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  • An Introduction to Solving Biological Problems with Python

    14 - 15 September 2015

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with Python https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-python-8def1e99-6a9b-4222-bf6a-9b880b0c5bf7 This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. The course website providing links to the course materials is [here](http://pycam.github.io). 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=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python_bioinfo-python_14-15.09.2015_1530918&CourseName=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python&CourseDate=14-15.09.2015&CourseDuration=2&EventID=1530918).'' 2015-09-14 08:30:00 UTC 2015-09-15 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • An Introduction to Solving Biological Problems with R

    17 - 18 September 2015

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with R https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-r-f6753f46-d38b-4ca7-b5ec-0a5096758884 This course provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented. The course website providing links to the course materials is [here](http://cambiotraining.github.io/r-intro/). 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=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R_bioinfo-rintro_17-18.09.2015_1539928&CourseName=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R&CourseDate=17-18.09.2015&CourseDuration=2&EventID=1539928).'' 2015-09-17 08:30:00 UTC 2015-09-18 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • An Introduction to MATLAB for biologists

    21 - 22 September 2015

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to MATLAB for biologists https://tess.elixir-europe.org/events/an-introduction-to-matlab-for-biologists-7f896236-bcd6-4d99-a37a-9fd806400875 This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. 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=An%20Introduction%20to%20MATLAB_bioinfo-MATLAB_21-22.09.2015_1538915&CourseName=An%20Introduction%20to%20MATLAB&CourseDate=21-22.09.2015&CourseDuration=2&EventID=1538915).'' 2015-09-21 08:30:00 UTC 2015-09-22 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • An Introduction to Solving Biological Problems with PERL

    23 - 24 September 2015

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with PERL https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-perl-05688fa0-4e4a-45eb-9e34-4cae88d372b9 This course is aimed at those new to programming and provides an introduction to programming using Perl. During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures. The course will be taught using the online [Learning Perl](http://sofiarobb.com/learning-perl-toc/) materials created by [Sofia Robb](http://stajich.bioinformatics.ucr.edu/members/sofia-robb) of the [University of California Riverside](http://www.ucr.edu/). The course website providing links to the course materials is [here](http://bit.ly/cambridgeperl). 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=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20PERL_bioinfo-perlintro_23-24.09.2015_1487628&CourseName=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20PERL&CourseDate=23-24.09.2015&CourseDuration=2&EventID=1487628).'' 2015-09-23 08:30:00 UTC 2015-09-24 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Statistical Analysis using R

    25 September 2015

    Cambridge, United Kingdom

    Elixir node event
    Statistical Analysis using R https://tess.elixir-europe.org/events/statistical-analysis-using-r-1150fce7-58b6-42f7-9780-d5a9fccd67aa Statistics are an important part of most modern studies and being able to effectively use a statistical package will help you to understand your results. This course provides an introduction to some statistical techniques through the use of the R language. Topics covered include: Chi2 and Fisher tests, descriptive statistics, t-test, analysis of variance and regression. Students will run analyses using statistical and graphical skills taught during the session. The course manual can be found [here](http://www.bioinformatics.babraham.ac.uk/training/R_statistics_course_manual.pdf). 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=Statistical%20analysis%20using%20R_bioinfo-statsR_25.09.2015_1503968&CourseName=Statistical%20analysis%20using%20R&CourseDate=25.09.2015&CourseDuration=1&EventID=1503968).'' 2015-09-25 08:30:00 UTC 2015-09-25 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Evidence-Based Teaching: What We Know and How to Use It

    30 September 2015

    Cambridge, United Kingdom

    Elixir node event
    Evidence-Based Teaching: What We Know and How to Use It https://tess.elixir-europe.org/events/evidence-based-teaching-what-we-know-and-how-to-use-it-6bb6528b-2668-4330-8940-31cdd6d13919 What are the cognitive differences between novices, competent practitioners, and experts? Do different people really have different learning styles? Do flipped classrooms actually work better than regular lectures? This tutorial will explore recent research in these areas and more, and show participants how to apply that research in the classroom to improve teaching. This tutorial is a condensed version of the instructor training program that Software Carpentry has been running for the past three years. In it, we will explore a handful of research results in educational psychology, and see how to use those findings to build more effective lessons. Greg Wilson is the Executive Director of the [Software Carpentry Foundation](http://www.software-carpentry.org/scf/index.html), a volunteer non-profit organization that teaches researchers basic lab skills for scientific computing. 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=Evidence-%20Based%20Teaching:%20What%20We%20Know%20and%20How%20to%20Use%20It%20_bioinfo-teach_30.09.2015_1561050&CourseName=Evidence-%20Based%20Teaching:%20What%20We%20Know%20and%20How%20to%20Use%20It%20&CourseDate=30.09.2015&CourseDuration=0.5&EventID=1561050).'' 2015-09-30 12:00:00 UTC 2015-09-30 15:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Introduction to Galaxy: Data Manipulation and Visualisation

    21 October 2015

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Galaxy: Data Manipulation and Visualisation https://tess.elixir-europe.org/events/introduction-to-galaxy-data-manipulation-and-visualisation-ac87f263-0323-4f73-adcc-f08c5e9a2ccb [Galaxy](http://galaxyproject.org/) is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses. This introductory course will cover Galaxy's basic functionality, simple data manipulation and visualization. This event is mostly targeted at first time users. Further information is available from the course [ website](http://galaxycam.github.io/). 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=Introduction%20to%20Galaxy%20:%20Data%20Manipulation%20and%20Visualisation_bioinfo-galaxy01_1544762_21.10.2015&CourseName=Introduction%20to%20Galaxy%20:%20Data%20Manipulation%20and%20Visualisation&CourseDate=21.10.2015&CourseDuration=1&EventID=1544762).'' 2015-10-21 08:30:00 UTC 2015-10-21 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: Introduction to EMBL-EBI resources

    26 October 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Introduction to EMBL-EBI resources https://tess.elixir-europe.org/events/embl-ebi-introduction-to-embl-ebi-resources-9a2f3b4c-f159-4cfa-b989-c271bb07d017 This workshop is an introduction to [EMBL-EBI](http://www.ebi.ac.uk/) and the life science data resources it provides. Participants will be shown how to navigate the website and search for appropriate database resources and tools, whilst also highlighting resources such as [Train online](http://www.ebi.ac.uk/training/online/) (our e-learning portal) and the literature resources at [Europe PMC](https://europepmc.org/). The timetable for this event can be found [here](http://www.ebi.ac.uk/training/workshop/embl-ebi-introduction-embl-ebi-resources). This workshop will not focus on a set of specific resources; for more focused workshops please see the others within this series (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:%20Introduction%20to%20EMBL-EBI%20resources_bioinfo-ebi_26.10.2015_1531245&CourseName=EMBL-EBI:%20Introduction%20to%20EMBL-EBI%20resources&CourseDate=26.10.2015&CourseDuration=0.5&EventID=1531245).'' 2015-10-26 09:30:00 UTC 2015-10-26 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 [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Mouse Genome Informatics workshop

    27 October 2015

    Cambridge, United Kingdom

    Elixir node event
    Mouse Genome Informatics workshop https://tess.elixir-europe.org/events/mouse-genome-informatics-workshop-579098c1-61f1-486d-9df2-c1cec673442e [Mouse Genome Informatics (MGI)](http://www.informatics.jax.org) is the international database resource for the laboratory mouse and provides integrated genetic, genomic, and biological data to facilitate the study of human health and disease. MGI is a free, highly curated resource and offers web and programmatic access to a complete catalogue of mouse genes and genome features, functional annotations, a comprehensive catalogue of mutant and knockout alleles, phenotype and human disease model annotations, gene expression, variation and sequence data. This workshop will be composed of ~20min overview and ~1 hour hands-on, interactive tutorial. 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=Mouse%20Genome%20Informatics%20workshop_bioinfo-mgi_27.10.2015_1541354&CourseName=Mouse%20Genome%20Informatics%20workshop&CourseDate=27.10.2015&CourseDuration=0.5&EventID=1541354).'' 2015-10-27 10:00:00 UTC 2015-10-27 12:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] other model organisms studies human diseases or developmental biology Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: Exploring Protein Sequence and Functional Information with UniProt

    28 October 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Exploring Protein Sequence and Functional Information with UniProt https://tess.elixir-europe.org/events/embl-ebi-exploring-protein-sequence-and-functional-information-with-uniprot-79a69522-e7bc-4fa7-bb33-4177e45d39ba This workshop will give an introduction to the resources provided by [UniProt](http://www.uniprot.org/). Participants will be shown, and given hands-on experience in, how to navigate the website, search for data and run analysis tools. The session also covers what the sources of our data are and how they are curated. A basic introduction into accessing UniProt Knowledgebase programmatically will be given as well. The timetable for this event can be found [here](http://www.ebi.ac.uk/training/workshop/exploring-protein-sequence-and-functional-information-uniprot-0). 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=Exploring%20Protein%20Sequence%20and%20Functional%20Information%20with%20UniProt_bioinfo-uniprot_28.10.2015_1393059&CourseName=Exploring%20Protein%20Sequence%20and%20Functional%20Information%20with%20UniProt&CourseDate=28.10.2015&CourseDuration=1&EventID=1393059).'' 2015-10-28 13:30:00 UTC 2015-10-28 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 [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: Interactions & Pathways - IntAct

    30 October 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Interactions & Pathways - IntAct https://tess.elixir-europe.org/events/embl-ebi-interactions-pathways-intact-8c2813f8-9562-4c57-a89f-ece15d65dd28 This workshop will give an introduction to the protein interaction database [IntAct](http://www.ebi.ac.uk/intact) and the Complex Portal service. You will also briefly learn how to visualise protein interactions using the Cytoscape application. The timetable for this event can be found [here](http://www.ebi.ac.uk/training/events/2015/interactions-pathways-intact). 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%20:%20Interactions%20and%20Pathways%20-%20IntAct_bioinfo-ebiintact_30.10.2015_1392930&CourseName=EMBL-EBI%20:%20Interactions%20and%20Pathways%20-%20IntAct&CourseDate=30.10.2015&CourseDuration=0.5&EventID=1392930).'' 2015-10-30 09:30:00 UTC 2015-10-30 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 [] protein-DNA and protein-small molecular interactions. Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • 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-212b5023-8662-45d9-83ba-8cd966e010cc 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 [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: An Introduction to Sequence Searching

    3 November 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: An Introduction to Sequence Searching https://tess.elixir-europe.org/events/embl-ebi-an-introduction-to-sequence-searching-ab223602-e076-4d7a-8498-ca0003a86ecd This workshop introduces the area of sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases. This session will include tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages. 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 or register Interest by linking [here](http://marstons.bio.cam.ac.uk/course-booking/?CourseID=bioinfo-ebiseqsearch_EMBL-EBI%20:%20An%20Introduction%20to%20Sequence%20Searching_03.11.2015_1392893&CourseName=Bioinformatics:%20EMBL-EBI%20:%20An%20Introduction%20to%20Sequence%20Searching&CourseDate=03.11.2015&CourseDuration=1&EventID=1392893).'' 2015-11-03 14:00:00 UTC 2015-11-03 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: Introduction to ontologies

    4 November 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Introduction to ontologies https://tess.elixir-europe.org/events/embl-ebi-introduction-to-ontologies-e489d398-b01f-4427-8bd3-7cf71af5ab18 This workshop will give an introduction to the basic concepts of ontologies and how they are useful in biological applications. After a brief overview of some existing resources, we will focus on the Gene Ontology, annotations made using the Gene Ontology and tools leveraging those for biomedical discovery. 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=bioinfo-onto_EMBL-EBI:%20Introduction%20to%20ontologies_4.11.2015_1555216&CourseName=EMBL-EBI:%20Introduction%20to%20ontologies&CourseDate=4.11.2015&CourseDuration=1&EventID=1555216).'' 2015-11-04 09:30:00 UTC 2015-11-04 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 [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC

    18 November 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC https://tess.elixir-europe.org/events/embl-ebi-network-analysis-with-cytoscape-and-psicquic-7ff314c2-1fea-4b62-9321-3265a50eabea This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks. The timetable for this event can be found [here](http://www.ebi.ac.uk/training/workshop/network-analysis-cytoscape-and-psicquic). 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=Network%20Analysis%20with%20Cytoscape%20and%20PSICQUIC_bioinfo-ebinetworks_18.11.2015_1538946&CourseName=Network%20Analysis%20with%20Cytoscape%20and%20PSICQUIC&CourseDate=18.11.2015&CourseDuration=1&EventID=1538946).'' 2015-11-18 09:30:00 UTC 2015-11-18 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 [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Biological data analysis using InterMine

    26 November 2015

    Cambridge, United Kingdom

    Elixir node event
    Biological data analysis using InterMine https://tess.elixir-europe.org/events/biological-data-analysis-using-intermine-04ca2b51-ce2f-42ec-922a-e97c5496f55f [InterMine](http://intermine.org/) is a freely available data warehouse and analysis software system that has been used to create a suite of databases for the analysis of large and complex biological data sets. InterMine-based data analysis platforms are available for many organisms including [mouse](http://www.mousemine.org/mousemine/begin.do), [rat](http://ratmine.mcw.edu/ratmine/begin.do), [budding yeast](http://yeastmine.yeastgenome.org/yeastmine/begin.do), [plants](https://apps.araport.org/thalemine/begin.do), [nematodes](http://www.wormbase.org/tools/wormmine/begin.do), [fly](http://www.flymine.org/), [zebrafish](http://www.zebrafishmine.org/) and more recently [human](http://www.humanmine.org/). The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. We have recently re-designed the InterMine interface to provide a more intuitive user-experience. This workshop will provide an overview of key features of the new interface and how this can be used to interrogate genomic and proteomic data. 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=Biological%20data%20analysis%20using%20InterMine_bioinfo-intermine_26.11.2015_1539952&CourseName=Biological%20data%20analysis%20using%20InterMine&CourseDate=26.11.2015&CourseDuration=0.5&EventID=1539952).'' 2015-11-26 09:30:00 UTC 2015-11-26 12:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] or who need to search against several biological datasets to gain knowledge of a gene/gene set biological process or function. The course may also be of interest to bioinformaticians who wish to familiarise themselves with the InterMine suite of databases although the webservices will not be covered in detail. Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Analysis of high-throughput sequencing data with Bioconductor

    30 November - 2 December 2015

    Cambridge, United Kingdom

    Elixir node event
    Analysis of high-throughput sequencing data with Bioconductor https://tess.elixir-europe.org/events/analysis-of-high-throughput-sequencing-data-with-bioconductor-febb90db-ed89-4495-a02f-4be0a2f9d323 This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment. The course timetable is available [here](https://drive.google.com/file/d/0B5BzNXp93Gp5b1VHYS1ZQUl5RmM/view?usp=sharing). 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=Analysis%20of%20High-throughput%20sequencing%20data%20with%20Bioconductor_bioinfo-ngsbioc_30.11-02.12.2015_1528113&CourseName=Analysis%20of%20High-throughput%20sequencing%20data%20with%20Bioconductor&CourseDate=30.11-02.12.2015&CourseDuration=3&EventID=1528113).'' 2015-11-30 09:30:00 UTC 2015-12-02 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Bioinformatics resources for exploring disease related data

    3 December 2015

    Cambridge, United Kingdom

    Elixir node event
    Bioinformatics resources for exploring disease related data https://tess.elixir-europe.org/events/bioinformatics-resources-for-exploring-disease-related-data-f37e2957-c1c5-49e4-a2cc-7500c8881010 This workshop will introduce students to EMBL-EBI, the databases and services it offers, and basic concepts in bioinformatics that will be of use to their disease related research work. It will explain the role of the EBI in curating and sharing biological data with scientists around the world and introduce basics for locating relevant data and information of interest. Sessions with trainers from [Ensembl](http://www.ensembl.org/), [ArrayExpress](https://www.ebi.ac.uk/arrayexpress/) and the [GWAS catalog](https://www.ebi.ac.uk/gwas/) will introduce practical skills in browsing genes and variation in a genomic context, in exploring SNP-trait associations and will show how further understanding can be gained on the location and level of gene expression across the body. 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=Bioinformatics%20resources%20for%20exploring%20disease%20related%20data_bioinfo-resdisease_3.12.2015_1650733&CourseName=Bioinformatics%20resources%20for%20exploring%20disease%20related%20data&CourseDate=3.12.2015&CourseDuration=1&EventID=1650733).'' 2015-12-03 09:30:00 UTC 2015-12-03 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Introduction to Scientific Figure Design

    4 December 2015

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Scientific Figure Design https://tess.elixir-europe.org/events/introduction-to-scientific-figure-design-eca409dd-6c99-47a4-a000-579315bd9d95 This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Further information and access to the course materials is [here](http://www.bioinformatics.babraham.ac.uk/training.html#figuredesign). 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=Introduction%20to%20Scientific%20Figure%20Design_bioinfo-figdes_4.12.2015_1503983&CourseName=Introduction%20to%20Scientific%20Figure%20Design&CourseDate=4.12.2015&CourseDuration=1&EventID=1503983).'' 2015-12-04 09:30:00 UTC 2015-12-04 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Introduction to Scientific Figure Design - Webcast Event

    4 December 2015

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Scientific Figure Design - Webcast Event https://tess.elixir-europe.org/events/introduction-to-scientific-figure-design-webcast-event-bce8e5b2-5054-4785-a50d-50fa2dd71a48 This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Further information and access to the course materials is [here](http://www.bioinformatics.babraham.ac.uk/training.html#figuredesign). 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=Introduction%20to%20Scientific%20Figure%20Design%20-%20webcast%20event_bioinfo-figdeswe_4.12.2015_1634028&CourseName=Introduction%20to%20Scientific%20Figure%20Design-%20webcast%20event&CourseDate=4.12.2015&CourseDuration=1&EventID=1634028).'' 2015-12-04 09:30:00 UTC 2015-12-04 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Image Analysis for Biologists

    7 - 9 December 2015

    Cambridge, United Kingdom

    Elixir node event
    Image Analysis for Biologists https://tess.elixir-europe.org/events/image-analysis-for-biologists-430a40a2-f58b-402a-8b11-a84221bc28f2 This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines. On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package. On day 2, we will focus on machine learning and computer vision for the analysis of images in cell biology. We will introduce the methodology in a series of lectures and show their application in the hands-on session. These practical sessions will be based on [CellCognition](http://www.cellcognition.org/), a tool for the analysis of live cell imaging data. On day 3, we will describe the open [Icy platform](http://icy.bioimageanalysis.org/) developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager). The timetable can be found [here](https://drive.google.com/file/d/0B5BzNXp93Gp5MnBPU0RKOV9TOEU/view?usp=sharing). This event is sponsored by the [Systems Microscopy NoE](http://www.systemsmicroscopy.eu/). 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=Image%20Analysis%20for%20Biologists%20_7-9.12.2015_1544771&CourseName=Image%20Analysis%20for%20Biologists&CourseDate=7-9.12.2015&CourseDuration=3&EventID=1544771).'' 2015-12-07 09:30:00 UTC 2015-12-09 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Introduction to RNA-seq and ChIP-seq data analysis

    10 - 11 December 2015

    Cambridge, United Kingdom

    Elixir node event
    Introduction to RNA-seq and ChIP-seq data analysis https://tess.elixir-europe.org/events/introduction-to-rna-seq-and-chip-seq-data-analysis-dc8a0018-b45f-42a6-9e25-57dee3b9155f The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughout sequencing (HTS) assays: ChIP-seq and RNA-seq. This course starts with a brief introduction to the transition from capillary to high-throughput sequencing (HTS) and discusses quality control issues, which are common among all HTS datasets. Next, we will present the alignment step and how it differs between the two analysis workflows. Finally, we focus on dataset specific downstream analysis, including peak calling and motif analysis for ChIP-seq and quantification of expression, transcriptome assembly and differential expression analysis for RNA-seq. The timetable for this event can be found [here.](https://drive.google.com/file/d/0B5BzNXp93Gp5LS1ILUNXZzRMa2c/view?usp=sharing) 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=Introduction%20to%20RNA-seq%20and%20ChIP-seq%20data%20analysis_bioinfo-RNA-seq_10-11.12.2015_1544785&CourseName=Introduction%20to%20RNA-seq%20and%20ChIP-seq%20data%20analysis&CourseDate=10-11.12.2015&CourseDuration=2&EventID=1544785).'' 2015-12-10 09:30:00 UTC 2015-12-11 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • EMBL-EBI: Transcriptomics Data and Tools

    15 December 2015

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI: Transcriptomics Data and Tools https://tess.elixir-europe.org/events/embl-ebi-transcriptomics-data-and-tools-49fac7ad-ce6a-430a-a6d9-46dc6f364dc9 This workshop will give an introduction to the functional genomics resources provided by EMBL-EBI and hands-on practical experience of searching and accessing appropriate data and information. The session will also cover data submission to [ArrayExpress](https://www.ebi.ac.uk/arrayexpress/) using Annotare. 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=bioinfo-ebitrans_EMBL-EBI:-%20Transcriptomics%20Data%20and%20Tools_15.12.2015_1393017&CourseName=EMBL-EBI:%20Transcriptomics%20Data%20and%20Tools&CourseDate=15.12.2015&CourseDuration=1&EventID=1393017).'' 2015-12-15 09:30:00 UTC 2015-12-15 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 [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • An Introduction to Solving Biological Problems with R

    16 - 17 December 2015

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with R https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-r-9cd068f6-285b-4412-b969-b5682d04b0c7 This course provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented. The course website providing links to the course materials is [here](http://cambiotraining.github.io/r-intro/). 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=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R_bioinfo-rintro_16-17.12.2015_1568450&CourseName=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R&CourseDate=16-17.12.2015&CourseDuration=2&EventID=1568450).'' 2015-12-16 09:30:00 UTC 2015-12-17 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Postdocs and Staff members from the University of Cambridge Institutions and other external Institutions or individuals workshops_and_courses [] []
  • Basic statistics and data handling

    7 - 9 December 2016

    Cambridge, United Kingdom

    Elixir node event
    Basic statistics and data handling https://tess.elixir-europe.org/events/basic-statistics-and-data-handling This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lecture, workshop and hands-on practice – and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics – so that they can begin to see how they can be applied to their own work, and to also help with better critical evaluation of the work of others. Covering: Basic statistics concepts and practice: power, variability, false discovery, t-test, effect size, simulations to understand what a p-value means. On day 3 will use some practical statistics examples in R to introduce concepts in data presentation for publication. Covering: Some practical examples of statistics in R. Visualising and publishing your data. Course materials are available [here](https://bioinformatics-core-shared-training.github.io/winter-school2016/). This event is sponsored by [CRUK](http://www.cancerresearchuk.org/). 2016-12-07 09:30:00 UTC 2016-12-09 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Basic statistics and data handling

    3 - 5 April 2017

    Cambridge, United Kingdom

    Elixir node event
    Basic statistics and data handling https://tess.elixir-europe.org/events/basic-statistics-and-data-handling-eefdec71-300e-43f3-ae60-9d17eab0f745 This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals – and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics – so that they can begin to see how they can be applied to their own work, and to also help with better critical evaluation of the work of others. Covering: Basic statistics concepts and practice: power, variability, false discovery, t-test, effect size, simulations to understand what a p-value means. On day 3 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction. Course materials are available [here](https://github.com/cambiotraining/stats-intro). This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). Please note that all participants attending this course will be charged a registration fee of £150. 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=2034285&course-title=Basic%20statistics%20and%20data%20handling).'' 2017-04-03 08:30:00 UTC 2017-04-05 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals 42 workshops_and_courses first_come_first_served HDRUK
  • Basic statistics and data handling

    30 August - 1 September 2017

    Cambridge, United Kingdom

    Elixir node event
    Basic statistics and data handling https://tess.elixir-europe.org/events/basic-statistics-and-data-handling-fda886f9-cdd0-4250-a213-f6ac55f8ff59 This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals – and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics – so that they can begin to see how they can be applied to their own work, and to also help with better critical evaluation of the work of others. Covering: Basic statistics concepts and practice: power, variability, false discovery, t-test, effect size, simulations to understand what a p-value means. On day 3 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction. Course materials are available [here](https://github.com/cambiotraining/stats-intro). This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). 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=2156934&course-title=Basic%20statistics%20and%20data%20handling).'' 2017-08-30 08:30:00 UTC 2017-09-01 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Basic statistics and data handling

    28 February - 2 March 2018

    Cambridge, United Kingdom

    Elixir node event
    Basic statistics and data handling https://tess.elixir-europe.org/events/basic-statistics-and-data-handling-1f3b186f-2e06-42c1-b334-c99034f541b8 This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals – and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics – so that they can begin to see how they can be applied to their own work, and to also help with better critical evaluation of the work of others. Covering: Basic statistics concepts and practice: power, variability, false discovery, t-test, effect size, simulations to understand what a p-value means. On day 3 we will continue to explore core concepts of statistics, focusing on linear regression and multiple testing correction. Course materials are available [here](https://github.com/cambiotraining/stats-intro). This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). 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=2235484&course-title=Basic%20statistics%20and%20data%20handling).'' 2018-02-28 09:30:00 UTC 2018-03-02 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Variant Discovery with GATK4

    16 - 19 July 2018

    Cambridge, United Kingdom

    Elixir node event
    Variant Discovery with GATK4 https://tess.elixir-europe.org/events/variant-analysis-with-gatk-1c39207f-184f-4cb6-a01e-2e4ee6aa4ee3 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 germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises. *Day 1: Introduction to Genomics, GATK Best Practices and Pipelining *Day 2: Germline short variant discovery (SNPs + Indels) *Day 3: Somatic variant discovery (SNVs + Indels + CNVs) *Day 4: Writing pipelines with WDL and running them in FireCloud 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. 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://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2483603&course-title=Variant%20Discovery%20with%20GATK4).'' 2018-07-16 08:30:00 UTC 2018-07-19 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Genomics Data visualisation Data mining Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Variant Discovery with GATK4

    8 - 11 July 2019

    Cambridge, United Kingdom

    Elixir node event
    Variant Discovery with GATK4 https://tess.elixir-europe.org/events/variant-discovery-with-gatk4 This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the [Broad’s Genome Analysis Toolkit (GATK)](https://www.broadinstitute.org/gatk/), using “Best Practices” developed by the GATK methods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are 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. If you are an experienced GATK user, you will gain a deeper understanding of how the GATK works under-the-hood and how to improve your results further, especially with respect to the latest innovations. *Day 1: Introductory and Overview. The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey. *Day 2: Germline Short Variant Discovery. Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself. *Day 3: Somatic Variant Discovery. Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity. *Day 4: Pipelining. Over the first three days, you would have learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery. 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 hands-on GATK tutorials in this workshop will be conducted on [Terra](https://terra.bio/), a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2858057&course-title=Variant%20Discovery%20with%20GATK4).'' 2019-07-08 08:30:00 UTC 2019-07-11 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Genomics Data visualisation Data mining Bioinformatics University of Cambridge Bioinformatics Training [] The course is aimed primarily at mid-career scientists – especially those whose formal education likely included statisticsbut who have not perhaps put this into practice since.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
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