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Rebecca Wattam
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.
Read more
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.
Read more
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.
Register for this course and see more details by visiting:
OpenCourser.com/course/0v2k7p/bacterial
What's inside
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.
Read more
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.
Read more
Assembly
This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the BV-BRC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process.
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.
Annotation
This lesson provides step-by-step instructions for annotating a genome from contigs using the BV-BRC Bacterial Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process.
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.
Comprehensive Genome Analysis
This lesson provides step-by-step instructions for assembling, annotating, and performing an automated analysis of a genome from a set of bacterial sequence reads using the BV-BRC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service.
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.
Codon-Based Phyogenetic Trees
This lesson provides step-by-step instructions for generating a codon-based phylogentic tree from a set of genomes using the BV-BRC Codon Tree Service. Exercises are included to enhance comprehension and build proficiency in using the service.
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.
Similar Genome Finder
This lesson provides step-by-step instructions for finding genomes (and associated taxonomy) in BV-BRC similar to your genome or sequences using the Similar Genome Finder Service. Exercises are included to enhance comprehension and build proficiency in using the service.
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.
Protein Family Sorter
This lesson provides step-by-step instructions for using the BV-BRC Protein Family Sorter to compare presence, absence, and counts of proteins in protein families across a set of genomes. Exercises are included to enhance comprehension and build proficiency in using the tool.
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.
Proteome Comparison
This lesson provides step-by-step instructions for using the BV-BRC Proteome Comparison Service to compare a set of genomes against a reference genome, feature group, or FASTA file. Exercises are included to enhance comprehension and build proficiency in using the tool.
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.
Good to know
Good to know
Know what's good ,
what to watch for , 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
Highly rated bacterial bioinformatics course
Learners say this is an excellent course that provides very informative and easy-to-understand lessons on bacterial genome analysis. Many enjoyed the assignments and the in-depth explanations of the PATRIC database. Some learners note that the course is updated regularly and suggest that the lessons be refreshed accordingly.
Clear and Knowledgeable
"The instructor, Rebecca Wattam, explains everything in detail and speaks very clearly."
Useful Tool for Analysis
"It is a very good course to start to analyze biodata"
"I am glad that I have met with BV-BRC. I will use their services in my future bacterial or viral studies."
"very useful course , can solve a lot of problem in bacterium genome analysis easily"
Engaging and Well-Explained
"Very informative Presentation"
"Easy and understandable. "
"Very Informative Course, I recommended "
Focus on Tutorials Rather Than Concepts
"having completed the first 2 weeks, I think the course title is misleading. The lessons aren't so much about concepts in bacterial bioinformatics as they are tutorials for PATRIC."
Course Needs Updating
"It was a very useful and easy-to-learn course. But I noticed that the database has been updated and there are a lot more changes and features available than the ones that are taught in the present lectures."
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
Show steps
Refresh your understanding of molecular biology to strengthen your foundation for the course.
Browse courses on
Molecular Biology
Show steps
-
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
Show steps
Gather useful bacterial genomics resources for future reference and continued learning.
Show steps
-
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
Show steps
Engage in peer review of proteome comparisons to enhance your understanding and critical analysis skills.
Show steps
-
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
Expand to see all activities and additional details
Show all eight activities
Tutorials on Genome Annotation
Show steps
Follow tutorials on genome annotation to supplement your learning and expand your knowledge.
Browse courses on
Genome Annotation
Show steps
-
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
Show steps
Practice performing genome assembly to improve comprehension and proficiency.
Browse courses on
Assembly
Show steps
-
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
Show steps
Reinforce your understanding of protein family analysis by working through practice exercises.
Show steps
-
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
Show steps
Create a codon-based phylogenetic tree to demonstrate your understanding of phylogenetic analysis.
Browse courses on
Comparative Genomics
Show steps
-
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
Show steps
Demonstrate your proficiency in comprehensive genome analysis by creating a detailed report.
Browse courses on
Genome Analysis
Show steps
-
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
Review Molecular Biology Concepts
Show steps
Refresh your understanding of molecular biology to strengthen your foundation for the course.
Browse courses on
Molecular Biology
Show steps
Show steps
Show steps
- 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
Show steps
Gather useful bacterial genomics resources for future reference and continued learning.
Show steps
Show steps
Show steps
- 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
Show steps
Engage in peer review of proteome comparisons to enhance your understanding and critical analysis skills.
Show steps
Show steps
Show steps
- 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
Expand to see all activities and additional details
Show all eight activities
Tutorials on Genome Annotation
Show steps
Follow tutorials on genome annotation to supplement your learning and expand your knowledge.
Browse courses on
Genome Annotation
Show steps
Show steps
Show steps
- 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
Show steps
Practice performing genome assembly to improve comprehension and proficiency.
Browse courses on
Assembly
Show steps
Show steps
Show steps
- 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
Show steps
Reinforce your understanding of protein family analysis by working through practice exercises.
Show steps
Show steps
Show steps
- 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
Show steps
Create a codon-based phylogenetic tree to demonstrate your understanding of phylogenetic analysis.
Browse courses on
Comparative Genomics
Show steps
Show steps
Show steps
- 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
Show steps
Demonstrate your proficiency in comprehensive genome analysis by creating a detailed report.
Browse courses on
Genome Analysis
Show steps
Show steps
Show steps
- 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:
Genomicist
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.
Bioinformatician
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.
Microbiologist
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.
Molecular Biologist
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.
Scientist
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.
Phylogeneticist
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.
Data Scientist
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.
Computational Biologist
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.
Researcher
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.
Physician Assistant
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.
Epidemiologist
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.
Biomedical Engineer
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.
Healthcare Data Analyst
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.
Medical Physicist
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.
Pharmacist
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.
For more career information including salaries, visit:
OpenCourser.com/course/0v2k7p/bacterial
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.
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.
Save
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.
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.
Save
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.
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.
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.
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.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/0v2k7p/bacterial
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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
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Good to know
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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