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.

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Read about what's good

what should give you pause

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

Deep dive into genome assembly

According to learners, this course offers a deep dive into the algorithms behind genome assembly, focusing heavily on De Bruijn graphs and their practical application to a real-world biological problem. Students find the programming challenges are rigorous and rewarding, providing a strong foundation in computational biology and algorithmic problem-solving. However, some learners note that the course is very challenging and may require a stronger programming or mathematical background than initially anticipated. The assignments often require significant time and effort, and while the lectures are generally clear, a few reviewers felt certain theoretical concepts could be explained better.

Generally clear, some concepts challenging.

"The lectures were mostly clear and well-paced, explaining difficult concepts step-by-step."

"While the instructors are knowledgeable, I found some theoretical explanations a bit hard to follow at times."

"Video quality and explanations were good, though I often needed to rewatch segments."

"Could use more visual aids or simpler examples for the most complex algorithmic parts."

Applies theory to biological problem.

"Using the E. coli outbreak as a case study made the material incredibly engaging and relevant."

"Connecting the algorithms to a real biological problem was very motivating."

"The course does a great job of showing how theoretical computer science is applied in bioinformatics."

"Loved working on a problem inspired by a real historical event."

Excellent coverage of assembly algorithms.

"Provides a really solid understanding of the De Bruijn graph approach to genome assembly."

"I appreciated the deep dive into the underlying algorithms, not just how to use tools."

"Explains complex concepts like Eulerian paths and cycles very well in the context of biology."

"This course is perfect if you want to understand the 'how' and 'why' behind genome assembly software."

Exercises are difficult but deeply rewarding.

"The programming assignments were incredibly challenging, pushing my understanding, but solving them felt very rewarding."

"Loved how the assignments built upon each other; they are tough but solidify the concepts."

"Be prepared to spend significant time on the coding problems, they are not trivial."

"Found the algorithmic challenges in the assignments the most valuable part of the course."

Demands solid programming/math skills.

"This course assumes a stronger background in algorithms and programming than I had; it was a steep learning curve."

"If you aren't comfortable with Python and graph theory, you will struggle immensely."

"Wish the prerequisites were clearer about the required level of comfort with data structures and algorithms."

"Definitely not for beginners in programming or bioinformatics."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Genome Assembly Programming Challenge with these activities:

Review Sequencing Technology Concepts

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Refresh your memory on the core concepts of DNA sequencing. This will make learning about genome assembly in this course easier.

Browse courses on DNA Sequencing

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Read a short summary of the Sanger sequencing method
Watch a video on next-generation sequencing methods
Review your notes or textbook on sequencing technologies

Learn about de Bruijn graphs

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A de Bruijn graph is a data structure that is central to genome assembly. Working through a tutorial on it will strengthen your understanding of this concept.

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Find a tutorial on de Bruijn graphs
Work through the tutorial, taking notes
Try to apply the concepts you learned to a simple example

Participate in the course discussion forums

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Helping others understand genome assembly will reinforce your own learning and identify areas you need to improve.

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Visit the course discussion forums
Answer questions asked by other students
Ask for help if you have questions
Provide feedback on other students' responses

Four other activities

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Practice assembling small sequences using de Bruijn graphs

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Getting hands-on experience with assembling small sequences will prepare you for developing your own assembler for E. coli X.

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Find a practice problem or dataset with small sequences
Assemble the sequences using a de Bruijn graph
Check your results

Attend a workshop on genome assembly

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Attending a workshop will provide you with insights from experts in the field and allow you to network with other professionals.

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Find a workshop on genome assembly that fits your schedule and interests
Register for the workshop
Attend the workshop and participate actively
Follow up with any contacts you make at the workshop

Build a genome assembler in your favorite programming language

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Applying your knowledge to build something concrete will help you deeply understand genome assembly. You'll also develop valuable coding skills.

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Choose a programming language
Design the architecture of your assembler
Implement the assembler
Test your assembler on small sequences
Optimize your assembler for performance

Volunteer at a local biotech lab

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Working in a lab will provide hands-on experience in the techniques and technologies used in genome assembly.

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Find a local biotech lab that is willing to take volunteers
Contact the lab and ask about volunteer opportunities
Complete any required training or orientation
Perform tasks assigned by the lab staff

Career center

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

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.

See salaries and explore the career path for Computational Biologist

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.

See salaries and explore the career path for Bioinformatics Scientist

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.

See salaries and explore the career path for Genome Assembler

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.

See salaries and explore the career path for Biomedical Engineer

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.

See salaries and explore the career path for Biostatistician

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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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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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.

See salaries and explore the career path for Geneticist

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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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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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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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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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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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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