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CourseraData Structures and AlgorithmsFree courseCertificate

Genome Assembly Programming Challenge

This specialization is a mix of theory and practice: you will learn algorithmic techniques for solving various computational problems and will implement about 100 algorithmic coding problems in a programming language of your choice. No other online course in Algorithms even comes close to offering you a wealth of programming challenges that you may face at your next job interview. To prepare you, we invested over 3000 hours into designing our challenges as an alternative to multiple choice questions that you usually find in MOOCs. Sorry, we do not believe in multiple choice questions when it c

Created by: Alexander S. Kulikov

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Course Description

In Spring 2011, thousands of people in Germany were hospitalized with a deadly disease that started as food poisoning with bloody diarrhea and often led to kidney failure. It was the beginning of the deadliest outbreak in recent history, caused by a mysterious bacterial strain that we will refer to as E. coli X. Soon, German officials linked the outbreak to a restaurant in LAbeck, where nearly 20% of the patrons had developed bloody diarrhea in a single week. At this point, biologists knew that they were facing a previously unknown pathogen and that traditional methods would not suffice - computational biologists would be needed to assemble and analyze the genome of the newly emerged pathogen.To investigate the evolutionary origin and pathogenic potential of the outbreak strain, researchers started a crowdsourced research program. They released bacterial DNA sequencing data from one of a patient, which elicited a burst of analyses carried out by computational biologists on four continents. They even used GitHub for the project: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wikiThe 2011 German outbreak represented an early example of epidemiologists collaborating with computational biologists to stop an outbreak. In this Genome Assembly Programming Challenge, you will follow in the footsteps of the bioinformaticians investigating the outbreak by developing a program to assemble the genome of the E. coli X from millions of overlapping substrings of the E.coli X genome.Do you have technical problems? Write to us: coursera@hse.ru

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Instructor Details

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Alexander S. Kulikov is a research fellow at St. Petersburg Department of Steklov Mathematical Institute of the Russian Academy of Sciences and a visiting professor at University of California, San Diego. His scientific interests include algorithms for NP-hard problems and circuit complexity. In St. Petersburg, he runs Computer Science Club and Computer Science Center.

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Reviews

3.9

30 reviews in total

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By Omar M on 28-Aug-19

The topic is very interesting but it is very rushed and it is very challenging to pass the test

By Priyansh B on 28-Jul-19

May be the course would have given more hints. But a learned a lot from the projects.

By Tamas S on 8-Jun-19

Felt a little bit adrift from the general flow of topics in the other courses. Of course this called a challenge for a reason, but it's funny that you can pass this course doing barely anything actually related to genome assembly as there are other problems for each week as well.

By Chan Y F on 16-Apr-19

A little bit difficult

By Daniel C on 23-Dec-18

This course takes considerably more time than the previous ones per week. There isn't a lot of teaching content because it's supposed to be simulating a real-life project. I personally am not interested in bioinfometrics and string assembly, so I don't feel very motivated.I am happy that I have finished this course and I have learned a lot. I also honed my C++ skills through the many programming assignments; this is one of the reasons I decided to take this over other specializations. The main reason for the 3 stars is that I could have spent the same amount time to learn more about algorithms, instead of thinking about problems I am not particularly interested. Also, there won't be help from the teachers, but the forum community is great.

By Zac B on 4-Oct-18

Most challenging course I've taken on Coursera so far, so be prepared. However, I'm definitely a far better programmer due to it!

By Joseph G N on 19-Sep-18

Nice exercises were difficult and interesting. You can learn a lot of in this course not only to solve bioinformatic problems

By Alexandr S on 5-Aug-18

I would like to say thank you to all who have created this course and specialization! Good material, excellent lecturers!

By Henry R on 28-Jul-18

Not bad, but you had better attend Bioinformatics Specialization so you could understand what tutors lecture.

By John B on 15-Jun-18

There were countless errors in the descriptions of the programming problems, not just "ambiguities" or "open ended problem definitions" but quantitatively incorrect specific statements (length of inputs, structure of inputs, etc). Many of these issues have been pointed out in the forums, but remain uncorrected as of June 2018.

By Alexander C on 8-Jun-18

I did not enjoy this course. I did not like the following things:1) It was advertizing a different course (Bioinformatics or something like that) too hard for my taste.2) The problem statements were often incorrect. In particular what is related to the size of inputs. I have wasted too much time because of these issues. For example, the problem statement says that there will be 400 lines of input. After wasting an hour and a half trying to find a cause of a segmentation error I am reading on the forum a message THAT IS ONE YEAR OLD saying that there are in fact 1618 lines of input.3) The final problem (genome assembler) has a very tight memory limit if you consider the size of the input. Solving it within the memory limit would require special skills that are not covered by the material in this course. Or maybe I (and other people on the forum) are just not smart enough.4) There are almost no lectures. All you have to work with seems to be a 60-page extract from a book.

By Pablo E M M on 3-Jun-18

Greate course

Showing 12 of 30 reviews

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Overall Score : 78 / 100