Bioinformatics Contest 2018


About this course

Bioinformatics Institute, ITMO University, Rosalind,  and Stepik announce the second online programming competition – Bioinformatics Contest 2018!

If you are interested in Bioinformatics, enjoy solving complex problems and have experience in the field of Computer Science, Molecular Biology, Genomics and Machine Learning, do not hesitate to join the contest.

The competition consists of two rounds:

  1. Qualification round will last one week, February 3–11 (11:59 AM UTC+0)
  2. Final round will last 24 hours on February 24  (11:59 AM UTC+0) .  

Both rounds will be held online, submissions will be auto-graded in real time. Contest scoreboard: http://mon.stepik.org.

To participate you will need to:

  1. Register or log in on Stepik (it is free).
  2. Press the “join this course” button in the upper right corner of this webpage.
  3. Press green "Learn" button the upper right corner of this webpage. 

After that, you will be able to get acquainted with examples of problems and find out more about the rules in the first part of this course. The Contest problems will appear right before the start day. 

Participants will need to solve bioinformatics problems using programming. The goal is to correctly solve as many problems as possible. Some of them will be ones with exact answers and some – with the approximate answers. For problems with exact answers, you need to submit a code in one of the supported programming languages that will be executed on a number of tests. These problems are focused on algorithms and data structures. For problems with approximate answers, the test inputs should be presented as downloadable files. Your task is to find the best possible solution for these tests and upload them to the testing system. Participation in the Contest is individual, winners will be rewarded.

Details and subscription to the news: bioinf.me/contest

Contest 2017:
Results of last year's Contest are also published online. Problem sets are availavle at stepik.org/945.

Who is this course for

Meet the Instructors

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Bioinformatics Institute
Bioinformatics Institute is located in St.Petersburg, Russia and operates since 2010.

Bioinformatics Institute is the first non-governmental non-commercial bioinformatics research and educational institution in Russia.

Bioinformatics Institute’s mission is to educate the new generation of highly qualified specialists in the field of bioinformatics and to popularize Bioinformatics in Russia.

The Institute's programs and events are open to students and professionals with Mathematics, Software Engineering, or Biology background. Apart from several offline educational initiatives, we develop a series of open online courses.

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ITMO University
ITMO University is one of the leading Russian universities in the field of information technologies and photonics, one of the few Russian universities that received the status of a national research university in 2009. ITMO University is one of 21 universities-participants of Russian Academic Excellence Project “5-100”.
Today ITMO University educates more than 11,000 students and employs more than 1,100 lecturers and 1,200 PhDs, including 110 foreign professors. ITMO University is the only 7-time winner of the World programming competition ACM ICPC and an alma mater to the most of the top-ranked competitive programmers.
The University’s mission is to generate cutting-edge knowledge, implement innovative findings and prepare an elite workforce capable of working in a fast-paced world and ensuring progress in science and technology.

Course content

Qualification Round
Final Round

Learners' reviews

Let me just start by saying this competition was really fun and had a lot of cool, challenging problems. I really enjoyed it, and wanted to take a little bit of time to provide feedback on each problem. Sorry in advance if it’s long-winded! 1. Quals Problem 1 – As a first-time competitor, I have mixed feelings about this problem. The only trick was finding the ATP equations. I’m not sure I liked having to hunt that down as it felt like annoying domain knowledge instead of being a test of problem-solving and/or coding. However, once found, the problem was fairly straight-forward and it felt good to be mostly through qualifying just on that problem. 2. Quals Problem 2 – This problem was clearly the hardest of the qualification problems. I like the way the second part built on the results of the first part. Unfortunately, I was only able to solve the third part through an entirely different approach (essentially a branch-and-bound brute force is how I did it). I wish that third part had been more closely related to the first two since those seemed to have clever, efficient solutions (granted this could just be me failing to see a clever solution). 3. Quals Problem 3 – I loved this problem. I knew how to generally tackle it very quickly based on similar problems from basic bioinformatics class, but it was different enough to provide a good challenge. This problem also very elegantly increased in difficulty, allowing for quick gathering of partial points with the final problem culminating in the greatest challenge/reward. If I was a teacher, I would seriously consider using this problem for a homework assignment on dynamic programming. 4. Finals Problem 1 – This was my least favorite problem of the whole competition. It seemed to require fairly extensive domain knowledge that I couldn’t find and/or didn’t understand. Somehow, I managed to solve part 1, but couldn’t figure out how to adapt that approach to part 2. I’m going to review the tests later to see if I can reverse-engineer it. Regardless, I wish the problem had either had a clear-cut, simple example (as many others do) or a clearer explanation of the problem. 5. Final Problem 2 – Very well designed problem and my overall favorite in terms of algorithmic design. The problem sufficiently increased in difficulty for each part and I think I see how to fully solve part 3 now. My one critique is that some of the language was confusing. For example, on the main page it says “directed acyclic graph” and then later on the problem pages “undirected version …” even though solving the problem is still a directed graph. The language may be technically correct, but it was very confusing until I knew the tests were passing and the graph at least operated as a directed graph. 6. Finals Problem 3 – I have mixed feelings about it depending on what the competition was trying to accomplish. I solved the problem through a combination of publicly available tools (i.e. aligners), programming, and then what was essentially computer-aided assembly. If the expectation is to know some of that domain knowledge, then I think this was one of the better problems in the competition and I really enjoyed working to solve it. However, I can’t imagine trying to solve this problem without that domain knowledge. 7. Finals Problem 4 – Conceptually, I like this problem, but it seemed pretty easy. In my case, I just ran some overlap tools (aka, domain knowledge) and then clustered based on the output. The time to spin it up and run on everything was small, and after tinkering a little bit I simply moved on to other problems. My scores were approximately the same as others, so I imagine they did the same or very similar. However, without that domain knowledge this problem was probably quite challenging. 8. Finals Problem 5 – Thematically, this was definitely my favorite problem in the finals. It was conceptually really interesting, but this problem was really, really challenging in my opinion. Going in, I don’t think I realized just how challenging this problem was going to be (I should’ve realized this is a tie-breaker and spent less time on it, so that’s really on me). Technically speaking, this problem was very difficult to work on through the Stepik UI since it requires so much feedback. I’m not sure I would recommend this type of problem in the future (although I did really enjoy breeding my cows :D). Overall, I found this to be a really awesome experience and I highly recommend anyone seeing this to go check out the problems even though the competition is over now. Looking forward to hopefully continuing this competition in the coming years!
The Stepik team out-did themselves again this year. Great and challenging problems! (with the usual dose of difficulty-induced frustration, but it wouldn't be the same without it)
The problems presented this year were a substantial improvement on last year, with good relevance to biological situations. I didn't feel like I was inside a computer science test this time, which was good -- no "we don't want you to brute force this, so we're making the problem *really* difficult, and it needs an inspirational twist to get any points at all". I have a issue with Problem 1, as it is a domain-knowledge problem with a specific answer that is not readily accessible to me, and no partial points are awarded. The problem creators seem to think that the confusion and frustration gives an air of authenticity to the problem, but this authenticity is removed by prohibiting discussion between participants. The problem felt a bit like asking for the number of steps between the second and third floors of Delores' Mansion, with random flavour text added that has no relevance to the answer, such as, "mansions are large buildings that frequently have multiple storeys. Usually you use stone for step construction in mansions, but in this case wooden steps were used."

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