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Access Bioinformatics Databases with Biopython

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.

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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

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

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Refreshing Python programming skills will strengthen the foundation for learning Biopython.

Browse courses on Python Programming

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Review basic Python syntax and data structures.
Practice writing simple Python programs.

Summarize Course Materials and Prepare Study Guide

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Summarizing course materials will help consolidate knowledge and improve retention.

Browse courses on Study Guide

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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

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Participating in a study group will provide a collaborative environment for learning and discussing Biopython applications.

Browse courses on Collaboration

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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

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Show all seven activities

Follow Tutorials on Structural Data Analysis with Biopython

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Following tutorials will provide a structured approach to learning structural data analysis techniques using Biopython.

Browse courses on Biopython

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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

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Writing a blog post will reinforce understanding of key Biopython concepts and improve communication skills.

Browse courses on Technical Writing

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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

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Practice parsing sequences using Biopython to improve understanding of sequence formats and improve coding skills.

Browse courses on Biopython

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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

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Creating a script to access and visualize data from NCBI will enhance practical skills in data retrieval and visualization.

Browse courses on Data Access

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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

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.

See salaries and explore the career path for Bioinformatics Scientist

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.

See salaries and explore the career path for Computational Biologist

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.

See salaries and explore the career path for Data Scientist

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.

See salaries and explore the career path for Biostatistician

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.

See salaries and explore the career path for Software Engineer

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.

See salaries and explore the career path for Database Administrator

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.

See salaries and explore the career path for Business 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.

See salaries and explore the career path for Systems Analyst

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.

See salaries and explore the career path for Consultant

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.

See salaries and explore the career path for Entrepreneur

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.

See salaries and explore the career path for Technical Writer

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.

See salaries and explore the career path for Teacher

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.

See salaries and explore the career path for Researcher

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.

See salaries and explore the career path for Science Writer

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.

See salaries and explore the career path for Project Manager

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.

Protein Science

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.

An Introduction to Bioinformatics Algorithms

Save

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.

An Introduction to Bioinformatics Algorithms

Paperback

Check price

An Introduction to Bioinformatics Algorithms

Kindle Edition

Check price

Bioinformatics Computing

Save

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.

Bioinformatics Computing

Paperback

$$$

Bioinformatics and Molecular Evolution

Save

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.

Bioinformatics and Molecular Evolution

Paperback

Bioinformatics and Molecular Evolution

Kindle Edition

$$$$

BIOS Instant Notes in Bioinformatics

Save

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.

BIOS Instant Notes in Bioinformatics

Paperback

Check price

BIOS Instant Notes in Bioinformatics

Kindle Edition

Check price

BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS...

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Provides a practical guide to using bioinformatics tools to analyze biological data.

Bioinformatics: A Practical Guide To The Analysis...

Paperback

Processes of Life

Save

Provides a philosophical perspective on bioinformatics, examining the conceptual foundations of the field.

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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

Share and help others discover this course.

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