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Bhagesh Hunakunti
In this 1-hour long project-based course, you will learn how to access, parse, and visualize data from various bioinformatics sequence and structural online databases such as ENTREZ, PDB, KEGG and NCBI using Biopython.
You will also interact with various bioinformatics file formats such as FASTA, PDB, GENBANK and XML along with various parsers to read and modify these files using Biopython.
Note: This course works best for learners who are based in the North America region. We’re currently working on providing the same experience in other regions.
Register for this course and see more details by visiting:
OpenCourser.com/course/077pte/access
What's inside
Syllabus
Project Overview
By the end of this project, you will learn to access, parse, and visualize data from various bioinformatics sequence and structural online databases such as ENTREZ, PDB, KEGG and NCBI using Biopython. you will also interact with various bioinformatics file formats such as FASTA, PDB, GENBANK and XML along with various parsers to read and modify these files using Biopython.
Good to know
Good to know
Know what's good ,
what to watch for , and
possible dealbreakers
Develops skills in data access and visualization from online databases using Biopython, which is standard in bioinformatics and necessary for exploring biological data
Leverages various bioinformatics file formats, including FASTA, PDB, GENBANK, and XML, which is crucial for working with biological data
Taught by Bhagesh Hunakunti, an experienced professional in the field of Bioinformatics
Emphasizes working with bioinformatics sequence and structural online databases
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Reviews summary
Engaging bioinformatics course
Learners say this bioinformatics course is engaging, informative, and well-taught. They applaud the instructor for their hard work and excellent teaching. While the walkthrough of how to use Biopython is very informative, some learners wish that the quiz was more in depth on reusing the programs that were just written. Other learners note that the discussion forum was not as active as they would have liked.
Walkthrough of Biopython is informative.
"While the walkthrough of how to use Bio[ython was very informative, I wished that the quiz was more in depth on reusing the programs that were just written."
Instructor is excellent.
"Such a fascinating topic and so well taught! Bravo!"
"I applaud the instructor for his hard work and excellent teaching."
Discussion forum is not active.
"Overall, the course is a good start. It is easy to understand and follow, provided you have some knowledge of the subject."
"You can definitely build on this project for your portfolio."
"I gave only 4 stars because the discussion forum was not as active."
"I haven't received any responses for my queries till date."
Quiz could be more in depth.
"While the walkthrough of how to use Bio[ython was very informative, I wished that the quiz was more in depth on reusing the programs that were just written."
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 Access Bioinformatics Databases with Biopython with these
activities:
Review Basic Python Programming
Show steps
Refreshing Python programming skills will strengthen the foundation for learning Biopython.
Browse courses on
Python Programming
Show steps
-
Review basic Python syntax and data structures.
-
Practice writing simple Python programs.
Summarize Course Materials and Prepare Study Guide
Show steps
Summarizing course materials will help consolidate knowledge and improve retention.
Browse courses on
Study Guide
Show steps
-
Review and understand the course materials, including lectures and resources.
-
Identify and extract key concepts, definitions, and examples.
-
Organize and summarize the extracted information into a study guide.
Join a Study Group Focused on Biopython Applications
Show steps
Participating in a study group will provide a collaborative environment for learning and discussing Biopython applications.
Browse courses on
Collaboration
Show steps
-
Identify or create a study group focused on Biopython applications.
-
Attend regular study sessions and actively participate in discussions.
-
Collaborate on projects or assignments related to Biopython.
Four other activities
Expand to see all activities and additional details
Show all seven activities
Follow Tutorials on Structural Data Analysis with Biopython
Show steps
Following tutorials will provide a structured approach to learning structural data analysis techniques using Biopython.
Browse courses on
Biopython
Show steps
-
Identify reputable tutorials on structural data analysis with Biopython.
-
Follow the tutorials step-by-step, experimenting with the code and data provided.
-
Apply the learned techniques to analyze real-world structural data.
Write a Blog Post Explaining Key Biopython Concepts
Show steps
Writing a blog post will reinforce understanding of key Biopython concepts and improve communication skills.
Browse courses on
Technical Writing
Show steps
-
Identify the key concepts to be covered in the blog post.
-
Research and gather information from reliable sources.
-
Write a clear and concise blog post, explaining the concepts and providing examples.
-
Proofread and edit the blog post for accuracy and clarity.
Practice Sequence Parsing Using Biopython
Show steps
Practice parsing sequences using Biopython to improve understanding of sequence formats and improve coding skills.
Browse courses on
Biopython
Show steps
-
Review sequence formats such as FASTA, PDB, and GenBank.
-
Install Biopython and import the necessary modules.
-
Explore and practice using Biopython's built-in functions for sequence parsing.
-
Write code to parse and extract specific information from various sequence formats.
Build a Script to Access and Visualize Data from NCBI
Show steps
Creating a script to access and visualize data from NCBI will enhance practical skills in data retrieval and visualization.
Browse courses on
Data Access
Show steps
-
Design the script's functionality and interface.
-
Write code to connect to NCBI's databases and retrieve data.
-
Implement data visualization techniques to present the retrieved data in an informative way.
-
Test and refine the script to ensure accuracy and efficiency.
Review Basic Python Programming
Show steps
Refreshing Python programming skills will strengthen the foundation for learning Biopython.
Browse courses on
Python Programming
Show steps
Show steps
Show steps
- Review basic Python syntax and data structures.
- Practice writing simple Python programs.
Summarize Course Materials and Prepare Study Guide
Show steps
Summarizing course materials will help consolidate knowledge and improve retention.
Browse courses on
Study Guide
Show steps
Show steps
Show steps
- Review and understand the course materials, including lectures and resources.
- Identify and extract key concepts, definitions, and examples.
- Organize and summarize the extracted information into a study guide.
Join a Study Group Focused on Biopython Applications
Show steps
Participating in a study group will provide a collaborative environment for learning and discussing Biopython applications.
Browse courses on
Collaboration
Show steps
Show steps
Show steps
- Identify or create a study group focused on Biopython applications.
- Attend regular study sessions and actively participate in discussions.
- Collaborate on projects or assignments related to Biopython.
Four other activities
Expand to see all activities and additional details
Show all seven activities
Follow Tutorials on Structural Data Analysis with Biopython
Show steps
Following tutorials will provide a structured approach to learning structural data analysis techniques using Biopython.
Browse courses on
Biopython
Show steps
Show steps
Show steps
- Identify reputable tutorials on structural data analysis with Biopython.
- Follow the tutorials step-by-step, experimenting with the code and data provided.
- Apply the learned techniques to analyze real-world structural data.
Write a Blog Post Explaining Key Biopython Concepts
Show steps
Writing a blog post will reinforce understanding of key Biopython concepts and improve communication skills.
Browse courses on
Technical Writing
Show steps
Show steps
Show steps
- Identify the key concepts to be covered in the blog post.
- Research and gather information from reliable sources.
- Write a clear and concise blog post, explaining the concepts and providing examples.
- Proofread and edit the blog post for accuracy and clarity.
Practice Sequence Parsing Using Biopython
Show steps
Practice parsing sequences using Biopython to improve understanding of sequence formats and improve coding skills.
Browse courses on
Biopython
Show steps
Show steps
Show steps
- Review sequence formats such as FASTA, PDB, and GenBank.
- Install Biopython and import the necessary modules.
- Explore and practice using Biopython's built-in functions for sequence parsing.
- Write code to parse and extract specific information from various sequence formats.
Build a Script to Access and Visualize Data from NCBI
Show steps
Creating a script to access and visualize data from NCBI will enhance practical skills in data retrieval and visualization.
Browse courses on
Data Access
Show steps
Show steps
Show steps
- Design the script's functionality and interface.
- Write code to connect to NCBI's databases and retrieve data.
- Implement data visualization techniques to present the retrieved data in an informative way.
- Test and refine the script to ensure accuracy and efficiency.
Career center
Learners who complete Access Bioinformatics Databases with Biopython will develop knowledge and skills
that may be useful to these careers:
Bioinformatics Scientist
Bioinformatics Scientist
A Bioinformatics Scientist uses computational tools to analyze and interpret biological data. This role requires skills in programming, data analysis, and biology. Taking the course Access Bioinformatics Databases with Biopython can help you build a foundation in bioinformatics and gain proficiency in using Biopython, a popular Python library for accessing and parsing biological data. This course will provide you with the skills and knowledge necessary to succeed as a Bioinformatics Scientist.
Computational Biologist
Computational Biologist
A Computational Biologist uses computer science and mathematics to solve problems in biology. This role requires skills in programming, data analysis, and biology. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is essential for a Computational Biologist. This course will provide you with a strong foundation in bioinformatics and help you succeed in this field.
Data Scientist
Data Scientist
A Data Scientist uses data analysis and machine learning to solve problems in various industries. This role requires skills in programming, data analysis, and statistics. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is a valuable skill for a Data Scientist. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Biostatistician
Biostatistician
A Biostatistician uses statistics to analyze and interpret biological data. This role requires skills in statistics, data analysis, and biology. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is a valuable skill for a Biostatistician. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Software Engineer
Software Engineer
A Software Engineer designs, develops, and maintains software applications. This role requires skills in programming, software development, and problem-solving. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is a valuable skill for a Software Engineer. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Database Administrator
Database Administrator
A Database Administrator manages and maintains databases. This role requires skills in database management, data analysis, and programming. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is a valuable skill for a Database Administrator. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Business Analyst
Business Analyst
A Business Analyst analyzes business processes and systems to identify areas for improvement. This role requires skills in business analysis, data analysis, and problem-solving. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is a valuable skill for a Business Analyst. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Systems Analyst
Systems Analyst
A Systems Analyst designs, develops, and maintains computer systems. This role requires skills in systems analysis, programming, and problem-solving. The course Access Bioinformatics Databases with Biopython can help you develop the skills necessary to access, parse, and visualize biological data, which is a valuable skill for a Systems Analyst. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Consultant
Consultant
A Consultant provides advice and support to organizations on a variety of topics. This role requires skills in consulting, problem-solving, and communication. The course Access Bioinformatics Databases with Biopython may be useful for a Consultant who is working with organizations in the biotechnology or pharmaceutical industries. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Entrepreneur
Entrepreneur
An Entrepreneur starts and runs their own business. This role requires skills in entrepreneurship, business management, and problem-solving. The course Access Bioinformatics Databases with Biopython may be useful for an Entrepreneur who is starting a business in the biotechnology or pharmaceutical industries. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Technical Writer
Technical Writer
A Technical Writer creates and maintains technical documentation. This role requires skills in writing, editing, and technical knowledge. The course Access Bioinformatics Databases with Biopython may be useful for a Technical Writer who is writing documentation for bioinformatics software or databases. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Teacher
Teacher
A Teacher teaches students at a variety of levels. This role requires skills in teaching, communication, and subject-matter expertise. The course Access Bioinformatics Databases with Biopython may be useful for a Teacher who is teaching bioinformatics or biology. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Researcher
Researcher
A Researcher conducts research in a variety of fields. This role requires skills in research, data analysis, and problem-solving. The course Access Bioinformatics Databases with Biopython may be useful for a Researcher who is working on a project that involves biological data. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Science Writer
Science Writer
A Science Writer writes about scientific topics for a variety of audiences. This role requires skills in writing, editing, and scientific knowledge. The course Access Bioinformatics Databases with Biopython may be useful for a Science Writer who is writing about bioinformatics or biological data. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
Project Manager
Project Manager
A Project Manager plans, executes, and controls projects. This role requires skills in project management, leadership, and problem-solving. The course Access Bioinformatics Databases with Biopython may be useful for a Project Manager who is working on a project that involves biological data. This course will provide you with a foundation in bioinformatics and help you succeed in this field.
For more career information including salaries, visit:
OpenCourser.com/course/077pte/access
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
Access Bioinformatics Databases with Biopython.
Save
Provides a broad overview of bioinformatics, covering topics such as sequence analysis, molecular evolution, protein structure, and gene expression. It good introductory text for those new to the field, and it provides a solid foundation for further study.
Provides a comprehensive overview of bioinformatics methods and applications, covering topics such as sequence analysis, molecular evolution, protein structure, and gene expression. It good reference for both students and researchers in the field.
Provides a practical guide to using computers to solve bioinformatics problems. It covers topics such as sequence alignment, phylogenetic inference, gene finding, and protein structure prediction. It valuable resource for both students and researchers in the field.
Provides a comprehensive overview of bioinformatics and molecular evolution, covering topics such as sequence analysis, molecular evolution, protein structure, and gene expression. It good reference for both students and researchers in the field.
Provides a gentle introduction to bioinformatics, covering topics such as sequence analysis, molecular evolution, protein structure, and gene expression. It good introductory text for those new to the field, and it provides a solid foundation for further study.
Provides a practical guide to using bioinformatics tools to analyze biological data.
Save
Provides a philosophical perspective on bioinformatics, examining the conceptual foundations of the field.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/077pte/access
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Effort
1 hour
Level
Intermediate
Via
Coursera
Institution
Coursera Project Network
Instructor
Bhagesh Hunakunti
Language
English
Good to know
Develops skills in data access and visualization from online databases using Biopython, which is standard in bioinformatics and necessary for exploring biological data
Leverages various bioinformatics file formats, including FASTA, PDB, GENBANK, and XML, which is crucial for working with biological data
Taught by Bhagesh Hunakunti, an experienced professional in the field of Bioinformatics
Emphasizes working with bioinformatics sequence and structural online databases
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