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DTSTART;TZID=Europe/Stockholm:20211115T080000
DTEND;TZID=Europe/Stockholm:20211119T170000
DTSTAMP:20260413T191753
CREATED:20210706T064513Z
LAST-MODIFIED:20210706T065837Z
UID:10000403-1636963200-1637341200@www.scilifelab.se
SUMMARY:RNA-seq data analysis ONLINE
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of  online lectures and computer practicals. The workshop will be held online. \n\n\n\nImportant dates\n\n\n\nApplication open: August 27\, 2021Application deadline: October 15\, 2021 \n\n\n\nResponsible teacher/s \n\n\n\nJohan Reimegård\, Julie Lorent \n\n\n\nContact information for questions regarding the course\n\n\n\nedu.rnaseq@nbis.se \n\n\n\nCourse fee\n\n\n\nThis online workshop has no fee. However\, if you accept a position and do not participate you will be invoiced* 1300 kr \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nTopics covered will include: \n\n\n\nRNA seq introductionRNA seq read mapping programsRNA seq QC analysisDifferential expression analysisGene set enrichment analysis\n\n\n\nMore details about the course can be found at the previous year’s webpage \n\n\n\nThe course will follow similar structure and topics.  \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\nBasic knowledge in Linux and RSteady and fast internet connection to be able to follow the workshop.Your own laptop with the following specs:At least 6 GB of RAM. Operating system Win10\, OS X or LinuxAt least 30 GB of free storage\n\n\n\nDesirable: \n\n\n\nExperience working with NGS data analysis or completed the NBIS workshop “Introduction to Bioinformatics using NGS data”Experience working in R or completed the NBIS course “R Programming Foundations for Life Scientists”\n\n\n\nDue to our best practise to have a high teacher to student ratio we have set the number of participants to a maximum of 20 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\n\n\n\n\n\nLink to application
URL:https://www.scilifelab.se/event/rna-seq-data-analysis-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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DTSTART;TZID=Europe/Stockholm:20211115T090000
DTEND;TZID=Europe/Stockholm:20211119T143000
DTSTAMP:20260413T191753
CREATED:20210909T083631Z
LAST-MODIFIED:20210909T084003Z
UID:10000443-1636966800-1637332200@www.scilifelab.se
SUMMARY:ELIXIR Tools for Reproducible Research - ONLINE
DESCRIPTION:Elixir / NBIS course 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\, Verena Kutschera \n\n\n\nContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\nApplication\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: September 1 \n\n\n\nApplication deadline: October 15 \n\n\n\nConfirmation to accepted participants: October 22 \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.*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\nIn this course you will learn how to make your data analyses reproducible. In particular\, you will learn: \n\n\n\ngood practices for data analysishow to use the version control system git to track edits and collaborate on codinghow to use the package and environment manager Condahow to use the workflow managers Snakemake and Nextflowhow to use R Markdown to generate automated reportshow to use Jupyter notebooks to document your ongoing analysishow to use Docker and Singularity to distribute containerized computational environments\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/elixir-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:20211122T080000
DTEND;TZID=Europe/Stockholm:20211126T170000
DTSTAMP:20260413T191753
CREATED:20210706T071301Z
LAST-MODIFIED:20210706T071802Z
UID:10000404-1637568000-1637946000@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data - ONLINE
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within 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:  August 16\, 2021  \n\n\n\nApplication closes: October 10\, 2021 \n\n\n\nConfirmation to accepted students:  October 15\, 2021 \n\n\n\nResponsible teachers  \n\n\n\nMalin 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. \n\n\n\nPlease note that NBIS cannot invoice individuals \n\n\n\nCourse content\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\nAfter this workshop you should be able to: \n\n\n\nDescribe the basic principles of next generation sequencing.Use the Linux command line interface to manage simple file processing operations\, and organize directory structures.Connect to and work on a remote high performance compute cluster.Apply programs in Linux for analysis of NGS data.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.Explain common NGS file formats.Interpret quality control of NGS reads.Explain the steps involved in variant calling using whole genome sequencing data.Independently perform a basic variant calling workflow on example data.Explain the steps involved in differential gene expression using RNA seq data.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\nHave relevant previous experience in sequencing or analysis.Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.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\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\n\n\n\n\n\nLink to application\n\n\n\n\nThe application opens on August 16\, 2021.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online-2/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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