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Bacterial Bioinformatics

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses BV-BRC, the Bacterial and Viral Bioinformatics Resource Center (merger of PATRIC, IRD and ViPR, the three former resources), as the platform for analysis. BV-BRC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. BV-BRC also provides a private workspace where users can upload and analyze their own data.

Course participants will gain skills needed to do comparative analysis of bacterial genomes, starting with raw sequence data.The lessons in the first module cover genome assembly, annotation, phylogenetic tree construction, and protein family / proteome comparisons. Each lesson builds on the previous, creating a complete baseline analysis workflow.

NOTE: The exercises in this course were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

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Syllabus

Introduction

This lesson provides an introduction to BV-BRC, the Bacterial and Viral Resource Integration Center (formerly PATRIC), a Bioinformatics Resource Center dedicated to supporting bacterial research. BV-BRC provides comprehensive bacterial genomic data with integrated analysis tools and visualizations. BV-BRC also provides a private workspace where users can upload and analyze their own data. BV-BRC will serve as the platform for the analysis methods covered in this module. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

Traffic lights

Read about what's good

what should give you pause

and possible dealbreakers

Provides a comprehensive introduction to bacterial genomics

Suitable for learners with basic knowledge of genomics and bioinformatics

Familiarizes learners with the BV-BRC platform

Emphasizes practical application through hands-on exercises

May require additional knowledge or resources for advanced learners

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Reviews summary

Practical bacterial bioinformatics with bv-brc

According to students, this course offers an invaluable hands-on approach to bacterial bioinformatics, primarily utilizing the BV-BRC platform. Learners highly praise the clear, step-by-step instructions and practical exercises, which are deemed highly relevant for research and facilitate immediate application. While it provides a strong foundation in key analysis tasks like genome assembly and annotation, a few learners noted that it is best suited for those with existing bioinformatics knowledge, as it may be challenging for absolute beginners. The structured approach, where each lesson builds on the previous, is also a positive aspect, though some found the content less engaging at times.

Repetitive note about PATRIC transition noted by learners.

"The only minor point is the outdated mention of PATRIC, but the system is intuitive enough that it wasn't a major issue."

"I found some of the initial setup slightly confusing, perhaps due to the PATRIC to BV-BRC transition, but once past that, the flow was smooth."

"My only criticism is the repetitive mention of PATRIC, which could be streamlined in the course material itself."

Logically progresses through a complete analysis workflow.

"Each lesson builds on the previous, creating a complete baseline analysis workflow."

"The course is well-organized and covers a wide range of genomic analysis tasks. I liked how it progressed logically from assembly to comparative analysis."

"I particularly appreciated the modules on genome assembly and annotation; they were hands-on and directly applicable to my research."

Gain skills directly applicable to bacterial genomics research.

"This course is an absolute gem... The step-by-step instructions for using BV-BRC are incredibly clear and the practical exercises truly solidify understanding."

"Highly recommend! As a researcher, I needed to get up to speed with BV-BRC quickly, and this course delivered. The hands-on nature meant I could immediately apply what I learned."

"Fantastic course for anyone in bacterial genomics! The clear explanations and practical exercises using BV-BRC made complex concepts accessible. This course is invaluable for wet lab biologists."

"Excellent course for researchers using BV-BRC. The hands-on approach is what makes it stand out. I use BV-BRC daily now, thanks to this course."

Could be more engaging, deeper dives into 'why' sometimes needed.

"While the tools covered are important, I felt the course could be more engaging. Some parts felt a bit like following a manual rather than a dynamic learning experience."

"The exercises are good, but I wished for more troubleshooting guidance or deeper dives into the 'why' behind certain steps."

Requires basic bioinformatics knowledge, not for beginners.

"It's definitely for those with some prior bioinformatics knowledge, not absolute beginners."

"My main feedback would be that a basic understanding of bioinformatics concepts is essential to get the most out of it."

"I found this course quite challenging to follow. It assumes a level of familiarity with bioinformatics concepts and even the BV-BRC interface that I didn't possess."

"Perhaps more foundational content is needed, or a clearer prerequisite statement."

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 Bacterial Bioinformatics with these activities:

Review Molecular Biology Concepts

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Refresh your understanding of molecular biology to strengthen your foundation for the course.

Browse courses on Molecular Biology

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Review your notes from previous molecular biology courses
Read introductory articles or textbooks on molecular biology
Take practice quizzes or tests to assess your understanding

Compile Bacterial Genomics Resources

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Gather useful bacterial genomics resources for future reference and continued learning.

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Review the introduction to BV-BRC lesson
Explore the BV-BRC website
Bookmark helpful resources
Create a reference list or annotated bibliography

Peer Review Proteome Comparisons

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Engage in peer review of proteome comparisons to enhance your understanding and critical analysis skills.

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Review the proteome comparison lesson
Compare the proteomes of different genomes using the BV-BRC Proteome Comparison Service
Share your results with a peer
Provide feedback on your peer's results

Five other activities

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Show all eight activities

Tutorials on Genome Annotation

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Follow tutorials on genome annotation to supplement your learning and expand your knowledge.

Browse courses on Genome Annotation

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Review the genome annotation lesson
Identify relevant tutorials on genome annotation
Complete the tutorials
Apply what you have learned to your own genome analysis

Practice Assembly

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Practice performing genome assembly to improve comprehension and proficiency.

Browse courses on Assembly

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Review the assembly lesson
Assemble a sample genome using the BV-BRC Genome Assembly Service
Analyze your results
Repeat steps 2-3 with different sample genomes

Protein Family Analysis Exercises

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Reinforce your understanding of protein family analysis by working through practice exercises.

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Review the protein family sorter lesson
Complete the protein family sorter exercises
Analyze your results
Repeat steps 2-3 with different datasets

Create a Codon-Based Phylogenetic Tree

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Create a codon-based phylogenetic tree to demonstrate your understanding of phylogenetic analysis.

Browse courses on Comparative Genomics

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Review the codon-based phylogenetic tree lesson
Generate a codon-based phylogenetic tree using the BV-BRC Codon Tree Service
Interpret your results
Write a report summarizing your findings

Develop a Comprehensive Genome Analysis Report

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Demonstrate your proficiency in comprehensive genome analysis by creating a detailed report.

Browse courses on Genome Analysis

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Review the comprehensive genome analysis lesson
Assemble, annotate, and analyze a genome using the BV-BRC Comprehensive Genome Analysis Service
Interpret your results
Write a comprehensive report summarizing your findings

Career center

Learners who complete Bacterial Bioinformatics will develop knowledge and skills that may be useful to these careers:

Bioinformatician

A Bioinformatician uses computer science, mathematics, and statistics to analyze biological data. This course may be useful for Bioinformaticians, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Bioinformatician

Computational Biologist

Computational Biologists develop and apply computational tools and techniques to solve biological problems. This course may be useful for Computational Biologists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Computational Biologist

Data Scientist

A Data Scientist uses data to solve problems and make decisions. This course may be useful for Data Scientists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of data science projects, including developing new machine learning algorithms, building predictive models, and visualizing data.

See salaries and explore the career path for Data Scientist

Genomicist

A Genomicist studies the structure and function of genomes. This course may be useful for Genomicists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Genomicist

Microbiologist

A Microbiologist studies microorganisms, including bacteria. This course may be useful for Microbiologists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Microbiologist

Molecular Biologist

A Molecular Biologist studies the structure and function of molecules, including DNA. This course may be useful for Molecular Biologists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Molecular Biologist

Phylogeneticist

A Phylogeneticist studies the evolutionary relationships among different groups of organisms. This course may be useful for Phylogeneticists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Phylogeneticist

Researcher

A Researcher conducts scientific research. This course may be useful for Researchers, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Researcher

Scientist

A Scientist conducts scientific research. This course may be useful for Scientists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of research projects, including studying the evolution of bacteria, identifying new drug targets, and developing new diagnostic tests.

See salaries and explore the career path for Scientist

Biomedical Engineer

A Biomedical Engineer designs and develops medical devices and technologies. This course may be useful for Biomedical Engineers, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of biomedical engineering projects, including developing new diagnostic tests, designing new medical devices, and developing new treatments for bacterial infections.

See salaries and explore the career path for Biomedical Engineer

Epidemiologist

An Epidemiologist studies the distribution and determinants of health-related states or events in specified populations. This course may be useful for Epidemiologists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of epidemiological studies, including studying the spread of bacterial infections, identifying risk factors for bacterial infections, and developing new strategies for preventing and controlling bacterial infections.

See salaries and explore the career path for Epidemiologist

Healthcare Data Analyst

A Healthcare Data Analyst collects, analyzes, and interprets healthcare data to improve patient care. This course may be useful for Healthcare Data Analysts, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of healthcare data analysis projects, including developing new models for predicting the spread of bacterial infections, identifying new risk factors for bacterial infections, and developing new strategies for preventing and controlling bacterial infections.

See salaries and explore the career path for Healthcare Data Analyst

Medical Physicist

A Medical Physicist applies the principles of physics to medicine. This course may be useful for Medical Physicists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of medical physics projects, including developing new imaging techniques for diagnosing bacterial infections, designing new radiation therapies for treating bacterial infections, and developing new methods for preventing and controlling bacterial infections.

See salaries and explore the career path for Medical Physicist

Pharmacist

A Pharmacist dispenses medications and provides information about their use. This course may be useful for Pharmacists, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of pharmacy practice settings, including developing new strategies for preventing and controlling bacterial infections, providing information to patients about bacterial infections, and providing consultations to physicians about the use of antibiotics.

See salaries and explore the career path for Pharmacist

Physician Assistant

A Physician Assistant provides healthcare services under the supervision of a physician. This course may be useful for Physician Assistants, as it provides training in using bioinformatics databases, tools, and methods to analyze bacterial genomes. The skills learned in this course can be applied to a variety of clinical settings, including diagnosing and treating bacterial infections, providing preventive care to patients, and providing education to patients about bacterial infections.

See salaries and explore the career path for Physician Assistant

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 Bacterial Bioinformatics.

An Introduction to Molecular Ecology

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Provides a comprehensive overview of bacterial genomics, including methods for genome sequencing, assembly, annotation, and analysis. It valuable reference for researchers in the field of bacterial genomics.

An Introduction to Molecular Ecology

Paperback

$$$

Protein Science

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Provides a comprehensive overview of bioinformatics, including methods for genome sequencing, assembly, annotation, and analysis. It valuable resource for researchers in the field of bioinformatics.

BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS...

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Provides a practical guide to bioinformatics, including methods for genome sequencing, assembly, annotation, and analysis. It valuable resource for researchers in the field of bioinformatics.

Bioinformatics: A Practical Guide To The Analysis...

Paperback

Bioinformatics

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Provides a comprehensive overview of genomics and bioinformatics, including methods for genome sequencing, assembly, annotation, and analysis. It valuable resource for researchers in the field of genomics and bioinformatics.

Bioinformatics: An Introduction (Computational...

Hardcover

$$$

Bioinformatics: An Introduction (Computational...

Kindle Edition

$$$

Microbial Ecology

Save

Provides a comprehensive overview of microbial ecology, including methods for genome sequencing, assembly, annotation, and analysis. It valuable resource for researchers in the field of microbial ecology.

Microbial Ecology: Fundamentals and Applications...

Hardcover

$$$

Experimental Techniques in Bacterial Genetics

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Provides a comprehensive overview of bacterial molecular genetics, including methods for genome sequencing, assembly, annotation, and analysis. It valuable resource for researchers in the field of bacterial molecular genetics.

Experimental Techniques in Bacterial Genetics

Paperback

Check price

Experimental Techniques in Bacterial Genetics

Kindle Edition

Check price

Active Assessment: Assessing Scientific Inquiry

Save

Provides a comprehensive overview of bacteriophage biology, including methods for genome sequencing, assembly, annotation, and analysis. It valuable resource for researchers in the field of bacteriophage biology.

Active Assessment: Assessing Scientific Inquiry...

Paperback

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Effort

The first module in the course contains 8 lessons, each taking approximately 1-3 hours to complete

Level

Intermediate

Via

Coursera

Institution

University of Virginia

Instructor

Rebecca Wattam

Language

English

Transcripts

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Traffic lights

Read about what's good

what should give you pause

and possible dealbreakers

Provides a comprehensive introduction to bacterial genomics

Suitable for learners with basic knowledge of genomics and bioinformatics

Familiarizes learners with the BV-BRC platform

Emphasizes practical application through hands-on exercises

May require additional knowledge or resources for advanced learners

Bacterial Bioinformatics

Two deals to help you save

What's inside

Syllabus

Traffic lights

Save this course

Reviews summary

Practical bacterial bioinformatics with bv-brc

Activities

Career center

Reading list

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