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  • EMBL-EBI: Interactions & Pathways - Reactome

    3 November 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Interactions & Pathways - Reactome https://tess.elixir-europe.org/events/embl-ebi-interactions-pathways-reactome This workshop will give an introduction to the [Reactome](http://www.reactome.org) pathway database website and analysis tools, using short presentations and practical hands-on exercises. The session will also explain where to learn more, get help, and how to become involved in adding more pathway information to Reactome. Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://marstons.bio.cam.ac.uk/course-booking/?CourseID=EMBL-EBI:%20Interactions%20and%20Pathways%20-%20Reactome_bioinfo-ebireactome_3.11.2015_1392944&CourseName=EMBL-EBI:%20Interactions%20and%20Pathways%20-%20Reactome&CourseDate=3.11.2015&CourseDuration=0.5&EventID=1392944).'' 2015-11-03 09:30:00 UTC 2015-11-03 13:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] This workshop is aimed at researchers who want to learn about pathways or identify pathways relevant to a set of moleculesGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Using the Ensembl Genome Browser

    27 November 2015

    Cambridge, United Kingdom

    Elixir node event
    Using the Ensembl Genome Browser https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-b763c62e-9dff-40c2-b9bf-82369f4a1911 The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. There may be some tools and topics that do not apply to non-vertebrates; if you have any questions about this, please email the Ensembl Outreach Project Leader, [mailto:emily@ebi.ac.uk Emily Perry]. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://marstons.bio.cam.ac.uk/course-booking/?CourseID=Using%20the%20Ensembl%20Genome%20Browser_bioinfo-ensbrow_2015.11.27_1528909&CourseName=Using%20the%20Ensembl%20Genome%20Browser&CourseDate=2015.11.27&CourseDuration=1&EventID=1528909).'' 2015-11-27 09:30:00 UTC 2015-11-27 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] The workshop is primarily targeted at wetlab researchersand we customise the course for species of interest and to include total beginners to our browser up through frequent usersGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Variant Analysis with GATK

    13 - 14 June 2016

    Cambridge, United Kingdom

    Elixir node event
    Variant Analysis with GATK https://tess.elixir-europe.org/events/variant-analysis-with-gatk-3624e45d-cd74-4297-bc4c-d40298e39632 This workshop will focus on the core steps involved in calling variants with the [Broad’s Genome Analysis Toolkit](https://www.broadinstitute.org/gatk/), using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq­ specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery. The workshop is composed of one day of lectures (including many opportunities for Q&A) and one day of hands­on training. On the first day, we explain the rationale, theory and application of our Best Practices for Variant Discovery in high­-throughput sequencing data. On the second day, we walk attendees through hands­on exercises that teach how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to various use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK, dealing with problems, and using third­party tools such as Samtools, IGV and RStudio. Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non ­human data, and we will address some questions regarding adaptations that are needed for analysis of non­ human data, but we will not go into much detail on those points. The timetable can be found [here](http://bioinfotraining.bio.cam.ac.uk/postgraduate/specialized/gatk). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://marstons.bio.cam.ac.uk/course-booking/?CourseID=Variant%20Analysis%20with%20GATK%20_13-14.06.2016_1572767&CourseName=Variant%20Analysis%20with%20GATK&CourseDate=13-14.06.2016&CourseDuration=2&EventID=1572767).'' 2016-06-13 08:30:00 UTC 2016-06-14 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR RNA-Seq Genomics Exome sequencing Data visualisation Data mining ChIP-seq Bioinformatics University of Cambridge Bioinformatics Training [] The lecture­ based component of the workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATKseeking an introductory course into the toolsor who are already GATK users seeking to improve their understanding of and proficiency with the tools.The hands­on component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • EMBL-EBI: Interactions & Pathways - Reactome

    28 February 2017

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Interactions & Pathways - Reactome https://tess.elixir-europe.org/events/embl-ebi-interactions-pathways-reactome-f28ac773-8e34-44b5-ad1d-7a4b8e311f04 This workshop will give an introduction to the [Reactome](http://www.reactome.org) pathway database website and analysis tools, using short presentations and practical hands-on exercises. The session will also explain where to learn more, get help, and how to become involved in adding more pathway information to Reactome. Further information can be found [here](https://www.ebi.ac.uk/training/events/2015/interactions-pathways-reactome-1). Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1994156&course-title=EMBL-EBI:%20Interactions%20and%20Pathways%20-%20Reactome).'' 2017-02-28 09:00:00 UTC 2017-02-28 11:45:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] This workshop is aimed at researchers who want to learn about pathways or identify pathways relevant to a set of moleculesGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
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