Summer School on Bioinformatics

In this post, dear reader, I will briefly talk about how 100+ people can have fun with knowledge for a week of summer fun.
I tried to describe the event so that even a person who is completely out of topic, what I am talking about, would still read with interest and understand everything.
In general, this is a post about our bioinformatics school, which was held from July 29 to August 4 near Moscow. For details - under the cat.
Carefully, traffic, all photos without katov!


Participants, organizers and some school speakers.

Introduction

So, around April, the Institute of Bioinformatics began accepting applications for competitive selection in summer school. It was declared that this would be a week-long training in various disciplines in the field of bioinformatics, taking place somewhere near Moscow with payment of accommodation.
I must say here, and I believe that it will be interesting to the reader, who so far feels "not in the subject", that for the moment I described, I was connected with bioinformatics only by the completed course "Algorithms in Bioinformatics" at the Computer Science Club . By the way, I also got to this course almost by accident, I just wanted to hear something new.
I myself come from the St. Petersburg Institute of Technology, from the Faculty of Information Technology and Management, I develop software, mainly in C ++ and C ++ Qt. In general, as you can see, the most common techie. I had no acquaintances in bioinformatics, except the distant, at that time, comrade who visited all this and advised.
I submitted an application, and in July I was notified that I was accepted and that I, like all participants, would be paid for a transfer from Moscow State University to the boarding house, where everything would pass, and back, as well as accommodation and meals.
')

School

The first day was different from all the others primarily because the classes were held at the Department of Biology, Moscow State University. I had to come in a day, so I spent the night with a friend in an apartment, whose windows just looked out onto the MSU steeple. I was sure that being in the area of ​​direct eye contact from the desired point, I would get there without difficulty. However, in the morning I was a little surprised that the buses did not go around with quite obvious routes around me, and most Muscovites could not clearly answer how to get there. I will skip the long story full of obscene language, and I will only say that I got to the venue only thanks to other participants who met on my way.

By the way, about the participants, under the terms of the recruitment, anyone could apply, but preference was given to IT specialists and biologists. This duality was reflected both in the school organization itself: the participants were divided into streams, biologists and informatics, respectively, and in symbolism: T-shirts issued to each showed a flower and a computer. The truth about whether it is a computer, we all have not decided. There were options like: worldwalk, stove, TV, MacOS window, etc. Other options can be offered in the comments :)


Fan and oven with hood Flower and computer.

And of course there were already mature bioinformatics at the school, that is, both. And later, we were told in confidence that we tried to mix the flows in the rooms so that there was an exchange of knowledge.

In addition to T-shirts, we were given a badge, notebook, pen and other attribution of school sponsors, as well as a schedule in front of an audience at the Faculty of Biology at Moscow State University. You can pay attention to the fact that classes for streams are sometimes different.
On the first day, it was immediately interesting and very little incomprehensible (which I was afraid of), the lecture “Genetic reprogramming of somatic cells: what bioinformatics gives us” about stem cells was especially interesting. I will mention in the course of the article only some lectures without a special description of their content, because all the videos will be available soon on this page , and if you are interested in something, you can watch the lecture.
After all the performances, we went to the boarding house near Mendeleevo. On the way, I realized how bad it is to live in Moscow - the road we drove for 2.5 hours.


Place of residence and training.

In the boarding house there was everything necessary for learning - the Internet (albeit constantly falling from the load), the audience, the boards, the sockets.
We engaged in a lot, often from 10 to 7 in the evening, sometimes more. But if a person is tired - no one prevented him from walking through nature instead of practicing or sleeping.
I was also pleased with the following organizational point: the so-called “coffee breaks” - coffee breaks between lectures, where, besides the coffee itself, there was tea and cookies or other buns.


Coffee break

The second day was also quite simple, everything was clear even to an uninitiated person, told (computer scientists, biologists had something else in parallel) about the basics of microbiology, cell structure, organelles, etc. There was also a small task with unit tests and a python pipeline.
In the evening there was an occupation-game with the assembly of the genome. The point is this: you are given a lot of sheets of reads and your team should collect them as soon as possible and record the resulting genome. Who will cope faster and better than all - that and sneakers. Our team won :) The game is useful because if someone else did not understand what a genome assembly is, then it will clearly understand it. Well, she's just fun.


Our team with a prize.


Another good team :)


Correct answer.

The next day, Sergei Nurk’s lecture on de Bruin’s graphs and their use for genome assembly was very much in the subject — now the people who played the assembly last night could figure out how to do the same thing on the computer, quickly and efficiently.
I also remember a couple of startups in bioinformatics. There were a lot of interesting conversations and new information, I understood how the system of grants works, I listened to people who already have experience in this field and told their stories.

Honestly, I don’t remember from what day, but pretty soon they started to enter into the tradition of the night, and some even have early morning parties. They included social and board games: Hat , Mafia , Evolution , well, and someone has alcohol. Not all participated in such public initiatives, but the majority. There was a funny moment when a mini-bar near the players was organized from the scanty stocks of liquor. I think this funny feature was remembered by everyone who was there :)


Minibar in the background while playing.

There were also presentations of students, the so-called mini-conference. It turned out interesting, a lot of serious projects, a lot of talented guys. The presentations were also recorded, so who is interested in looking at the future of bioinformatics - wait until the materials from the school are uploaded to the site. There were 13 speeches for 2 couples, I will not single out anyone, because it will be subjective, but there is something to see.

On Friday and Saturday, they talked about BLAST, or rather, about its device. BLAST is a tool for finding similarities between protein and nucleotide sequences. The lecture dealt with statistical methods, allowing to evaluate the significance of the coincidences of these sequences and to distinguish
truly non-random coincidences from random. In general, hooray, this is the former native theory of probability and mat. statistics.
On Saturday, I also listened about the dynamics of synthetic networks of gene regulation, I was very interested, I didn’t know about this before. In this area, they are engaged in researching, using mathematical modeling tools, the peculiarities of the functioning of real gene networks that control various processes in the body. With the help of these models, it is possible to predict and analyze the complex dynamics of gene networks and on this basis to purposefully construct synthetic networks and cellular systems with given individual and collective properties.

And then we were photographed (the first photo in the post), many were photographed :) There is even a gif . After the group photo, there were a couple more lectures, and then a farewell evening, with food and drinks, kindly provided by the organizers, socializing, games, and even dancing. Comrade Andrei Afanasyev, the speaker who drove the car with the speakers, is responsible for the latter :) In general, for a full evening lamplight (and someone had a night spilled over in the morning), there was only a fire with stories. In any case, it was unpleasant to part, only got used to each other.

Conclusion

In general, the school was a success and a success with a bang. In the first place, of course, in social terms - people got acquainted, and acquaintances in science mean a lot, would not be surprised if in the future these guys start joint projects or decide to link their lives with bioinformatics thanks to this school. It's great when studying takes place in an informal atmosphere, in a pleasant company of people with whom you communicate and have fun in the evening. This is great when real experts and practitioners pass on the experience to you, who are well aware of how everything that has been said happens, and not the teachers who read the textbook, as it happens in low-quality universities. And of course it’s great to feel that you are taking root in a really demanded area, in the science of the future, which is still just gaining momentum. But, as always, you need patience and determination.

This school was the first in the practice of our organizers (see thanks) and for the first time, in my subjective view, an ordinary participant, all in the highest category. Yes, we had some unpleasant moments that did not depend on the organizers, for example, a wonderful epidemic of sore throat, but in the end they made fun of the same sore throat rather than feared it (see the certificate). Otherwise, there is nothing to complain about, which is rare in our country, there are only wishes and the desire to get there again.


Certificate of participation of the school.

Afterword

Thanks

Once again I express my gratitude for the efforts and the opportunity to get a bunch of pleasant emotions, on behalf of all the school participants, to the following comrades:




And, of course, to all the speakers, as well as to us, the participants.

For participants

Thank you for this cool week, everything turned out very warm and friendly. I miss the nightly gatherings in the hallway.
Do not scatter, but it is as usual, as friends in the VC added each other and forgot. Will not work :)

For habrovchan and just readers who live in St. Petersburg

The Institute of Bioinformatics continues to recruit students for the Algorithmic Bioinformatics and Bioinformatics for Biologists programs.

For everyone else

The organizers said that perhaps next year the school will be held again, this time planned in St. Petersburg. If you liked what was described, dear reader, then be sure to try your luck in a year and submit an application.

All science, bye.