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DTSTART;TZID=Europe/Stockholm:20231106T090000
DTEND;TZID=Europe/Stockholm:20231110T170000
DTSTAMP:20260407T223841
CREATED:20230818T135627Z
LAST-MODIFIED:20230915T130032Z
UID:10000955-1699261200-1699635600@www.scilifelab.se
SUMMARY:DDLS Population genomics in practice
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of hands-on and practical skills for the analyses of population genomics data. \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-08-17 \n\n\n\nApplication closes: 2023-09-30 \n\n\n\nConfirmation to accepted students: 2023-10-10 \n\n\n\nCourse Leader and teachers: Per Unneberg (CL)\, Nikolay Oskolkov\, Jason Hill\, André Soares \n\n\n\nIn case you miss information on any of the above dates\, please contact: edu.population-genomics-in-practice@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an introduction to commonly used methods in population genomics. As the focus of the course is on hands-on work\, the topics have been designed to cover the fundamental analyses that are common in many population genomics studies. The course consists of lectures and exercises\, with a focus on the practical aspects of analyses. Whereas lectures introduce some background theory\, their primary aim is to set the stage for accompanying exercises. \n\n\n\nTopics covered will include: \n\n\n\n\nFoundations of population genetics\n\n\n\nIntroduction to simulation and the coalescent\n\n\n\nBasics of variant calling\n\n\n\nVariant filtering and sequence masks\n\n\n\nCharacterization and interpretation of DNA sequence variation\n\n\n\nCalculation and interpretation of summary statistics from variation data\n\n\n\nInvestigating population structure with admixture modelling and principal component analyses\n\n\n\nDemographic modelling using sequentially Markovian coalescent models and linkage disequilibrium\n\n\n\nSelection scans\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ndescribe the different forces of evolution and how they influence genetic variation\n\n\n\nunderstand and interpret genealogical trees and how they relate to genetic variation data\n\n\n\ndescribe the basics of the coalescent\n\n\n\nperform simple coalescent simulations with msprime\n\n\n\nrun simple SLiM forward simulation models\n\n\n\ndescribe and run the steps of a variant calling pipeline\, including quality control of raw reads\, read mapping\, and variant calling\n\n\n\nknow how and when to filter raw variant calls using manual coverage filters\n\n\n\ndescribe and calculate nucleotide diversity from variation data\n\n\n\nanalyse population structure with admixture modelling and dimensionality reduction methods\n\n\n\nperform demographic modelling with sequential Markovian coalescent models\n\n\n\ndescribe methods that identify regions undergoing adaptation and selection\n\n\n\nrun selection scans\, score identified regions and interpret findings in the context of genome annotations\n\n\n\n\n\n\n\n\n\n\nEntry Requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge in R or Python\n\n\n\nBasic knowledge of variant calling\, or the equivalent of NBIS course “Introduction to Bioinformatics using NGS data”\n\n\n\nBasic knowledge of population genetics\n\n\n\nBasic understanding of frequentist statistics\n\n\n\nA computer\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with analysis of NGS and other omic data\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/population-genomics-in-practice/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231113T090000
DTEND;TZID=Europe/Stockholm:20231117T170000
DTSTAMP:20260407T223841
CREATED:20230607T141335Z
LAST-MODIFIED:20230607T141419Z
UID:10000906-1699866000-1700240400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within Swedish academia\, introducing the analysis of next generation sequencing data. \n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI) \n\n\n\nResponsible teachers: Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nContact information: edu.intro-ngs@nbis.se  \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jun 7\, 2023 \n\n\n\nApplication deadline: October 4\, 2023 \n\n\n\nConfirmation to accepted participants: Week 41 (October 9-12) \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 3000 SEK for academic participants\, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee.  \n\n\n\n\n\n\n\nCourse description\n\n\n\nThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.  \n\n\n\n\n\n\n\nCourse content\n\n\n\nBriefly\, the workshop covers the followings major topics: \n\n\n\n\nWorking on the UNIX/LINUX command line\n\n\n\nBioinformatic/NGS data formats and QC\n\n\n\nDNA variant calling workflow essentials\n\n\n\nRNA sequence analysis workflow essentials\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nAfter this workshop you should be able to: \n\n\n\n\nDescribe the basic principles of next generation sequencing.\n\n\n\nUse the Linux command line interface to manage simple file processing operations\, and organise directory structures.\n\n\n\nConnect to and work on a remote high performance compute cluster.\n\n\n\nApply programs in Linux for analysis of NGS data.\n\n\n\nSummarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.\n\n\n\nExplain common NGS file formats.\n\n\n\nInterpret quality control of NGS reads.\n\n\n\nExplain the steps involved in variant calling using whole genome sequencing data.\n\n\n\nIndependently perform a basic variant calling workflow on example data.\n\n\n\nDemonstrate hands-on experience with handling raw RNA sequencing data\, QC and quantification of gene expression.\n\n\n\nExplain the steps involved in differential gene expression using RNA seq data.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nTo be able to follow the workshop you need to: \n\n\n\n\nBYOL\, bring your own laptop configured according to precourse instructions.\n\n\n\nHave a background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable.\n\n\n\nTo get the maximum benefit from the workshop you should:\n\n\n\nHave a research project where you are currently using or are planning to use next generation sequencing.\n\n\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 30 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers\, and we will prioritise applications  from Swedish academia.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-3/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231120T090000
DTEND;TZID=Europe/Stockholm:20231124T160000
DTSTAMP:20260407T223841
CREATED:20230911T091422Z
LAST-MODIFIED:20230911T091932Z
UID:10000970-1700470800-1700841600@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research
DESCRIPTION:NBIS / ELIXIR-SE course is open for PhD students\, postdocs\, group leaders and core facility staff interested in making their computational analysis more reproducible. International applications are welcome\, but we will give approximately half of the participant slots to applicants from Swedish universities at minimum\, due to the national role NBIS plays in Sweden. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Erik Fasterius\, John SundhContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Sep 11\, 2023 \n\n\n\nApplication deadline: Oct 20\, 2023 \n\n\n\nConfirmation to accepted participants: Oct 27\, 2023 \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches\, coffee and snacks\, and course dinner. Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse description\n\n\n\nOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis\, e.g. bioinformatics or computational biology\, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete\, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study\, all the code and/or computational notebooks needed to produce results from the raw data\, and the computational environment or a complete description thereof. \n\n\n\nReproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly\, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! \n\n\n\n\n\n\n\nCourse content\n\n\n\nTopics covered \n\n\n\n\nGood practices for data analysis\n\n\n\nVersion control and collaborative code development\n\n\n\nPackage and environment management\n\n\n\nWorkflow management\n\n\n\nDocumentation and reporting\n\n\n\nContainerized computational environments\n\n\n\n\nLearning outcomes \n\n\n\nBy the end of the course the student will be able to: \n\n\n\n\nOrganize and structure computational projects\n\n\n\nTrack changes and collaborate on code using Git\n\n\n\nInstall packages and manage software environments using Conda\n\n\n\nStructure computational steps into workflows with Snakemake and Nextflow\n\n\n\nCreate automated reports and document their analyses with RMarkdown and Jupyter\n\n\n\nPackage and distribute computational environments using Docker and Singularity\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\n\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)\n\n\n\nSome knowledge in R and/or python is beneficial but not strictly required\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 20 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.  \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/nbis-elixir-se-tools-for-reproducible-research/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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