Genome Assembly Programming Challenge from Coursera

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 online course 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.

What's inside

Syllabus

The 2011 European E. coli Outbreak

In April 2011, hundreds of people in Germany were hospitalized with a deadly disease that often started as food poisoning with bloody diarrhea. 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. Within a few months, the outbreak had infected thousands and killed 53 people. To prevent the further spread of the outbreak, computational biologists all over the world had to answer the question “What is the genome sequence of E. coli X?” in order to figure out what new genes it acquired to become pathogenic. 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 deadly E. coli X strain. However, before you embark on building a program for assembling the E. coli X strain, we have to explain some genomic concepts and warm you up by having you solve a simpler problem of assembling a small virus.

Assembling Genomes Using de Bruijn Graphs

DNA sequencing approach that led to assembly of a small virus in 1977 went through a series of transformations that contributed to the emergence of personalized medicine a few years ago. By the late 1980s, biologists were routinely sequencing viral genomes containing hundreds of thousands of nucleotides, but the idea of sequencing a bacterial (let alone the human) genome containing millions (or even billions) of nucleotides remained preposterous and would cost billions of dollars. In 1988, three biologists (independently and simultaneously!) came up with an idea to reduce sequencing cost and proposed the futuristic and at the time completely implausible method of DNA arrays. None of these three biologists could have possibly imagined that the implications of his own experimental research would eventually bring him face-to-face with challenging algorithmic problems. In this module you will learn about the algorithmic challenge of DNA sequencing using information about short k-mers provided by DNA arrays. You will also travel to the 18the century to learn about the Bridges of Konigsberg and solve a related problem of assembling a jigsaw puzzle!

Genome Assembly Faces Real Sequencing Data

Our discussion of genome assembly has thus far relied upon various assumptions. In this module, we will face practical challenges introduced by quirks in modern sequencing technologies and discuss some algorithmic techniques that have been devised to address these challenges. Afterwards, you will assemble the smallest bacterial genome that lives symbiotically inside leafhoppers. Its sheltered life has allowed it to reduce its genome to only about 112,091 nucleotides and 137 genes. And afterwards, you will be ready to assemble the E. coli X genome!

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Features a hands-on assembly programming challenge to assemble the genome of E. coli X, providing learners with practical experience in genome assembly

Taught by highly accomplished instructors Pavel Pevzner, Alexander S. Kulikov, Neil Rhodes, and Michael Levin, who are recognized for their work in the field of bioinformatics

Explores the 2011 European E. coli Outbreak, a real-world example of how epidemiologists and computational biologists collaborated to stop an outbreak

Develops core skills in genome assembly and computational biology, which are in high demand in the fields of bioinformatics, medicine, and research

Suitable for learners with a background in biology, computer science, or a related field

Requires learners to have some familiarity with bioinformatics concepts and tools, but provides resources for those who need a refresher

Reviews summary

Engaging capstone in bioinformatics

Learners say this challenging capstone is great and very rewarding. The course pulls together everything learned in bioinformatics and makes it come together. Learners note that the assignments are difficult but feel that it is worth the effort. Some learners also wish there was more information available for the assignment.

Learners find the capstone very rewarding.

"Excellent."

"Great course, hard but it is worth."

"It was great! Really tough, but rewarding."

Learners wish there was more information available for the assignments.

"The last assignment was extremely frustrating."

"hi, this is a hard course and the videos are not sufficient."

"You're on your own here about how you approach the problems, although there is some nice supplemental material available in the form of introductory videos and a booklet walking you through the project."

Learners say this course is very challenging.

"Too hard."

"Why we are learn this is biology part"

"It is a challenging course, which makes it great."

Career center

Learners who complete Genome Assembly Programming Challenge will develop knowledge and skills that may be useful to these careers:

Genome Assembler

Genome assemblers are responsible for assembling genomes from raw sequencing data. This is a complex and challenging task, as genomes are often large and complex. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Genome Assembly.

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Computational Biologist

Computational Biology is the study of biology using mathematical and computational techniques. It combines computer science, applied mathematics, biology, and software engineering to understand biological systems. The Genome Assembly Programming Challenge is a course designed to teach students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Computational Biology.

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Bioinformatics Scientist

Bioinformatics is the use of computer science and information technology to analyze and interpret biological data. Bioinformatics is used in a variety of fields, including genetics, genomics, and drug discovery. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Bioinformatics.

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Biomedical Engineer

Biomedical engineers use engineering principles to design and build medical devices and equipment. They also work on developing new treatments and therapies for diseases. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Biomedical Engineering.

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Biostatistician

Biostatisticians use statistical methods to analyze biological data. They work on a variety of projects, including drug development, clinical trials, and public health research. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Biostatistics.

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Molecular Biologist

Molecular biologists study the structure and function of molecules, such as DNA, RNA, and proteins. They work on a variety of projects, including gene expression, genetic engineering, and drug development. Genome assembly is a central technique in molecular biology and is essential for understanding the genetic makeup of living organisms.

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Researcher

Researchers conduct scientific research to advance knowledge and understanding. They work on a variety of projects, including basic research, applied research, and development. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Research.

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Data Scientist

Data scientists use data to solve problems. They work on a variety of projects, including fraud detection, customer segmentation, and product development. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Data Science.

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Microbiologist

Microbiologists study microorganisms, such as bacteria, viruses, and fungi. They work on a variety of projects, including infectious disease research, drug development, and environmental microbiology. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Microbiology.

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Geneticist

Geneticists study genes and heredity. They work on a variety of projects, including genetic testing, gene therapy, and the development of new drugs. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Genetics.

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Pharmaceutical Scientist

Pharmaceutical scientists develop and test new drugs. They work on a variety of projects, including drug discovery, drug development, and clinical trials. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Pharmaceutical Science.

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Physician

Physicians diagnose and treat diseases. They work on a variety of projects, including patient care, research, and teaching. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Medicine.

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Medical Physicist

Medical physicists use physics to develop and improve medical treatments. They work on a variety of projects, including cancer treatment, imaging, and radiation therapy. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Medical Physics.

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Software Engineer

Software engineers design, develop, and maintain software applications. They work on a variety of projects, including web development, mobile development, and data science. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Software Engineering.

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Epidemiologist

Epidemiologists study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. The Genome Assembly Programming Challenge is a course that teaches students how to use computational techniques to assemble genomes. This course is a valuable resource for anyone interested in a career in Epidemiology.

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