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  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    16 September - 30 December 2019

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-92c9e794-2186-4766-8435-3273e0756322 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 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? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated: Next start dates: * September 2019 (date TBC) ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # 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. ### 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. ### 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. ## **Educator** ### 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 Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # 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 # CPD Approval 2019-09-16 09:00:00 UTC 2019-12-30 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    4 November - 16 December 2019

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-42ab9f65-c62d-4842-ba28-08d69c662855 # Overview * **Duration**: 3 weeks, 3 hours per week * Free * Certificate of achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (9 credits), Royal College of Nursing (9 credits) * **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? The increase in resistance of harmful bacteria to antibiotics is a major global threat to health. Here we explore bacterial genomes and the use of genome sequencing to identify and track these drug resistant bacteria. Join us to discover how genome research is helping scientists and healthcare professionals track disease outbreaks and prevent the rise of antibiotic resistant ‘superbugs’. ### Who is the course for? This course will be of interest to scientists, healthcare professionals, biomedical researchers and bioinformaticians. The course offers all learners an opportunity to learn about genomes, disease, and antimicrobial resistance. You require no previous knowledge of genome science to complete the course. ### What do people say about this course? "_I would definitely point students to this resource. Text, videos, and figures were all very well done._" Pablo Tsukayama, Assistant Professor of Microbiology "_A highlight of the course was the introduction to whole genome sequencing – new information for me._" Christine Laws, Medical Doctor “_Exchanging genetic information quickly throughout the world is clearly going to revolutionise the ability to combat disease._” Prue van der Hoorn, Artist # Programme and start dates ### Course start dates This course is repeated twice a year. ### What topics will you cover? * Diseases caused by bacteria * What bacterial genomes look like * Genome sequencing technology * Mechanisms of transmission and resistance * Genomic epidemiology – tracking the spread of bacterial pathogens * Antimicrobial resistance ### What will you achieve? By the end of the course, you'll be able to... * Explain why some bacteria are pathogenic * Explore the structure of bacterial genomes * Describe the uses of different genome sequencing technologies * Investigate how genome data are used to track the spread of bacterial disease * Discuss the role of genome sequencing in stopping the spread of antimicrobial resistance # Educators ## **Lead Educators** **[Dr Adam Reid][1]** I am a senior staff scientist at the Wellcome Sanger Institute near Cambridge in the United Kingdom. I'm interested in using genomics and bioinformatics to better understand infectious diseases. **[Dr Josie Bryant][2]** I am a Henry Wellcome Postdoctoral Fellow in the University of Cambridge, Department of Medicine. I am working on bacterial genomics and evolution with a focus on within-patient microbial diversity ### Dr Francesca Short I am a scientist at the Wellcome Sanger Institute. I am interested in using functional genomics techniques to understand infections caused by the bacterium _Klebsiella pneumoniae_. ## **Programme Lead Educator** **[Professor Nicholas Thomson][3]** 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. ### The course also features interviews with distinguished scientists, including: * **[Mathew Beale][4]** - Wellcome Sanger Institute * **[Daryl Domman][5]** - Wellcome Sanger Institute * **[Gal Horesh][6]** - Wellcome Sanger Institute * **[Catherine Ludden][7]** - London School of Hygiene and Tropical Medicine * **[Tapoka Mkandawire][8]** - Wellcome Sanger Institute * **[Julian Parkhill][9]** - Wellcome Sanger Institute * **Lindsay Pike** - Wellcome Sanger Institute * **[Michael Quail][10]** - Wellcome Sanger Institute * **[Susannah J. Salter][11]** - Wellcome Sanger Institute * **[Estee Torok][12]** - Addenbrooke’s Hospital and University of Cambridge [1]: http://www.sanger.ac.uk/people/directory/reid-adam-james [2]: https://www.infectiousdisease.cam.ac.uk/directory/josie-bryant [3]: http://www.sanger.ac.uk/people/directory/thomson-nicholas-robert [4]: http://www.sanger.ac.uk/people/directory/beale-mathew [5]: http://www.sanger.ac.uk/people/directory/domman-daryl [6]: http://www.sanger.ac.uk/people/directory/horesh-gal [7]: https://www.lshtm.ac.uk/aboutus/people/ludden.catherine [8]: http://www.sanger.ac.uk/people/directory/mkandawire-tapoka-t [9]: http://www.sanger.ac.uk/people/directory/parkhill-julian [10]: http://www.sanger.ac.uk/people/directory/quail-michael-andrew [11]: http://www.sanger.ac.uk/people/directory/salter-susannah-j [12]: https://www.infectiousdisease.cam.ac.uk/directory/et317@medschl.cam.ac.uk # 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 # CDP Approval 2019-11-04 09:00:00 UTC 2019-12-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    11 November - 23 December 2019

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-003b5554-1cac-45b9-ae71-cf1656ab62a3 # 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][1] and [Bacterial Genomes: Accessing and Analysing Microbial Genome Data][2] before joining this course. [1]: /our-events/bacterial-genomes-dna-protein-function-bioinformatics-online-sep19/ [2]: /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][1]. Older versions of ACT require Java 8 to run successfully. Java 8 can be downloaded from [this link][2]. [1]: https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html [2]: 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 2019-11-11 09:00:00 UTC 2019-12-23 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • 4th European Conference on Translational Bioinformatics - ECTB2019

    11 - 12 November 2019

    Granada, Spain

    Elixir node event
    4th European Conference on Translational Bioinformatics - ECTB2019 https://tess.elixir-europe.org/events/4th-european-conference-on-translational-bioinformatics-ectb2019 We are pleased to present the 4th European Conference on Translational Bioinformatics: Biomedical Big Data Supporting Precision Medicine (#ECTB2019). The fourth ECTB edition follows the successful precedent of previous editions organized in 2016 at the University of Copenhagen, Denmark, in 2017 at the European Bioinformatics Institute, UK and in 2018 at the Barcelona Biomedical Research Park (PRBB). ECTB2019 will bring together researchers, clinicians, developers, and companies interested in exchanging experiences on the translation of research and innovative developments into healthcare tools and services based on genomics and bioinformatics applications. The conference is organised in collaboration with the University of Granada, Fundación Progreso y Salud (FPS) and the Spanish National Bioinformatics Institute (INB/ELIXIR-ES). 2019-11-11 10:15:00 UTC 2019-11-12 16:00:00 UTC University of Granada, Fundación Progreso y Salud (FPS) and the Spanish National Bioinformatics Institute (INB/ELIXIR-ES) Facultad de Medicina de la Universidad de Granada, 11, Avenida de la Investigación, Granada, Spain Facultad de Medicina de la Universidad de Granada, 11, Avenida de la Investigación Granada Spain Biomedical science Genomics Bioinformatics Translational medicine University of Granada [] ResearchersCliniciansDevelopersCompanies meetings_and_conferences [] Translational researchTranslational Bioinformaticsbiomedical applicationsBig DataPrecision MedicineGenomicsBioinformaticsClinical BioinformaticstoolsservicesHealthcareApplications
  • Advances in Computational Biology Conference 2019

    28 - 29 November 2019

    Barcelona, Spain

    Elixir node event
    Advances in Computational Biology Conference 2019 https://tess.elixir-europe.org/events/advances-in-computational-biology-conference-2019 The first **Advances in Computational Biology conference – _Fostering collaboration among women scientists_** will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing with applications to biology from both the public and private sectors. One of the main purposes of the conference is to **visualize and promote the research done by women scientists** and for this reason, all presenters will be women, although the conference is open to everyone. We want to create a space to foster collaborations between scientists, providing an excellent opportunity to share ideas and build research networks. Topics included: - **Learning from Biological Sequences**: population genomics, evolutionary genomics, systems biology, transcriptomics, sequence analysis - **When Computational Biology meets Medicine**: biomedical applications, mutational landscapes, clinical genomics - **Machines Speeding up Research**: high performance computing, machine learning in the life sciences, imaging data analysis, dynamic simulations and algorithm development Key dates: - Open registration: May 6th, 2019 - Abstract submission opens: May 6th, 2019 - **Abstract submission deadline: July 1st, 2019** - Early bird registration deadline: September 15th, 2019 - Registration deadline: November 1st, 2019 - AdvCompBio Conference: November 28th - 29th, 2019 The programme will include poster and oral presentations, as well as keynotes from leading scientists in the computational biology and high-performance computing fields. The keynote speakers of the conference are: **Christine Orengo**, group leader of Orengo Group at University College London, **Natasa Przulj**, group leader of the Life Sciences – Integrative Computational Network Biology at the Barcelona Supercomputing Center and **Marie-Christine Sawley**, director of the Exascale Lab at Intel. The confirmed chairs of the conference are: **Alison Kennedy**, director of the STFC Hartree Centre, **Janet Kelso**, group leader of the Minerva Research Group for Bioinformatics at the Max Planck Institute for Evolutionary Anthropology, and **Nuria Lopez-Bigas**, leader of the Biomedical Genomics Research Group at the Institute for Research in Biomedicine Barcelona. Furthermore, the participants will have the opportunity to interact personally with female leaders in the fields of IT, academic research and politics that support the conference. The conference is organised by the Bioinfo4Women programme from the Barcelona Supercomputing Center (BSC-CNS) with the collaboration of IMIM-UPF Research Programme on Biomedical Informatics (GRIB), the Spanish National Bioinformatics Institute (INB/ELIXIR-ES) and the Universitat Politècnica de Catalunya (UPC). It is an affiliate conference of the International Society for Computational Biology (ISCB). 2019-11-28 09:00:00 UTC 2019-11-29 17:00:00 UTC La Pedrera, 92, Passeig de Gràcia, Barcelona, Spain La Pedrera, 92, Passeig de Gràcia Barcelona Barcelona Spain Imaging Machine learning Computational biology Computer science Biomedical science Sequence analysis Transcriptomics Evolutionary biology Population genomics Omics Systems biology Bioinformatics [] [] ResearchersPhD studentsPostdoctoral studentsComputer scienceComputational biologistsbioinformaticians meetings_and_conferences [] HPCBioinformaticsComputational BiologyArtificial IntelligenceGenomicsTranscriptomicsSystems biologyPopulation GenomicsEvolutinary genomicsSequence Analysisbiomedical applicationsmutational landscapesclinical genomicsImagingdynamic simulationsalgorithmsmachine learning
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