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Genome Assembly Programming Challenge

Data Structures and Algorithms,

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 Lübeck, 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/wiki The 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.

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Rating 3.8 based on 31 ratings
Length 4 weeks
Effort 3 weeks, 4-6 hours per week
Starts Jun 7 (3 weeks ago)
Cost $79
From University of California San Diego, National Research University Higher School of Economics, HSE University via Coursera
Instructors Alexander S. Kulikov, Michael Levin, Pavel Pevzner, Neil Rhodes
Download Videos On all desktop and mobile devices
Language English
Subjects Programming Science
Tags Computer Science Life Sciences Algorithms Bioinformatics Health Informatics

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capstone project

Besides, since this is the "capstone project", you are supposed to do it by yourself.The only negative point is that at the beginning of the specialization, they announced that there were going to be different options for the capstone project.

Good course and final capstone project.

I wish I had the choice of pursuing graph algorithms, when I signed up for the specialization with the promise of selecting one of the two Capstone projects.

There are already two dedicated courses by Pevzner and et al, which would have prepared us better for this too specialized and impractical Capstone project...

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Rating 3.8 based on 31 ratings
Length 4 weeks
Effort 3 weeks, 4-6 hours per week
Starts Jun 7 (3 weeks ago)
Cost $79
From University of California San Diego, National Research University Higher School of Economics, HSE University via Coursera
Instructors Alexander S. Kulikov, Michael Levin, Pavel Pevzner, Neil Rhodes
Download Videos On all desktop and mobile devices
Language English
Subjects Programming Science
Tags Computer Science Life Sciences Algorithms Bioinformatics Health Informatics

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