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Bioinformatics Capstone

Big Data in Biology

Pavel Pevzner and Phillip Compeau

In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.

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In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.

In particular, in a series of Application Challenges will see how genome assembly can be used to track the source of a food poisoning outbreak, how RNA-Sequencing can help us analyze gene expression data on the tissue level, and compare the pros and cons of whole genome vs. whole exome sequencing for finding potentially harmful mutations in a human sample.

Plus, hacker track students will have the option to build their own genome assembler and apply it to real data!

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What's inside

Syllabus

Assembly and Annotation of the SARS-CoV-2 Genome
Variant Detection and Classification of SARS-CoV-2
SARS-CoV-2 Spike Protein Structure Analysis
Read more

Good to know

Know what's good
, what to watch for
, and possible dealbreakers
Develops skills for analyzing gene expression data on the tissue level, which is highly relevant in both industry and academia
Builds a strong foundation for beginners in bioinformatics
Offers hands-on labs and interactive materials, which enhance the learning experience
Involves real-world data, which makes the learning more practical
Uses the BaseSpace cloud platform, which is relevant to industry
Taught by instructors who are recognized for their work in bioinformatics

Save this course

Save Bioinformatics Capstone: Big Data in Biology to your list so you can find it easily later:
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Reviews summary

Bioinformatics capstone: not recommended

Learners say this bioinformatics course is very difficult to complete due to broken links. While there are some engaging assignments, the final projects are based on difficult and time-consuming peer-reviews. Additionally, Coursera's learning policies can also slow down progress. Overall, most learners do not recommend this course.
Learning pace restricted
"This course, as others in Coursera catalog, suffer from Coursera's new learning policies, which deteriorate the learnang experience, significantly slowing progress towards completion."
Lengthy and difficult
"Every single final project are all based on peer-reviews."
"Peer-reviews take a loooong time."
"I have seen some submissions from 2 years ago!!"
Incomplete course materials
"Links were dead to the data set since a few years ago."
"The course cannot be completed due to absence of the valid URL"
"Important data for this course, as well as vital links, no longer exist."

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 Bioinformatics Capstone: Big Data in Biology with these activities:
Review Python Programming Basics
Refresh basic Python programming skills to enhance understanding and application of bioinformatics algorithms and tools.
Browse courses on Python Programming
Show steps
  • Review online tutorials or documentation
  • Solve practice problems or exercises
Review Linux basics
Reviewing Linux basics can help you be better prepared for this course's work in the BaseSpace cloud platform.
Browse courses on Linux
Show steps
  • Review basic Linux commands
  • Create and navigate directories
  • Edit files with a text editor
Organize Course Materials
Organize notes, assignments, quizzes, and exams to enhance understanding and retention of course materials.
Browse courses on Bioinformatics
Show steps
  • Gather all course materials
  • Create a filing system
  • Color-code or label materials
  • Review materials regularly
12 other activities
Expand to see all activities and additional details
Show all 15 activities
Find a mentor who can help you learn more about bioinformatics
Finding a mentor who can help you learn more about bioinformatics can help you accelerate your learning and improve your skills.
Show steps
  • Ask your friends, family, or colleagues for recommendations
  • Attend industry events and meetups
  • Use online resources like LinkedIn and Meetup to find potential mentors
Attend a BaseSpace cloud platform user group meeting
Attending a BaseSpace cloud platform user group meeting can help you connect with other users and learn about their experiences with the platform.
Show steps
  • Find a user group meeting in your area
  • Register for the meeting
  • Attend the meeting
Explore BaseSpace Cloud Tutorials
Utilize BaseSpace Cloud tutorials to strengthen understanding of the platform's capabilities and applications in bioinformatics.
Browse courses on Cloud Computing
Show steps
  • Identify relevant tutorials
  • Follow step-by-step instructions
  • Apply learned concepts to course scenarios
Follow BaseSpace cloud platform tutorials
Following BaseSpace cloud platform tutorials can help you learn how to use the platform's features and tools.
Show steps
  • Find tutorials on the BaseSpace website
  • Follow the steps in the tutorials
  • Take notes on what you learn
Create a Bioinformatics Resource Compilation
Assemble a collection of resources such as tools, datasets, and articles to enhance understanding and access to bioinformatics information.
Browse courses on Bioinformatics
Show steps
  • Identify relevant resources
  • Organize and categorize resources
  • Share the compilation with others
Practice Genome Assembly Challenges
Engage in repetitive exercises to solidify genome assembly skills and reinforce understanding of bioinformatics algorithms.
Browse courses on Genome Assembly
Show steps
  • Attempt a series of genome assembly challenges
  • Analyze results and identify areas for improvement
  • Repeat challenges to track progress
Practice using BaseSpace cloud platform tools
Practicing using BaseSpace cloud platform tools can help you become more proficient in using the platform.
Show steps
  • Create a new project in BaseSpace
  • Upload data to your project
  • Run analysis tools on your data
Join Bioinformatics Discussion Forum
Engage in discussions with peers to exchange ideas, clarify concepts, and broaden perspectives on bioinformatics.
Browse courses on Bioinformatics
Show steps
  • Find a relevant discussion forum
  • Introduce oneself and participate in discussions
  • Ask questions and share insights
Create a blog post or article about BaseSpace cloud platform
Creating a blog post or article about BaseSpace cloud platform can help you solidify your understanding of the platform and share your knowledge with others.
Show steps
  • Choose a topic to write about
  • Research your topic
  • Write your blog post or article
Participate in Bioinformatics Hackathons
Participate in hackathons to apply bioinformatics skills in a competitive and collaborative environment, fostering innovation and problem-solving abilities.
Browse courses on Bioinformatics
Show steps
  • Identify relevant hackathons
  • Form a team or work independently
  • Develop and submit a project
Contribute to the BaseSpace cloud platform open source project
Contributing to the BaseSpace cloud platform open source project can help you learn more about the platform and make it better for everyone.
Show steps
  • Find a project to contribute to
  • Read the project documentation
  • Make a contribution to the project
Develop a Genome Assembler
Build a genome assembler as a practical application of bioinformatics concepts, fostering in-depth understanding and problem-solving skills.
Browse courses on Genome Assembly
Show steps
  • Design the assembler algorithm
  • Implement the algorithm in a programming language
  • Test the assembler on real data

Career center

Learners who complete Bioinformatics Capstone: Big Data in Biology will develop knowledge and skills that may be useful to these careers:
Bioinformatics Scientist
A Bioinformatics Scientist must have strong analytical skills and be comfortable with coding to work with large amounts of biological data. They will use this data to help solve complex biological problems. This course may be useful in learning the necessary skills and knowledge to analyze biological data.
See salaries and explore the career path for Bioinformatics Scientist
Bioinformatics Analyst
A Bioinformatics Analyst will use their knowledge of computer science to manipulate information within biological data. With the help of computational tools, they will analyze this data to help make new discoveries in the field of biology. This course may be useful in learning the necessary techniques and tools to analyze different biological data, such as genome assemblies.
See salaries and explore the career path for Bioinformatics Analyst
Computational Biologist
A Computational Biologist will work in an interdisciplinary field that combines biology and computer science. They will use computational tools to analyze biological data and make new discoveries. This course may be useful in learning the necessary skills and knowledge to analyze biological data and solve biological problems.
See salaries and explore the career path for Computational Biologist
Research Scientist
A Research Scientist will conduct research in a variety of fields, including biology, chemistry, physics, and computer science. They will use their knowledge and skills to make new discoveries and develop new technologies. This course may be useful in learning the necessary skills and knowledge to conduct research in the field of bioinformatics.
See salaries and explore the career path for Research Scientist
Software Engineer
A Software Engineer will design, develop, and maintain software applications. They will use their knowledge of computer science to create software that meets the needs of users. This course may be useful in learning the necessary skills and knowledge to develop software applications for the field of bioinformatics.
See salaries and explore the career path for Software Engineer
Biostatistician
A Biostatistician will use their knowledge of statistics and biology to solve problems in the field of biology. They will use statistical methods to analyze biological data and make new discoveries. This course may be useful for building a foundation in analyzing biological data and working with large datasets.
See salaries and explore the career path for Biostatistician
Systems Analyst
A Systems Analyst will work with businesses to analyze their systems and processes. They will use their knowledge of computer science and business to identify areas for improvement and develop solutions. This course may be useful in learning the necessary skills and knowledge to analyze systems and processes in the field of bioinformatics.
See salaries and explore the career path for Systems Analyst
Science Writer
A Science Writer will communicate complex scientific information to the public. They will use their writing skills to make scientific research and discoveries accessible to a wider audience. This course may be useful in learning the necessary skills to communicate complex scientific information to the public.
See salaries and explore the career path for Science Writer
Healthcare Data Analyst
A Healthcare Data Analyst will work with large amounts of healthcare data to help improve the quality of care for patients. They will use their knowledge of statistics and computer science to analyze data and identify trends, patterns, and relationships that can be leveraged to make better predictions and provide better care to patients. This course may be useful for building a foundation in analyzing biological data and working with large datasets.
See salaries and explore the career path for Healthcare Data Analyst
Medical Physicist
A Medical Physicist will work in an interdisciplinary field that combines physics and medicine. They will use their knowledge of physics to develop new medical technologies and treatments. This course may be useful for building a foundation in analyzing biological data and working with large datasets.
See salaries and explore the career path for Medical Physicist
Health Informatics Specialist
A Health Informatics Specialist will work with healthcare data to improve the quality of care for patients. They will use their knowledge of computer science and healthcare to analyze data and identify trends, patterns, and relationships that can be leveraged to make better decisions. This course may be useful for building a foundation in analyzing biological data and working with large datasets.
See salaries and explore the career path for Health Informatics Specialist
Data Analyst
A Data Analyst will work with large amounts of data to help companies make better decisions. They will use their knowledge of statistics and computer science to analyze data and identify trends, patterns, and relationships that can be leveraged to make better predictions. This course may be useful for building a foundation in data analysis and working with large datasets.
See salaries and explore the career path for Data Analyst
Web Developer
A Web Developer will design and develop websites. They will use their knowledge of computer science and design to create websites that are both visually appealing and functional. This course may be useful in learning the necessary skills and knowledge to develop websites for the field of bioinformatics.
See salaries and explore the career path for Web Developer
Technical Writer
A Technical Writer will create user manuals, technical documentation, and other written materials to explain complex technical information. They will use their writing skills to make technical information accessible to a wider audience. This course may be useful in learning the necessary skills to communicate complex technical information to the public.
See salaries and explore the career path for Technical Writer
Biomedical Engineer
A Biomedical Engineer will work in an interdisciplinary field that combines engineering and biology. They will design and develop medical devices and technologies to solve problems in the field of medicine and healthcare. This course may be useful for building a foundation in analyzing biological data and working with large datasets.
See salaries and explore the career path for Biomedical Engineer

Reading list

We've selected seven 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 Bioinformatics Capstone: Big Data in Biology.
Cover image
An Introduction to Bioinformatics Algorithms
Save
Provides an introduction to bioinformatics algorithms, including topics such as sequence alignment, gene finding, and genome assembly.
An Introduction to Bioinformatics Algorithms
Paperback
Check
An Introduction to Bioinformatics Algorithms
Kindle Edition
Check
Cover image
BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS...
Save
Provides a comprehensive overview of bioinformatics, including topics such as sequence analysis, gene expression analysis, and genome annotation.
Bioinformatics: A Practical Guide To The Analysis...
Paperback
$$
Cover image
Bioinformatics Data Skills
Save
Provides a comprehensive overview of bioinformatics data skills, including data management, analysis, and visualization. Serves as a valuable reference for practicing bioinformaticians.
Bioinformatics Data Skills: Reproducible and Robust...
Paperback
$$
Bioinformatics Data Skills: Reproducible and Robust...
Kindle Edition
$$
Cover image
Bioinformatics Programming Using Python
Save
Provides an introduction to programming in Python for bioinformatics, including topics such as data structures, algorithms, and software development.
Bioinformatics Programming Using Python: Practical...
Paperback
$$
Bioinformatics Programming Using Python by Mitchell...
Unknown Binding
$$$
Bioinformatics Programming Using Python: Practical...
Kindle Edition
$$
Cover image
Gene Cloning and DNA Analysis
Save
Provides an overview of genomics, including topics such as genome structure, function, and evolution.
Gene Cloning and DNA Analysis: An Introduction
Paperback
$$$
Gene Cloning and DNA Analysis: An Introduction
Paperback
$$$$
Gene Cloning and DNA Analysis: An Introduction
Paperback
$$$$
Gene Cloning and DNA Analysis: An Introduction
Paperback
$$$$
Gene Cloning and DNA Analysis: An Introduction
Kindle Edition
$$$
Cover image
Statistical Methods in Bioinformatics
Save
Provides a solid foundation in statistical methods commonly used in bioinformatics. Serves as a valuable reference for understanding and applying statistical techniques in this field.
Statistical Methods in Bioinformatics: An...
Hardcover
$$$$
Statistical Methods in Bioinformatics: An...
Kindle Edition
$$$
Cover image
RNA-seq Data Analysis
Save
Offers a practical guide to RNA-Seq data analysis, covering experimental design, data analysis, and interpretation. Particularly valuable for researchers working with RNA-Seq data.
RNA-seq Data Analysis: A Practical Approach...
Hardcover
$$$
RNA-seq Data Analysis: A Practical Approach...
Kindle Edition
$$$

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Course image
Effort
3 weeks of study, 3-4 hours/week
Level
Intermediate
Via
Coursera
Institution
University of California San Diego
Instructors
Pavel Pevzner
Phillip Compeau
Language
English
This course belongs to a collection called Bioinformatics. It's comprised of seven courses:
  1. Molecular Evolution (Bioinformatics IV)
  2. Finding Mutations in DNA and Proteins (Bioinformatics VI)
  3. Finding Hidden Messages in DNA (Bioinformatics I)
  4. Comparing Genes, Proteins, and Genomes (Bioinformatics III)
  5. Genomic Data Science and Clustering (Bioinformatics V)
  6. Genome Sequencing (Bioinformatics II)
  7. Bioinformatics Capstone: Big Data in Biology (viewing)
Good to know
Develops skills for analyzing gene expression data on the tissue level, which is highly relevant in both industry and academia
Builds a strong foundation for beginners in bioinformatics
Offers hands-on labs and interactive materials, which enhance the learning experience
Involves real-world data, which makes the learning more practical
Uses the BaseSpace cloud platform, which is relevant to industry
Taught by instructors who are recognized for their work in bioinformatics
Share and help others discover this course.
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