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DTSTART;TZID=Europe/Stockholm:20250310T080000
DTEND;TZID=Europe/Stockholm:20250314T170000
DTSTAMP:20260408T083519
CREATED:20241212T094918Z
LAST-MODIFIED:20250207T090557Z
UID:10001416-1741593600-1741971600@www.scilifelab.se
SUMMARY:Workshop for Cryo-electron Tomography
DESCRIPTION:Location: UCEM facility (EM-building) and Chemical Biological Centre (KBC) building\, Umeå University\, Linnaeus väg 6\, Umeå \n\n\n\nDeadline for registration: 13 January 2025 \n\n\n\nCryo-electron tomography (cryo-ET) is a powerful structural technique. Its power comes from its versatility to study biological systems in vitro or in situ\, i.e. within cells or tissue. It has the ability to reach uncharted regions in biological systems at high resolution. Advancements in microscopes\, cameras\, and computation make it now possible to determine sub-10 Å 3-dimensional structures of molecules directly within cells. \n\n\n\nThis four-and-a-half-day workshop will cover cryo-ET workflows from sample preparation on EM grids to data processing and analysis. The workshop will be a mixture of lectures and practical sessions. Participants will get hands-on experience in sample preparation on EM grids (micropatterning)\, sample freezing (plunge freezing and high-pressure freezing)\, cryo-correlative light and electron microscopy (cryo-CLEM)\, cryo-focused ion beam milling (cryo-FIB)\, cryo-TEM tiltseries data collection\, and data processing and analysis (MotionCor2\, IMOD\, Dynamo). \n\n\n\nIt is compulsory that applicants have previous cryo-EM experience either with single-particle or already with cryo-tomography. \n\n\n\nThis workshop is supported by SciLifeLab\, CryoNET and Umeå University and organized by the Umeå Centre for Electron Microscopy (UCEM). \n\n\n\nContact email: erin.schexnaydre@umu.se
URL:https://www.scilifelab.se/event/workshop-for-cryo-electron-tomography/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2020/11/CryoEM.jpg
ORGANIZER;CN="UCEM Ume%C3%A5":MAILTO:hussein.haggag@umu.se
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DTSTART;TZID=Europe/Stockholm:20250324T080000
DTEND;TZID=Europe/Stockholm:20250328T170000
DTSTAMP:20260408T083519
CREATED:20250110T131412Z
LAST-MODIFIED:20250304T085100Z
UID:10001452-1742803200-1743181200@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\nResponsible teachers: Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nContact information: edu.intro-ngs@nbis.se   \n\n\n\nImportant dates\n\n\n\nApplication opens: 13-Jan-2025 \n\n\n\nApplication closes: 23-Feb-2025 \n\n\n\nConfirmation to accepted students: Week 9\, 2025 \n\n\n\nCourse fee\n\n\n\nThis online training event is subsidized by academic grants and thereby free of charge for academic participants. The fee for non-academic participants is 12 000 SEK.   \n\n\n\nNon-show fee: If you accept a position at the workshop but fail to attend without a valid reason (sickness or urgent family matter)\, you will be liable for a now-show fee  of 3000 SEK (for academic participants) or the full fee (for non-academic participants).  \n\n\n\nPlease note that NBIS cannot invoice individuals. \n\n\n\nApply here\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\nCourse content\n\n\n\nBriefly\, the workshop covers the followings major topics: \n\n\n\n●      Working on the UNIX/LINUX command line \n\n\n\n●      Bioinformatic/NGS data formats and QC \n\n\n\n●      DNA variant calling workflow essentials \n\n\n\n●      RNA sequence analysis workflow essentials \n\n\n\nLearning outcomes\n\n\n\nAfter this workshop you should be able to: \n\n\n\n●      Describe the basic principles of next generation sequencing. \n\n\n\n●      Use the Linux command line interface to manage simple file processing operations\, and organise 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●      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●      Demonstrate hands-on experience with handling raw RNA sequencing data\, QC and quantification of gene expression. \n\n\n\n●      Explain the steps involved in differential gene expression using RNA seq data. \n\n\n\nEntry requirements\n\n\n\nTo be able to follow the workshop you need to: \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\nSelection criteria\n\n\n\nIf we receive more applications than we have seats in the course\, 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-5/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
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DTSTART;TZID=Europe/Stockholm:20250331T080000
DTEND;TZID=Europe/Stockholm:20250403T170000
DTSTAMP:20260408T083519
CREATED:20241218T133816Z
LAST-MODIFIED:20250224T141503Z
UID:10001419-1743408000-1743699600@www.scilifelab.se
SUMMARY:Single-Cell RNA-Seq Data Analysis
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of single cell RNAseq analysis skills. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\nCourse dates: 31 March 2025 – 3 April 2025 and 10 April 2025 \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-12-18 \n\n\n\nApplication closes: 2025-02-28 \n\n\n\nConfirmation to accepted students: 2025-03-07 \n\n\n\nCourse Leader and teachers: Åsa Björklund (CL)\, Susanne Reinsbach (CL)\, Jennifer Fransson (CL) \n\n\n\nIn case you miss information on any of the above dates\, please contact: edu.sc [at] nbis.se \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee for academic participants. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 3000 SEK. For non-academic participants a course fee* of 12000 SEK  will be invoiced. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nRegister here\n\n\n\nCourse content\n\n\n\nThis workshop will introduce the best practice bioinformatics methods for analysing single cell RNA-seq data via a series of lectures and computer practicals. The total course duration is 5 days which includes 4 days of lectures and exercises followed by a “Bring Your Own Data” (BYOD) day where you get to practice your skills on a dataset of your choosing. Please note that the BYOD section will take place the week after the lectures. \n\n\n\nTopics covered will include: \n\n\n\n\nOverview of the current scRNAseq technologies\n\n\n\nBasic overview of pipelines for processing raw reads into expression values\n\n\n\nQuality control and normalization\n\n\n\nDimensionality reduction techniques\n\n\n\nData integration and batch correction\n\n\n\nDifferential gene expression\n\n\n\nClustering techniques\n\n\n\nCell type prediction\n\n\n\nTrajectory inference analysis\n\n\n\nComparison of Seurat\, Bioconductor and Scanpy toolkits\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to run analysis on your own data\, select appropriate analysis methods and interpret the results. \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\nYou are familiar with basic UNIX command line (bash)\n\n\n\nYou are familiar with either R and/or Python\n\n\n\nYou already understand the basics of NGS technologies\n\n\n\nYou are familiar with analyses of bulk RNA-sequencing data\n\n\n\nYou have full access to your computer (admin permissions). Instructions on installation will be sent by email to accepted participants.\n\n\n\n\nThe course accommodates 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. \n\n\n\nContact\n\n\n\neducation@nbis.se
URL:https://www.scilifelab.se/event/single-cell-rna-seq-data-analysis-2/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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