• Wellcome Connecting Science

Bacterial Genomes II: Accessing and Analysing Microbial Genome Data with Artemis

4.6 (67 reviews)

Learn more about genomic data, and how computational tools like Artemis can help us understand and track disease-causing bacteria.

17,616 enrolled on this course

Bacterial plate with bacterial growth held by a blue gloved hand, with behind it, an image of a keyboard with the first letters of the DNA bases C, T, G, A in primary colours

  • Duration

    3 weeks

  • Weekly study

    5 hours

  • Digital upgrade

    Free

  • Accreditation

    AvailableMore info
Overview
Syllabus
Accreditation
Start dates
Requirements
Educators
What's included
Learner reviews
More courses

Other courses you might like

This course isn't running right now. We can email you when it starts again, or check out these other courses you might like.

Wellcome Connecting Science
New

Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis

3 weeks

5 hrs per week

Free digital upgrade

Find out more
BoxPlay & FutureLearn

Applications of Calculus

3 weeks

2 hrs per week

Included in Unlimited

Find out more
Foundation for Rare Diseases & European Joint Programme on Rare Diseases

Diagnosing Rare Diseases: from the Clinic to Research and back

4.8 (52 reviews)

5 weeks

3 hrs per week

Included in Unlimited

Find out more

Browse more in Healthcare & Medicine and Science, Engineering & Maths

Biology & Biotechnology · Genetics · Medical Technology
View all courses

Find the right course for you

See your personalised recommendations based on your interests and goals.

Get started

Use computational tools to investigate microbial genomes

Applying increasingly powerful computation to genomics contributes to important medical breakthroughs.

On this course, you will discover the basic principles of microbial bioinformatics analysis, and comparative genomics. Using Artemis, a free genome browser, you will find out how to investigate whole bacterial genomes, and through the analysis of bacterial genes and proteins, you will explore the genomic features of pathogens.

By the end of this course, you will be able to use genomic data to increase your knowledge of microbial genomes.

Download video: standard or HD

Skip to 0 minutes and 9 seconds Research into bacterial genomes have been revolutionised by computer programmes. These programmes are in constant development, keeping up with the growing demands of researchers and technology. My name is Dr. Anna Protasio. I’m Dr. Christine Boinett. And I am Professor Pablo Tsukayama. Here at the Wellcome Sanger Institute, alongside collaborators from around the world, bioinformatitians and researchers work together to deliver the best tools for genome analysis. In this course, you’ll learn one of these tools called Artemis, an open-source genome browser that’s specially designed for bacterial genomes and their annotations. Together, we’ll explore the different functions in Artemis and unlock the features so that we can better understand the biology of the organism. You will learn through a combination of articles, screencasts, and interviews.

Skip to 0 minutes and 54 seconds You will join in productive discussions, sharing your findings and ideas with other learners. And together, we’ll be working on a real research problem. Join us in this new adventure, when we find out what lies behind bacterial genomes.

Syllabus

  • Week 1

    Welcome, Reference genomes and introduction to Artemis

    • Welcome to the Course

      Welcome to the Course

    • Reference genomes: Genome assemblies, construction, representation, and reliability

      Multi-FASTA files, Reference and draft bacterial genomes

    • The bacterial genome browser Artemis

      Introduction to Artemis, an open source genome browser

  • Week 2

    Genome annotation, GC (guanine-cytosine) content, and data access

    • Genome Annotation

      Genome annotation and file formats

    • Genomic regions have different content of Gs and Cs

      GC (guanine-cytosine) content as used to identify regions of the bacterial genome with particular characteristics, Pathogenicity islands

    • Data access

      Accessing whole bacterial genomes freely available on the internet, Analysing viral SARS-CoV-2 genome using Artemis

  • Week 3

    Consolidation and Peer Review Project

    • Artemis further practice

      Practice more with Artemis and learn a few more functionalities

    • A real case study where Artemis saves the day!

      Case study of the use of Artemis: explore the annotation of a bacterial genome and compare annotations in two genomes

    • Assignment completion, sharing learning, and peer review

      Peer review: complete your project's report and share it with other learners

    • Project resolution, Week 3 and the Course Summary

      Discussion of some answers to the Project, Review of Week 3 and the Course's Learning.

    • Assessment, discussion, reflection and acknowledgments

      End of the course: complete the multiple choice assessment, join in the concluding discussion and reflection, Plan next steps

    • Acknowledgements

      Acknowledgements to the course team

Who is this accredited by?

Royal College of Pathologists
Royal College of Pathologists:

RCPath has approved this course for 15 CPD credits. This applies to medical staff and clinical scientists in career grade posts who are enrolled with one of the Royal Colleges for CPD purposes.

When would you like to start?

  • Date to be announced

Add to Wishlist to be emailed when new dates are announced

Learning on this course

On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.

What will you achieve?

By the end of the course, you‘ll be able to...

  • Collect, access, and download whole bacterial genomes from public repositories
  • Investigate and navigate bacterial genomes and their annotation using Artemis
  • Identify genomic regions with low/high GC (guanine-cytosine) content, often associated with virulence
  • Perform simple comparative analyses between bacterial genomes

Who is the course for?

This course would benefit those interested in learning how to use tools to investigate bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Using analytical tools to access and probe genomes, learners will find out how to perform comparative analyses of genes and their protein products.

The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, microbiologists, and healthcare professionals. The opportunity to use online computational tools to probe bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students.

Bacterial Genomes: From DNA to Protein Function using Bioinformatics is a recommended pre-requisite. Scientific terminology is explained.

What software or tools do you need?

This course will give you an opportunity to learn about and use Artemis, a free genome browser and annotation tool. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of Artemis requires version 1.11 of Java to run successfully. Java can be downloaded from this link.

What do people say about this course?

A highlight of the course is the project.

"A highlight of the course is the project - it applies the newly acquired skill set."

Mqondisi Tshabalala

Who will you learn with?

Dr. Anna Protasio

I am a researcher in parasitology and computational biology at the University of Cambridge. I am passionate about bioinformatics and how we can use these tools to answer questions in biology.

Dr. Christine Boinett

I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques.

Pablo Tsukayama

I am a professor of microbiology at Universidad Peruana Cayetano Heredia and a visiting research scholar at the Wellcome Sanger Institute. I study how pathogen populations evolve and spread in Peru.

Martin Aslett

I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics.

Matthew Dorman

I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens.

Professor Nicholas Thomson

I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease.

Who developed the course?

Wellcome Connecting Science

Wellcome Connecting Science develops and delivers open postgraduates courses and conferences focused on biomedicine.

What's included?

Wellcome Connecting Science are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get:

  • Unlimited access to this course
  • Includes any articles, videos, peer reviews and quizzes
  • Tests to validate your learning
  • A PDF Certificate of Achievement to prove your success when you’re eligible

    • Learning on FutureLearn

    Your learning, your rules

    • Courses are split into weeks, activities, and steps to help you keep track of your learning
    • Learn through a mix of bite-sized videos, long- and short-form articles, audio, and practical activities
    • Stay motivated by using the Progress page to keep track of your step completion and assessment scores

    Join a global classroom

    • Experience the power of social learning, and get inspired by an international network of learners
    • Share ideas with your peers and course educators on every step of the course
    • Join the conversation by reading, @ing, liking, bookmarking, and replying to comments from others

    Map your progress

    • As you work through the course, use notifications and the Progress page to guide your learning
    • Whenever you’re ready, mark each step as complete, you’re in control
    • Complete 90% of course steps and all of the assessments to earn your certificate

    Want to know more about learning on FutureLearn? Using FutureLearn

    Learner reviews

    Learner reviews cannot be loaded due to your cookie settings. Please and refresh the page to view this content.

    Join the conversation on social media

    You can use the hashtag #FLaccess2analysis to talk about this course on social media.