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DTSTART;TZID=Europe/Stockholm:20250513T080000
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DTSTAMP:20260416T014421
CREATED:20250122T135937Z
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UID:10001459-1747123200-1747328400@www.scilifelab.se
SUMMARY:Advanced Data Visualization
DESCRIPTION:National course is open for PhD students\, postdocs\, group leaders\, core facility staff and other employees in all Swedish universities who are interested in learning to produce high quality figures for publication and presentation purposes. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\nImportant dates and information\n\n\n\nApplication opens: January 28\, 2025 \n\n\n\nApplication closes: March 31\, 2025 \n\n\n\nConfirmation to accepted students: April 11\, 2025 \n\n\n\nFormat: This workshop runs on-site in Lund. Teaching assistants and instructors will be available throughout the course to help you with exercises and questions. \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Markus Ringnér\, Louella Vasquez\, Katja Kozjek \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\nCourse fee\n\n\n\nThe fee for this on-site training is: \n\n\n\n\n2000 SEK for participants from academic institutions\n\n\n\n9500 SEK for participants from non-academic organisations\n\n\n\n\nThe fee includes lunches\, coffee breaks\, snacks\, and a course dinner. \n\n\n\nIf you accept a spot in the course but do not attend (no-show)\, the full fee will still be charged. *Please note that NBIS cannot invoice individuals directly. \n\n\n\nCourse content\n\n\n\nPeople with all expertise-levels in R and plotting are encouraged to apply. The course materials can be organized to match your level and the TAs would be happy to help you to attain your needs. \n\n\n\nThis course is designed to help researchers in visualizing their data through various techniques using R and Quarto. Participants will learn how to create publication-ready visualisations with R. Additionally\, the course also includes introductions to Quarto and dynamic plotting using tools like plotly\, OJS\, etc. The last day of the course includes interactive plotting that can be hosted on a web server\, enabling researchers to share and explore visualizations of their data. \n\n\n\nTopics covered will include: \n\n\n\n\nUsing the language of graphics: ggplot2\n\n\n\nBasic and advanced plotting in ggplot2\n\n\n\nSingle-cell data visualizations with Seurat\n\n\n\nQuarto notebooks and reports\n\n\n\nDynamic plotting with Quarto\n\n\n\nInteractive web apps with Shiny\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nHandle data in R for visualizations\n\n\n\nFamiliarize with ggplot2 functions and techniques\n\n\n\nCombine different data and/or different plots that are of publication-ready\n\n\n\nCreate interactive documents with Quarto for data exploration and analysis\n\n\n\nWrite your own simple Shiny app in R\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\nFamiliarity with R and R Studio\n\n\n\nPlotting using standard R graphics\n\n\n\nParticipants are expected to use their own computers with pre-installed R\, R Studio and different R packages (detailed instructions will be given upon acceptance).\n\n\n\n\nThe course can accommodate a maximum of 20 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\nAdditional information\n\n\n\nFor more details\, visit the webpage:\n\n\n\nFor beginner level \n\n\n\nFor advanced level (The content of this page is regularly updated until the course)
URL:https://www.scilifelab.se/event/advanced-data-visualization/
LOCATION:Medicon Village\, Scheelevägen 2\, Lund\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20250609T080000
DTEND;TZID=Europe/Stockholm:20250619T170000
DTSTAMP:20260416T014421
CREATED:20250121T125239Z
LAST-MODIFIED:20250121T125322Z
UID:10001457-1749456000-1750352400@www.scilifelab.se
SUMMARY:Raukr 2025 - Summer School - R beyond the basics
DESCRIPTION:Course description\n\n\n\nJoin us this June in the beautiful and historic town of Visby and sharpen your R skills with like-minded enthusiasts! As the use of R continues to flourish within the realms of Life Science and Bioinformatics – revolutionizing data transformation\, statistical analysis\, and the creation of visuals ready for publication – we are thrilled to offer a workshop dedicated to elevating your expertise with R. \n\n\n\nWe are excited to announce our invited guest instructors for this year: Jennifer Bryan (Posit)\, Christophe Dervieux (Posit) and Henrik Bengtsson (UCSF). \n\n\n\nPlease consider joining us for this enriching experience. For more details and to apply\, visit our homepage. We’d also greatly appreciate you sharing this opportunity with others who might be interested. \n\n\n\nCourse content\n\n\n\nWe will be covering a number of topics in R programming with focus on R features helpful in bioinformatics and computational biology data analyses workflow: \n\n\n\n\nReproducible research in R (Quarto\, Rmarkdown\, Renv)\n\n\n\nCollaborative work using Git and GitHub\n\n\n\nR code style guide & best practices\n\n\n\nCode debugging\, optimization and profiling\n\n\n\nParallelization and vectorization in R\n\n\n\nCrafting your own functions\n\n\n\nObject oriented programming and R classes: S3\, S4\, R6 and RC\n\n\n\nAnatomy of an R package: Creating your own package from scratch\n\n\n\nTidy data flow using tidyverse\n\n\n\nUsing the language of graphics: ggplot2\n\n\n\nDeveloping web applications using Shiny\n\n\n\nR and Python integration using reticulate\n\n\n\nTeam project work – developing data analyses workflow in R using acquired skills\n\n\n\n\nLearning outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nWork collaboratively and reproducibly in R\n\n\n\nOptimize R code\n\n\n\nUnderstand R code to a greater extent\n\n\n\nCreate better visualizations\n\n\n\nAnd more!\n\n\n\n\nEntry requirements\n\n\n\nThe course is aimed at both Ph.D. students and researchers within Life Sciences who are already using R for basic bioinformatics analyses and who would like to start using R at a more advanced level. In order for you and other participants to benefit the most\, you should consider yourself eligible if you are comfortable with reading and transforming data\, installing and using third-party packages and plotting using standard R graphics. \n\n\n\nWe offer places for participants from all over the world\, but there are a number of places reserved for participants from Sweden. Due to limited space the course can accommodate approximately 45 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\nBy participating in this workshop\, you agree to the NBIS Code of conduct: https://uppsala.instructure.com/courses/105973/pages/code-of-conduct \n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 9500 SEK for academic participants and 19 000 SEK for non-academic participants\, invoiced to the participant’s organization. If you accept a position and do not participate (no-show) you will still be invoiced at the standard fee. Please note that NBIS cannot invoice individuals. \n\n\n\nThe fee includes: \n\n\n\n\nParticipation in lectures and workshops\n\n\n\nMingle reception with snacks and drinks\n\n\n\nDaily breakfast/coffee\, lunch and afternoon coffee during the workshop\n\n\n\nOne official course dinner\n\n\n\nSurprise social activities\n\n\n\n\nNOT included in the fee: \n\n\n\n\nAccommodation\n\n\n\nTravel to and from Visby\n\n\n\nDaily dinners\n\n\n\n\nImportant information\n\n\n\nApplication opens: 13 Jan 2025 \n\n\n\nApplication closes: 06 Apr 2025 \n\n\n\nConfirmation to accepted participants: Rolling acceptance. \n\n\n\nResponsible teachers: Marcin Kierczak\, Sebastian DiLorenzo\, Roy Francis \n\n\n\nContact information: raukr@nbis.se \n\n\n\n\n\nRegister here\n\n\n\n\n\nCourse website
URL:https://www.scilifelab.se/event/raukr-2025-summer-school-r-beyond-the-basics/
LOCATION:B-huset\, Campus Gotland\, Cramérgatan 3\, Visby\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2025/01/RaukR.jpg
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20250915T080000
DTEND;TZID=Europe/Stockholm:20250919T170000
DTSTAMP:20260416T014421
CREATED:20250109T105219Z
LAST-MODIFIED:20250109T144332Z
UID:10001448-1757923200-1758301200@www.scilifelab.se
SUMMARY:Population Genomics in Practice
DESCRIPTION:The “Population Genomics in Practice” course is open for PhD students\, postdocs\, researchers\, and other employees in Swedish universities\, who need hands-on and practical skills to analyze population genomics data. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2025-01-13 \n\n\n\nApplication closes: 2025-05-15 \n\n\n\nConfirmation to accepted students: 2025-06-15 \n\n\n\nCourse Leader and teachers: Per Unneberg (CL)\, André E.R. Soares (CL)\, Nikolay Oskolkov\, Jason Hill \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\nCourse fee\n\n\n\nA course fee* of 3000 SEK for academic participants and 15000 SEK for non-academic participants 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\nRegister here\n\n\n\nCourse content\n\n\n\nThis workshop aims 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 modeling and principal component analyses\n\n\n\nDemographic modeling using sequentially Markovian coalescent models and linkage disequilibrium\n\n\n\nSelection scans\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\nAnalyze population structure with admixture modeling and dimensionality reduction methods\n\n\n\nPerform demographic modeling 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\nThe latest information about the course can be found on \n\n\n\nhttps://uppsala.instructure.com/courses/105981 \n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required to be able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge of R or Python\n\n\n\nBasic knowledge of variant calling\, or the equivalent of the 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 –omics 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-3/
LOCATION:BMC Trippelrummet\, Husargatan 3\, entrance C11\, Uppsala\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
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DTSTART;TZID=Europe/Stockholm:20260817T080000
DTEND;TZID=Europe/Stockholm:20260828T170000
DTSTAMP:20260416T014421
CREATED:20260408T064712Z
LAST-MODIFIED:20260408T065111Z
UID:10001798-1786953600-1787936400@www.scilifelab.se
SUMMARY:Integrated Structural Biology course\, 3rd edition
DESCRIPTION:Save the dates! Registration details will be shared soon. \n\n\n\nWelcome to the 3rd edition of the Integrated Structural Biology course\, organized by SciLifeLab and NordStruct. The course will take place over two weeks across Stockholm\, Linköping\, Lund\, and Gothenburg. \n\n\n\n\n\n\n\nDuring the course\, you will be introduced to a wide range of structural biology techniques available at research infrastructures in Sweden. The program combines lectures\, site visits\, and hands-on discussions\, offering opportunities for in-depth learning\, networking\, and project-specific discussions with experts. \n\n\n\nIn addition to the scientific program\, the course includes social activities such as dinners and informal gatherings\, providing further opportunities to connect with fellow participants and instructors. \n\n\n\nThe course will cover: \n\n\n\n\nCryo-EM\n\n\n\nNMR\n\n\n\nStructural proteomics\n\n\n\nCrystallography\n\n\n\nSAXS/SANS\n\n\n\nBiophysical characterization\n\n\n\nComputational aspects\, including AlphaFold\n\n\n\nProtein production\n\n\n\n\nThe program also includes student presentations and visits to key research infrastructures. \n\n\n\nPractical details\n\n\n\nThe course begins with three days in Stockholm\, followed by two days in Linköping to complete the first week. The second week starts in Lund and concludes with two days in Gothenburg. \n\n\n\nThe course fee is 7\,000 SEK and includes accommodation (four nights per week)\, lunches\, coffee breaks (fika)\, and organized travel between sites. Accommodation and local logistics will be arranged by the organizers. \n\n\n\nParticipants are expected to arrange their own travel to and from the course locations as follows: \n\n\n\n\nArrival in Stockholm on August 17 (no later than 10:00)\n\n\n\nDeparture from Linköping on August 21\n\n\n\nArrival in Lund on August 24 (before approximately 10:00–11:00)\n\n\n\nFinal departure from Gothenburg on August 28\n\n\n\n\nSchedule in short\n\n\n\n\n\nAugust 17  \n\n\n\n\n\nArrival in Stockholm\, set up computersProtein production and crystallography lectures \n\n\n\n\n\n\n\nAugust 18 \n\n\n\n\n\nCrystallography in practice (wet lab and computer) \n\n\n\n\n\n\n\nAugust 19 \n\n\n\n\n\nCryo-EM\, lecture and practicalTravel to Linköping \n\n\n\n\n\n\n\nAugust 20 \n\n\n\n\n\nAlphaFold and AI in structural biology \n\n\n\n\n\n\n\nAugust 21 \n\n\n\n\n\nBiophysical characterization \n\n\n\n\n\n\n\nAugust 24 \n\n\n\n\n\nArrival in LundGuest lecture and molecular Dynamicssite visit MAX IV and ESS \n\n\n\n\n\n\n\nAugust 25 \n\n\n\n\n\nSAXS/SANS lecture & practical \n\n\n\n\n\n\n\nAugust 26 \n\n\n\n\n\nStructural ProteomicsTravel to Gothenburg \n\n\n\n\n\n\n\nAugust 27 \n\n\n\n\n\nNMR \n\n\n\n\n\n\n\nAugust 28 \n\n\n\n\n\nIntegration of structural biology dataWrap-up\, good bye and travel home
URL:https://www.scilifelab.se/event/integrated-structural-biology-course-3rd-edition/
LOCATION:Stockholm\, Linköping\, Lund and Gothenburg
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2026/04/ISB2026_1.png
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