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Niema Moshiri,
Vikram Sirupurapu,
Sabeel Mansuri,
Pavel Pevzner,
and
Mikhail Rayko
In this course, you will follow in the footsteps of the bioinformaticians investigating the COVID-19 outbreak by assembling the SARS-CoV-2 genome. Whether you’re new to the world of computational biology, or you’re a bioinformatics expert seeking to learn about its applications in the COVID-19 pandemic, or somewhere in between, this course is for you! As you go through this journey, we will introduce and explain genomic concepts and give you many opportunities to practice your skills, and we will provide a series of problems with gradually increasing complexity. This first course will only discuss the assembly of the SARS-CoV-2 genome, but future courses in this series will explore follow-up bioinformatics analyses used in the COVID-19 pandemic.
Register for this course and see more details by visiting:
OpenCourser.com/course/af8zs6/hacking
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What's inside
Syllabus
Week 1
In Chapter 1, we will first travel back in time to learn about the history of the SARS outbreak of 2003. Next, we will travel to late 2019 to learn about the origins of SARS-CoV-2, a novel virus that wreaked havoc upon the world during the COVID-19 pandemic. Lastly, we will explore the biology behind this mysterious virus as we take our first steps towards Hacking COVID-19.
Read more
Syllabus
Week 1
In Chapter 1, we will first travel back in time to learn about the history of the SARS outbreak of 2003. Next, we will travel to late 2019 to learn about the origins of SARS-CoV-2, a novel virus that wreaked havoc upon the world during the COVID-19 pandemic. Lastly, we will explore the biology behind this mysterious virus as we take our first steps towards Hacking COVID-19.
Read more
Traffic lights
Traffic lights
Read about what's good
what should give you pause and
possible dealbreakers
Course belongs to an entire series of courses
Introduces common genomic concepts early on
Introduces modern technologies, such as DNA sequencing
Teaches learners how to use a genome assembly tool
Emphasizes the importance of quality assessment in bioinformatics
Provides multiple opportunities to practice skills
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Create your own learning path.
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Reviews summary
Foundations of viral genome assembly
According to learners, this course offers a strong, practical introduction to SARS-CoV-2 genome assembly, making complex bioinformatics concepts accessible. Many praise the clear explanations and hands-on labs with SPAdes and QUAST, noting their usefulness for building skills. Its timely focus on COVID-19 makes it highly relevant. While ideal for beginners, some with prior experience found the material basic. Common concerns include challenging lab setup and potentially outdated sequencing technology information, plus limited forum support.
Provides a solid introduction for newcomers to bioinformatics.
"It's a great starting point for anyone new to bioinformatics."
"The pace was good for beginners, but I wished for more advanced topics..."
"The course material felt a bit basic for someone with prior bioinformatics experience."
"I found this course perfect as someone with a biology background but new to coding."
The course's focus on SARS-CoV-2 makes it exceptionally timely.
"Excellent and timely course. The focus on SARS-CoV-2 made it incredibly relevant."
"This course is a must-take for anyone interested in applying bioinformatics to real-world problems like pandemics."
"The course provided a clear pathway to understanding SARS-CoV-2."
"The timely focus on COVID-19 made the content incredibly relevant."
Presents complex bioinformatics topics in an easy-to-understand format.
"The lectures were clear, and the practical labs... were incredibly useful."
"The course took a complex topic and broke it down into digestible, bite-sized modules."
"The clarity of explanation, especially for complex topics, was exceptional."
"I found the explanations of DNA sequencing... highly valuable."
Builds confidence in applying bioinformatics tools for genome assembly.
"The practical labs using SPAdes and QUAST were incredibly useful for hands-on learning."
"I gained practical skills I can immediately apply."
"The hands-on approach with practical exercises was exactly what I needed to build confidence."
"I found the practical application of SPAdes highly valuable for my understanding."
Some content may be outdated; community forum activity is limited.
"Outdated information on some of the sequencing technologies by the time I took it."
"While the core assembly concepts remain, the specific examples felt a little behind."
"The community forum was not very active, making debugging hard."
Some learners found setting up the technical environment challenging.
"The practical labs were challenging to set up without prior environment configuration experience."
"I struggled with the technical setup more than the bioinformatics concepts themselves."
"Getting the tools to work was frustrating."
"I think a more robust virtual environment would be beneficial."
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 Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen with these
activities:
Review high school biology
Show steps
Refresh foundatonal biology to prepare for course materials
Browse courses on
Biology
Show steps
-
Review major biology textbooks
-
Practice genetics problems
Follow the online Bioinformatics Tutorial Series by the European Bioinformatics Institute
Show steps
These tutorials will provide you with a comprehensive overview of bioinformatics concepts.
Browse courses on
Bioinformatics
Show steps
-
Watch the introductory videos on bioinformatics.
-
Complete the interactive exercises.
-
Read the provided articles and resources.
Read the book "Bioinformatics for Beginners"
Show steps
This introductory book will help you develop a solid foundation in bioinformatics to better prepare for the course.
View
Bioinformatics: A Practical Guide To The...
on Amazon
Show steps
-
Define bioinformatics and discuss its importance.
-
Explain the role of DNA and RNA in bioinformatics.
-
Describe the different types of bioinformatics databases.
Six other activities
Expand to see all activities and additional details
Show all nine activities
Complete the interactive exercises on the NCBI website
Show steps
These exercises will provide you with the practical experience you need to master the concepts of bioinformatics.
Browse courses on
NCBI
Show steps
-
Navigate the NCBI website and search for a specific gene.
-
Use the NCBI BLAST tool to align two sequences.
-
Create a phylogenetic tree using the NCBI TreeView tool.
Attend a Bioinformatics Workshop at a local university or research institution
Show steps
This is an excellent opportunity to learn from experts in the field and network with other bioinformatics professionals.
Browse courses on
Bioinformatics
Show steps
-
Research upcoming bioinformatics workshops in your area.
-
Register for a workshop that aligns with your interests.
-
Attend the workshop and actively participate in the activities.
Write a blog post about your experience learning bioinformatics
Show steps
This activity will help you reflect on what you have learned and share your knowledge with others.
Browse courses on
Bioinformatics
Show steps
-
Describe the challenges you faced while learning bioinformatics.
-
Share your tips for other students who are interested in learning bioinformatics.
-
Discuss the applications of bioinformatics in the real world.
Develop a bioinformatics software tool to analyze a specific biological dataset
Show steps
This project will allow you to apply your bioinformatics skills to solve a real-world problem.
Browse courses on
Bioinformatics
Show steps
-
Identify a biological dataset that you would like to analyze.
-
Design and develop a software tool to analyze the dataset.
-
Test and validate your software tool.
Volunteer as a mentor for other students in the bioinformatics course
Show steps
This experience is a great opportunity to reinforce your understanding of the material and help others succeed.
Browse courses on
Bioinformatics
Show steps
-
Meet with other students and provide guidance on bioinformatics concepts.
-
Assist students with completing assignments and projects.
-
Create study materials and resources for other students.
Participate in the International Gene Sequence Analysis Competition (iGSA)
Show steps
This is a great way to test your skills and compete with other bioinformatics students from around the world.
Browse courses on
Bioinformatics
Show steps
-
Register for the iGSA competition.
-
Analyze the provided gene sequences.
-
Submit your results and compete for prizes.
Review high school biology
Show steps
Refresh foundatonal biology to prepare for course materials
Browse courses on
Biology
Show steps
Show steps
Show steps
- Review major biology textbooks
- Practice genetics problems
Follow the online Bioinformatics Tutorial Series by the European Bioinformatics Institute
Show steps
These tutorials will provide you with a comprehensive overview of bioinformatics concepts.
Browse courses on
Bioinformatics
Show steps
Show steps
Show steps
- Watch the introductory videos on bioinformatics.
- Complete the interactive exercises.
- Read the provided articles and resources.
Read the book "Bioinformatics for Beginners"
Show steps
This introductory book will help you develop a solid foundation in bioinformatics to better prepare for the course.
View
Bioinformatics: A Practical Guide To The...
on Amazon
Show steps
Show steps
Show steps
- Define bioinformatics and discuss its importance.
- Explain the role of DNA and RNA in bioinformatics.
- Describe the different types of bioinformatics databases.
Six other activities
Expand to see all activities and additional details
Show all nine activities
Complete the interactive exercises on the NCBI website
Show steps
These exercises will provide you with the practical experience you need to master the concepts of bioinformatics.
Browse courses on
NCBI
Show steps
Show steps
Show steps
- Navigate the NCBI website and search for a specific gene.
- Use the NCBI BLAST tool to align two sequences.
- Create a phylogenetic tree using the NCBI TreeView tool.
Attend a Bioinformatics Workshop at a local university or research institution
Show steps
This is an excellent opportunity to learn from experts in the field and network with other bioinformatics professionals.
Browse courses on
Bioinformatics
Show steps
Show steps
Show steps
- Research upcoming bioinformatics workshops in your area.
- Register for a workshop that aligns with your interests.
- Attend the workshop and actively participate in the activities.
Write a blog post about your experience learning bioinformatics
Show steps
This activity will help you reflect on what you have learned and share your knowledge with others.
Browse courses on
Bioinformatics
Show steps
Show steps
Show steps
- Describe the challenges you faced while learning bioinformatics.
- Share your tips for other students who are interested in learning bioinformatics.
- Discuss the applications of bioinformatics in the real world.
Develop a bioinformatics software tool to analyze a specific biological dataset
Show steps
This project will allow you to apply your bioinformatics skills to solve a real-world problem.
Browse courses on
Bioinformatics
Show steps
Show steps
Show steps
- Identify a biological dataset that you would like to analyze.
- Design and develop a software tool to analyze the dataset.
- Test and validate your software tool.
Volunteer as a mentor for other students in the bioinformatics course
Show steps
This experience is a great opportunity to reinforce your understanding of the material and help others succeed.
Browse courses on
Bioinformatics
Show steps
Show steps
Show steps
- Meet with other students and provide guidance on bioinformatics concepts.
- Assist students with completing assignments and projects.
- Create study materials and resources for other students.
Participate in the International Gene Sequence Analysis Competition (iGSA)
Show steps
This is a great way to test your skills and compete with other bioinformatics students from around the world.
Browse courses on
Bioinformatics
Show steps
Show steps
Show steps
- Register for the iGSA competition.
- Analyze the provided gene sequences.
- Submit your results and compete for prizes.
Career center
Learners who complete Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen will develop knowledge and skills
that may be useful to these careers:
Bioinformatician
Bioinformatician
A Bioinformatician studies the overlap between computer science and biology, applying the principles of computer science and informatics to biological systems. They research and develop applications and methods for analyzing and understanding the vast amounts of data generated in the life sciences. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. It can help build a foundation for understanding the uses and possibilities of bioinformatics in the medical industry.
Computational Biologist
Computational Biologist
A Computational Biologist is a scientist who uses computer science techniques to understand biological data. Computational Biology combines computer science, applied mathematics, statistics, and engineering to analyze and interpret biological data. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. It can help build a foundation for understanding the uses and possibilities of computational biology in the medical industry.
Medical Scientist
Medical Scientist
A Medical Scientist will typically have an advanced degree in a biomedical field. They work in medical research and development to advance knowledge and improve human health. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome, which could lay the foundation for a research project.
Physician
Physician
Physicians are responsible for providing medical care to patients. They diagnose and treat diseases, perform surgeries, and conduct research. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome, which could help provide a deeper understanding of bioinformatics and its uses in the medical field.
Genetic Counselor
Genetic Counselor
Genetic Counselors help people understand and make informed decisions about genetic conditions. They work with patients and their families to provide information about the risks and benefits of genetic testing, and help them to develop a plan for managing their genetic health. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. It also introduces and explains genomic concepts, which could help genetic counselors better understand the genetic aspects of the COVID-19 pandemic.
Researcher
Researcher
Research Scientists design, conduct, and analyze studies to advance knowledge in their field. They may work in a variety of settings, including universities, government agencies, and private companies. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This could help researchers better understand how viruses work and develop new treatments and vaccines for infectious diseases.
Epidemiologist
Epidemiologist
Epidemiologists study the distribution and patterns of disease in a population. They use this information to develop and implement public health interventions to prevent and control disease outbreaks. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This could help epidemiologists better understand how the virus spreads and develop effective control measures.
Biomedical Engineer
Biomedical Engineer
Biomedical Engineers apply engineering principles and techniques to the medical field. They design and develop medical devices, implants, and other technologies to improve human health. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome, which is a critical step in understanding and treating the virus. By completing this course, biomedical engineers can gain a deeper understanding of the virus and develop more effective technologies to combat it.
Microbiologist
Microbiologist
Microbiologists study microorganisms, such as bacteria, viruses, and fungi. They research the growth, reproduction, and genetics of microorganisms, and how they affect human health and the environment. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome, which is a critical step in understanding and treating the virus. By completing this course, microbiologists can gain a deeper understanding of the virus and develop more effective strategies to combat it.
Virologist
Virologist
Virologists study viruses, which are small infectious agents that can cause disease in humans, animals, and plants. They research the structure, function, and genetics of viruses, and how they interact with their hosts. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This is a critical step in understanding and treating the virus. By completing this course, virologists can gain a deeper understanding of the virus and develop more effective strategies to combat it.
Pharmacist
Pharmacist
Pharmacists dispense medications and provide information about their use. They also work with physicians to develop and manage medication plans for patients. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful for pharmacists. It can provide them with a deeper understanding of the SARS-CoV-2 virus and how it can be treated. This knowledge can help pharmacists provide better care to their patients and help to prevent the spread of the virus.
Data Analyst
Data Analyst
Data Analysts collect, clean, and analyze data to identify trends and patterns. They use their findings to make recommendations and inform decision-making. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This could help data analysts develop new methods for tracking and analyzing the spread of the virus.
Software Engineer
Software Engineer
Software Engineers design, develop, and maintain software systems. They work with users to gather requirements, design and implement software solutions, and test and debug software. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This could help software engineers develop new tools and applications for tracking and analyzing the spread of the virus.
Computer Scientist
Computer Scientist
Computer Scientists research and develop new computing technologies. They work in a variety of fields, including artificial intelligence, computer graphics, and software engineering. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This could help computer scientists develop new methods for analyzing and interpreting biological data.
Biostatistician
Biostatistician
Biostatisticians apply statistical methods to solve problems in biology and medicine. They work with researchers to design studies, analyze data, and interpret results. This course, Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen, may be useful because it discusses the assembly of the SARS-CoV-2 genome. This could help biostatisticians develop new methods for analyzing and interpreting data on the spread and treatment of the virus.
For more career information including salaries, visit:
OpenCourser.com/course/af8zs6/hacking
Reading list
We've selected eight books
that we think will supplement your
learning. Use these to
develop background knowledge, enrich your coursework, and gain a
deeper understanding of the topics covered in
Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen.
Provides a comprehensive overview of molecular biology. It valuable resource for students and researchers who want to understand the fundamental principles of biology.
Introduces the fundamental principles of reproducible and robust research in bioinformatics. It provides a comprehensive overview of open source tools and workflows commonly used in the field.
Save
Provides a comprehensive overview of genomics. It valuable resource for students and researchers who want to understand the structure and function of genomes.
Provides a comprehensive overview of genome analysis. It valuable resource for students and researchers who want to understand the methods used to analyze genomes.
Provides a comprehensive overview of human molecular genetics. It valuable resource for students and researchers who want to understand the genetic basis of human health and disease.
Provides a practical guide to bioinformatics, with a focus on hands-on exercises and case studies. It will be particularly useful for learners who want to develop the practical skills necessary to use bioinformatics tools and techniques.
Provides a comprehensive overview of bioinformatics. It good resource for students and researchers who are new to the field.
Provides a gentle introduction to bioinformatics. It good resource for students and researchers who are new to the field.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/af8zs6/hacking
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Effort
6 hours to complete
Level
Introductory
Via
Coursera
Institution
University of California San Diego
Instructors
Niema Moshiri
Vikram Sirupurapu
Sabeel Mansuri
Pavel Pevzner
Mikhail Rayko
Language
English
Transcripts
Español
Français
Português
Deutsch
Italiano
中文
العربية
한국어
日本語
हिंदी
Nederlands
Svenska
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This course belongs to a
collection
called
Applied Bioinformatics. It's comprised of five courses:
- Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen (viewing)
- Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution
- Hacking COVID-19 — Course 2: Decoding SARS-CoV-2's Secrets
- Hacking COVID-19 — Course 3: Unraveling COVID-19's Origins
- Hacking COVID-19: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets
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