed only because we were already quite experienced in organizing events and several of us had experience with this technology. The idea of school-long hackathons is challenging and it is crucial to understand how much effort it will take before you even start to think about your school (e.g., at least 1 year before the school). But if you are sure that you will manage it will be an unforgettable experience for the participants — and for the speakers too. We find the idea of mixing two potentially related fields in one school really fortunate since it gives everybody an opportunity to learn at the school, not only the participants.

Final presentations of the hackathons

Social things? 2 of our participants came to the historical center of Lublin for 2–3 hours and were able to organise a scavenger hunt-type quest in the city. It was a sequence of riddles, connected to the history of the town, and all the participants divided into teams had to solve all of them as fast as they could and resolve a protein sequence in the end. It was amazing since it gave us an opportunity to get to know the city better and helped the participants to get to know each other!

We are solving the quest! (scary? nah, it was fun)

Lecture in a bar. Should I say more? Well, I will anyway.

That’s how it was.

One of the brilliant scientists that agreed to come to our school gave us an exciting intro on his projects (mutational rate across the genome and many other topics) in a bar. When I become a president of some country, or maybe not a country, all the PhD students will have a lecture in a bar once per week.
Our participants self-organised and went to do bouldering in a small team of 6 people. That was great. The thing that surprised us the most is that they did it without skipping lectures or workshops. Cool. Next time we will fill all the gaps in the schedule. Just kidding, we will leave one per day for a short nap at night.
Maybe we should mention pierogi. They were a big part of our school that year and probably next year too. Eating pierogi in the evening (as well as for lunch and for breakfast) makes scientific discussions easier. Only approximately half of the people from the NGSchool2018 knew Polish language, but all of us learned the language of pierogi.

Pie. Ro. Gi.

But what the participants of the school think? We asked…

Samantha Filipów, PhD student, #NGschool Team Member since 2019, participant in 2018

The very first thing I learned at #NGSchool2018 was how to juggle. Then it got even better! For me, a wet lab person, NGSchool workshops felt like stepping into a new dimension of biological sciences. I thought I would suffer but everybody was friendly and truly helpful. =) Passionate people, great social events, lectures held by leading experts and family atmosphere — that’s what NGSchool really is.

Anamaria Elek, NGSchool2018 participant, PhD student at CRG, Barcelona, Spain

Coming to NGSchool fresh after completing my Masters studies, and with both skillset and experience that were nowhere near extensive, I saw it primarily as an amazing learning opportunity. And it did not disappoint, as all the lectures and workshops were interesting and engaging, and hackatons were especially remarkable — some of the groups have done outstanding amount of work there that culminated in publication of their findings afterwards! Diverse background of the participants — ranging from computer scientists who never held a pipette, to wet lab biologists who never opened a terminal — combined with the crammed schedule and narrow one-week timeline, made the hackaton I attended feel like sort of a crash-course in NGS data generation and analysis. And I found this design quite rewarding, firstly because I got a hands-on introduction to some of the tools and methods that I was not familiar with before, and secondly — and not less importantly — because there were some aspects in which I happened to be more skilled than the rest and could therefore actively contribute to driving our mini-project to its conclusion. That general atmosphere of sharing skills and knowledge extended to lectures and workshops, as well. And while a lot has already been written about the unique sense of community among the participants, lecturers, mentors and organizers at NGSchool, it really cannot be overemphasized. A range of both planned and impromptu social activities, and an unspoken agreement that everyone was at the same social level here, created a brilliant atmosphere that made it easy to approach people and initiate discussions. I can’t imagine how else would I have talked about career prospects in academia and industry with senior staff scientist and PIs who certainly can offer a lot of advice on the topic, but whom you otherwise wouldn’t really go asking this out of the blue. Nor can I picture how else would I end up discussing the prospects of socios model for football clubs’ ownership with one of them, but that also happened at one point. It was just amazing how approachable and easy-going everyone was.
To draw the line, attending NGSchool 2018 was without doubt one of the most significant and at the same time enjoyable events that helped to shape my scientific path up to this point and I hope many others have and will experience the same and share this opinion.


#NGSchool2019: learning ex Machina

This year we are gonna provide a series of training in machine learning for bioinformatics. The topic is not logically similar to the previous 2 — we are not gonna discuss anything cutting edge, instead, we want to teach intermediate level data science to as many participants as we can. Of course, some of the lectures will be devoted to the new algorithms, but in general, the goal is to show the gold standards and a bit beyond.
We were able to invite speakers that cover not only the extensively used machine learning techniques such as random forest-based methods, Bayesian inference and Deep Learning but also cutting edge methods that are just making their way into the field of bioinformatics, such as Deep Generative Models, Reinforcement Learning or Natural Language Processing.
This year we will also have hackathons — but this time without the wet-lab part. Hopefully, it will be as exciting and useful as in the previous year, but with a “normal” amount of effort this time.
The lessons that we already learned before school? First, getting grants for such educational events is not easy. It was amazingly difficult and nerve-wracking this year. We got it — but having a plan B in terms of funding is always good. Thanks to all of our sponsors. Second, extensive usage of our network that was formed in previous years helped us with finding the right speakers.


#NGSchool2.0: To the Future!

We are still thinking about the next schools. What should be the topic? Whom should we invite? Who will organise this? In which country? Where will we get the financial/scientific support? Where should we post the ads about the new school? Nothing is known.
Many of us grew together with NGSchool, while obtaining valuable skills in both organising scientific events and science itself. As we progress and move to other positions, countries (even other continents) we feel it is time to give some oldfags a proper “vacation” and get some fresh blood on board, so they can also suffer experience the wonderful world of NGSchool!
So, if you feel that you’re cool enough (as cool as this post author, obviously) you have a unique chance to influence and change upcoming NGSchool editions — just drop us a line!

Kasia Kędzierska, PhD student at University of Oxford, NGSchool Society Vice President, #NGSchool2019 project coordinator

I joined during NGSchool2017 by providing some advice, as the school was taking place near Warsaw and I had experience in organising conferences there. I knew Leszek before as we worked together, but this was the very first time I met German and others — via emails. Since I was invited to give a workshop on ATAC-seq, I had the opportunity to experience the atmosphere of the school myself, and meet the mystery people I’ve been messaging for past months. Oh, what a school it was. Excellent training, amazing lectures and a friendly social environment. I still keep in touch with many people I met there! Not to mention coming back to the training materials.

To improve the organisation process and the school, we now work as a TEAM. NGSchool2018 was organised by a group of brilliant and enthusiastic people: Alina, Adrian, Angelika, German, Maja, Migdał, Natalia, Leszek and me. Everyone has contributed something unique and helped shape the event. Not to mention their time and dedication. It was a very ambitious idea — not only we held the hackathons for the very first time, but we also included the experimental part. All of this was possible because we were a team, and each one of us had their responsibilities. Because we continuously strive to learn and improve, we identified areas in which we can do better and decided to formalise our team. In September last year, NGSchool Society was established.

I have the pleasure to organise this year’s edition with 7 brilliant people — Alina, German, Gienio, Maja, Maciek, Leszek and Sam. We don’t always see eye to eye on everything and our Slack discussion go well into the night. Yet, it is the right type of disagreeing, the one that makes things better. It has indeed been a privilege, to see their enthusiasm and commitment; and see how our ideas come to life. Fingers crossed for this year’s edition as we are still putting the last touches!

The goal of the Society is to promote and support science. We do that by organising scientific events (and securing funding for such) and cooperation with scientific institutions and other scientists. We are always open to new volunteers! Do you want to shape the upcoming editions of NGSchool? Do you want to help promote science? Do you want to organise excellent and affordable training in computational biology for young, talented scientists? If your answer is yes (or even maybe) — don’t hesitate to contact us.

We are looking forward to welcoming you to the team :))

Best of luck and greetings!

The main author: German
Read, edited, but not necessarily approved by NGSchool TEAM (namely
Alina, Gienio, Kasia, 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.

The first part of the story is here.

The second is here.

More From Medium

Also tagged Science

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