Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)
30 November 2020 - 31 January 2021Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://coursesandconferences.wellcomegenomecampus.org/our-events/bacterial-genomes-compara-genomics-online-nov20/ https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-3e9f10a2-bd0a-4af3-bc39-0d11856143e2 # Overview * **Duration**: 3 weeks, 5 hours per week * Free * Certificate of achievement available on satisfactory completion * **Start Date**: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Disease outbreaks are still a big problem in our modern world. Comparison between two or more bacterial genomes can help improve understanding of the causes of pathogenicity and outbreaks of disease caused by bacteria. On this course you will learn how to use the free Artemis Comparison Tool (ACT). Developed at the Wellcome Sanger Institute, ACT will help you to visualise the comparison of genomes and analyse the results. ### Who is the course for? This course would benefit those interested in learning how to use tools to investigate and research bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Learners will gain experience in comparative genomics, using the Artemis Comparison Tool to probe, visualise and compare genomes, and analyse the results. This course will be of interest to anyone interested in microbiology, including undergraduates, post-graduates, biomedical researchers, microbiologists, bioinformaticians, teachers, and healthcare professionals. The opportunity to gain experience in using the Artemis Comparison Tool, a computational tool designed for comparative genomics, will also be of interest to all those who have studied our pre-requisite courses: those with an interest in genomics and disease outbreaks, teachers and their 16-18-year-old science and computing students. Ideally, you will have completed [Bacterial Genomes: From DNA to Protein Function Using Bioinformatics] and [Bacterial Genomes: Accessing and Analysing Microbial Genome Data] before joining this course. : /our-events/bacterial-genomes-dna-protein-function-bioinformatics-online-sep19/ : /our-events/bacterial-genomes-accessing-analysing-microbial-genome-data-feb19/ # Programme ### What topics will you cover? Week 1 * Introduction to comparative genomics * Introduction to ACT Week 2 * Analyse available data * Generate your own comparison files * Make your own comparisons in ACT Week 3 * Identify pseudogenes in Mycobacterium leprae using ACT * Peer review project: Comparative genomics on two clinically relevant plasmids from Shigella ### What will you achieve? By the end of the course, you'll be able to... * Explain the advantages of comparative genomics * Explore basic tools of ACT * Interpret results from already generated comparison files * Produce new comparisons and analyse results * Develop hypothesis based on results observation ### What software or tools do you need? This course will give you an opportunity to learn about and use Artemis Comparison Tool (ACT), a free tool used to display pairwise comparisons between two DNA sequences. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of ACT requires version 11 of Java to run successfully. Java 11 can be downloaded from [this link]. Older versions of ACT require Java 8 to run successfully. Java 8 can be downloaded from [this link]. : https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html : https://www.java.com/en/download/ # Educators ## Lead Educators ### Dr Anna Protasio I am a researcher in parasitology and life sciences. 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. ### Dr. Ulrike Böhme I am a researcher in parasitology at the Wellcome Sanger Institute where I work as biocurator for Plasmodium genomes. ### Dr. 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 as part of the Infection Genomics programme. ## Programme Lead Educator ### 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. # 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 2020-11-30 09:00:00 UTC 2021-01-31 23:59:59 UTC Wellcome Genome Campus - Advanced Courses  firstname.lastname@example.org   workshops_and_courses  comparativegenomicsHDRUK
WEBINAR: Harmonised analysis of childhood cancer data across international borders
21 January 2021WEBINAR: Harmonised analysis of childhood cancer data across international borders https://www.biocommons.org.au/events/kids-cancer https://tess.elixir-europe.org/events/webinar-harmonised-analysis-of-childhood-cancer-data-across-international-borders The development of personalised treatments that target rare paediatric cancer subtypes can be enhanced through global collaboration. But geography and rules to protect personal data in different jurisdictions can make the sharing and comparing of essential data difficult or even impossible. The Australian BioCommons Zero Childhood Cancer Flagship project is a collaborative partnership between ZERO Childhood Cancer, D3b at Children’s Hospital of Philadelphia, Seven Bridges (SB), Australian Research Data Commons and the Australian BioCommons to unite and harmonise the analysis of paediatric cancer data sets from Australia (ZERO) and the US (Kids First Data Resource) using the cloud-based Cavatica analysis platform. The project allows ZERO and Kids First workflows and analysis tools to be used interchangeably and seamlessly across both datasets, effectively aggregating the separate datasets into a single virtual pan-continental dataset. This webinar will highlight the outcomes of the project and how the platform can be used to enhance human genomics studies and patient outcomes. Future plans will also be discussed. **Presenters**: Mark Cowley (Children's Cancer Institute), Jack DiGiovanna (Seven Bridges), Allison Heath (Children’s Hospital of Philadelphia) **Date/time**: 21 Jan 2021 - 11:00-12:00 AEDT / 10:00-11:00 AEST / 10:30 - 11:30 ACST / 8:00-9:00 AWST 2021-01-21 11:00:00 UTC 2021-01-21 12:00:00 UTC Australian BioCommons Australia, Australia Australia Australia    500  first_come_first_served CancergenomicsCloud computing
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