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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.
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.
Read more
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.
Read more
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!
Register for this course and see more details by visiting:
OpenCourser.com/course/2ybldf/bioinformatics
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
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
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Show steps
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
Review Python Programming Basics
Show steps
Refresh basic Python programming skills to enhance understanding and application of bioinformatics algorithms and tools.
Browse courses on
Python Programming
Show steps
Show steps
Show steps
- Review online tutorials or documentation
- Solve practice problems or exercises
Review Linux basics
Show steps
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
Show steps
Show steps
- Review basic Linux commands
- Create and navigate directories
- Edit files with a text editor
Organize Course Materials
Show steps
Organize notes, assignments, quizzes, and exams to enhance understanding and retention of course materials.
Browse courses on
Bioinformatics
Show steps
Show steps
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
Show steps
Finding a mentor who can help you learn more about bioinformatics can help you accelerate your learning and improve your skills.
Show steps
Show steps
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
Show steps
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
Show steps
Show steps
- Find a user group meeting in your area
- Register for the meeting
- Attend the meeting
Explore BaseSpace Cloud Tutorials
Show steps
Utilize BaseSpace Cloud tutorials to strengthen understanding of the platform's capabilities and applications in bioinformatics.
Browse courses on
Cloud Computing
Show steps
Show steps
Show steps
- Identify relevant tutorials
- Follow step-by-step instructions
- Apply learned concepts to course scenarios
Follow BaseSpace cloud platform tutorials
Show steps
Following BaseSpace cloud platform tutorials can help you learn how to use the platform's features and tools.
Show steps
Show steps
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
Show steps
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
Show steps
Show steps
- Identify relevant resources
- Organize and categorize resources
- Share the compilation with others
Practice Genome Assembly Challenges
Show steps
Engage in repetitive exercises to solidify genome assembly skills and reinforce understanding of bioinformatics algorithms.
Browse courses on
Genome Assembly
Show steps
Show steps
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
Show steps
Practicing using BaseSpace cloud platform tools can help you become more proficient in using the platform.
Show steps
Show steps
Show steps
- Create a new project in BaseSpace
- Upload data to your project
- Run analysis tools on your data
Join Bioinformatics Discussion Forum
Show steps
Engage in discussions with peers to exchange ideas, clarify concepts, and broaden perspectives on bioinformatics.
Browse courses on
Bioinformatics
Show steps
Show steps
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
Show steps
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
Show steps
Show steps
- Choose a topic to write about
- Research your topic
- Write your blog post or article
Participate in Bioinformatics Hackathons
Show steps
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
Show steps
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
Show steps
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
Show steps
Show steps
- Find a project to contribute to
- Read the project documentation
- Make a contribution to the project
Develop a Genome Assembler
Show steps
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
Show steps
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
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.
Bioinformatics Analyst
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.
Computational Biologist
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.
Research Scientist
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.
Software Engineer
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.
Biostatistician
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.
Systems Analyst
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.
Science Writer
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.
Healthcare Data Analyst
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.
Medical Physicist
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.
Health Informatics Specialist
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.
Data Analyst
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.
Web Developer
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.
Technical Writer
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.
Biomedical Engineer
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.
For more career information including salaries, visit:
OpenCourser.com/course/2ybldf/bioinformatics
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.
Provides an introduction to bioinformatics algorithms, including topics such as sequence alignment, gene finding, and genome assembly.
Provides a comprehensive overview of bioinformatics, including topics such as sequence analysis, gene expression analysis, and genome annotation.
Provides a comprehensive overview of bioinformatics data skills, including data management, analysis, and visualization. Serves as a valuable reference for practicing bioinformaticians.
Provides an introduction to programming in Python for bioinformatics, including topics such as data structures, algorithms, and software development.
Provides an overview of genomics, including topics such as genome structure, function, and evolution.
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.
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.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/2ybldf/bioinformatics
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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:
- Molecular Evolution (Bioinformatics IV)
- Finding Mutations in DNA and Proteins (Bioinformatics VI)
- Finding Hidden Messages in DNA (Bioinformatics I)
- Comparing Genes, Proteins, and Genomes (Bioinformatics III)
- Genomic Data Science and Clustering (Bioinformatics V)
- Genome Sequencing (Bioinformatics II)
- 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
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