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DTSTART;TZID=Europe/Stockholm:20220328T090000
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DTSTAMP:20260409T110001
CREATED:20211216T145021Z
LAST-MODIFIED:20220110T113421Z
UID:10000502-1648458000-1648832400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data - ONLINE
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within or affiliated to Swedish academia. This workshop is organized by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nDue to the Covid-19 situation\, this workshop will be held online. \n\n\n\nIf you have questions regarding the workshop\, please email: edu.intro-ngs@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication opens:  10 January 2022 \n\n\n\nApplication closes: 27 February 2022 \n\n\n\nConfirmation to accepted students:  Week 9\, 2022 \n\n\n\nResponsible teachers:  Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK workshop fee* \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nThis is an intense one-week beginner level workshop that introduces the analysis of next generation sequencing (NGS) 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\nAfter this workshop you should be able to: \n\n\n\n●      Use the Linux command line interface to manage simple file processing operations and organize directory structures. \n\n\n\n●      Connect to and work on a remote high performance compute cluster. \n\n\n\n●      Apply programs in Linux for analysis of NGS data. \n\n\n\n●      Describe the basic principles of NGS. \n\n\n\n●      Summarise 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\n●      Explain common NGS file formats. \n\n\n\n●      Interpret quality control of NGS reads. \n\n\n\n●      Explain the steps involved in variant calling using whole genome sequencing data. \n\n\n\n●      Independently perform a basic variant calling workflow on example data. \n\n\n\n●      Explain the steps involved in differential gene expression using RNA seq data. \n\n\n\n●      Independently perform differential gene expression analysis on example data. \n\n\n\nEntry requirements\n\n\n\nA background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to: \n\n\n\n●      Have relevant previous experience in sequencing or analysis. \n\n\n\n●      Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing. \n\n\n\n●      It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others. \n\n\n\n\n\n\n\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\nDue to the high volume of applications from Swedish institutions\, we currently do not accept international applicants. \n\n\n\n\n\n\n\n\nAPPLICATION
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online-3/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T080000
DTEND;TZID=Europe/Stockholm:20220407T170000
DTSTAMP:20260409T110001
CREATED:20211202T132557Z
LAST-MODIFIED:20211202T132705Z
UID:10000497-1649145600-1649350800@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. \n\n\n\nNote: We follow the recommendations and guidelines from Swedish authorities and Folkhälsomyndigheten. The course is designed to be an interactive face-to-face event. However\, we follow the situation carefully and will deliver the course online if needed. \n\n\n\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\nAPPLICATION\n\n\n\n\n\n\n\n\nContact: edu.intro-dm@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication is open now \n\n\n\nApplication closes: 2022-03-15 \n\n\n\nConfirmation to accepted students: 2022-03-21 \n\n\n\nCourse fee\n\n\n\n1500 SEK paid by invoice to NBIS. This includes lunches\, coffee and snacks. Please note that NBIS cannot invoice individuals. \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 several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nEntry requirements\n\n\n\nNo previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. \n\n\n\nInstallation instructions will be provided before the course starts. \n\n\n\nCourse content\n\n\n\nTopics covered will include: \n\n\n\n  • Open Science and FAIR in practice \n\n\n\n  • Organising data\, files and folders in research projects \n\n\n\n  • Versioning data\, documents and scripts with Git \n\n\n\n  • Describing data with metadata \n\n\n\n  • Cleaning tabular data and metadata with OpenRefine \n\n\n\n  • Submitting data to public data repositories \n\n\n\n  • Writing basic recipes for data analysis and visualisation with R \n\n\n\n(Links to an external site.) \n\n\n\n\n\n\n\nLearning objectives: \n\n\n\n  • To get acquainted with\, and reflect upon\, the principles of Open \n\n\n\nScience and FAIR \n\n\n\n  • To understand the importance of metadata\, and how it affects \n\n\n\n“FAIRness” \n\n\n\n  • To learn how to organise files to make project work more efficient \n\n\n\n  • To learn to clean up messy tabular data and metadata \n\n\n\n  • To learn how to find\, and submit to\, relevant public repositories for \n\n\n\ndata publication \n\n\n\n  • To learn to apply simple version control practices on files \n\n\n\n  • To learn to start using R to analyse data
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-2/
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:20220425T090000
DTEND;TZID=Europe/Stockholm:20220429T153000
DTSTAMP:20260409T110001
CREATED:20220131T095506Z
LAST-MODIFIED:20220201T080802Z
UID:10000518-1650877200-1651246200@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
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: John Sundh\, Erik Fasterius \n\n\n\nContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nAPPLICATION\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Feb 1\, 2022 \n\n\n\nApplication deadline: Mar 25\, 2022 \n\n\n\nConfirmation to accepted participants: Apr 1\, 2022 \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2\,000 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \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\nCourse content\n\n\n\nTopics covered: \n\n\n\nGood practices for data analysisVersion control and collaborative code developmentPackage and environment managementWorkflow managementDocumentation and reportingContainerized computational environments\n\n\n\n\n\n\n\nLearning outcomesBy the end of the course the student will be able to: \n\n\n\nOrganize and structure computational projectsTrack changes and collaborate on code using GitInstall packages and manage software environments using CondaStructure computational steps into workflows with Snakemake and NextflowCreate automated reports and document their analyses with RMarkdown and JupyterPackage and distribute computational environments using Docker and Singularity\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)A computer with a webcamYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseSome knowledge in R and/or python is beneficial but not strictly required\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-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220427T080000
DTEND;TZID=Europe/Stockholm:20220429T170000
DTSTAMP:20260409T110001
CREATED:20220125T121449Z
LAST-MODIFIED:20220128T090507Z
UID:10000517-1651046400-1651251600@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R - Lund
DESCRIPTION:National course open for PhD students (prioritized)\, postdocs\, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus Ringner \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\naPPLY HERE\n\n\n\n\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jan 31\, 2022 \n\n\n\nApplication deadline: Mar 18\, 2022 \n\n\n\nConfirmation to accepted participants: Mar 25\, 2022 \n\n\n\nCourse fee\n\n\n\nThis training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nThis course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. \n\n\n\nCourse content\n\n\n\nIn this course you will learn how to visualize your data in R. \n\n\n\nIn particular\, you will learn: \n\n\n\n·          how to format the data necessary for ggplot \n\n\n\n·          how to make bar-charts\, box-plots and others using ggplot \n\n\n\n·          how to make PCA plots in ggplot \n\n\n\n·          how to use R packages for heatmaps \n\n\n\n·          how to plot data on maps using R (optional) \n\n\n\n·          how to plot and handle phylogenetic trees in R (optional) \n\n\n\n·          how to make interactive plots in R using Rshiny \n\n\n\n·          how to host a Rshiny app in one of the available servers \n\n\n\nLearning outcomes\n\n\n\nBy the end of the course the participant will be able to: \n\n\n\n·          handle data in R for visualizations \n\n\n\n·          apply the grammar efficiently in ggplot to get the desired plot \n\n\n\n·          combine different data and/or different plots that are of publication-grade \n\n\n\n·          write your own simple Rshiny app \n\n\n\n·          deploy Rshiny apps in public servers.  \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\nfamiliarity with using R and Rstudioa computer with R and Rstudioyou will be asked to install different R packages necessary for the course prior to the course. \n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 25 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/workshop-on-data-visualization-in-r-lund/
LOCATION:Retina D227\, Biologihuset\, Sölvegatan 35\, Lund\, 223 62
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
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