Mohammed Abdul Jawad

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

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

FREE ONLINE COURSE (with a PDF Certificate of Achievement to prove your success when you’re eligible)

  • Duration: 3 weeks

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


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.



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?

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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.


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.


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. 
  • Matthew Dorman: I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens. 
  • 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. 
  • 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 Genome Campus Advanced Courses and Scientific Conferences: 
Wellcome Genome Campus Advanced Courses and Scientific Conferences provides open postgraduate courses and conferences focused on biomedicine.


What's included?

Wellcome Genome Campus Advanced Courses and Scientific Conferences 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

To register and join the course, visit: https://www.futurelearn.com/courses/bacterial-genomes-access-and-analysis

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