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DTSTART;TZID=Europe/Stockholm:20230508T090000
DTEND;TZID=Europe/Stockholm:20230512T170000
DTSTAMP:20260408T234602
CREATED:20230330T125745Z
LAST-MODIFIED:20230330T130447Z
UID:10000846-1683536400-1683910800@www.scilifelab.se
SUMMARY:Workshop in Metabolomics using Nuclear Magnetic Resonance Spectroscopy 
DESCRIPTION:Linköping University together with the Swedish NMR Centre and SwedNMR are pleased to invite to a Workshop in Metabolomics using Nuclear Magnetic Resonance Spectroscopy 8th to 12th of May\, 2023 at Linköping University. The workshop aims to give an overview of NMR based metabolomics for PhD-students and researchers that will apply this technique in their own research. Lectures and seminars/workshops on; overview of metabolomics\, introduction to NMR\, experimental design\, biobanking of samples\, workflow\, sample preparation strategy\, application of multivariate data analysis and clinical applications. The workshop contains practical laboratory exercises using NMR. For PhD students it is also possible to participate in the workshop as a 3hp course. In connection to the workshop a mini-symposium will be organised the 9th of May.  \n\n\n\n\n\n\n\nOrganizers: Swedish NMR Centre and Linköping University \n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\nWorkshop website\n\n\n\n\n\nMini symposium website\n\n\n\n\n\nApplication closes: April 15\, 2023
URL:https://www.scilifelab.se/event/workshop-in-metabolomics-using-nuclear-magnetic-resonance-spectroscopy/
LOCATION:Berzeliussalen\, Entrance 65\, Campus US\, Linköping University
CATEGORIES:Course
ORGANIZER;CN="Swedish NMR Centre":MAILTO:info@nmr.gu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230605T080000
DTEND;TZID=Europe/Stockholm:20230609T170000
DTSTAMP:20260408T234602
CREATED:20230317T162228Z
LAST-MODIFIED:20230531T095005Z
UID:10000841-1685952000-1686330000@www.scilifelab.se
SUMMARY:1st cryoNET course on advanced single particle cryo-EM analysis
DESCRIPTION:CryoNet is a Nordic network in cryogenic electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryogenic electron microscopy as a strong pillar of Nordic life science research. \n\n\n\nThe core of the network is constituted by the cryo-EM facilities at University of Copenhagen\, Aarhus University\, Stockholm University and Umeå University. \n\n\n\nWe are happy to announce the 1st cryoNET course on advanced single particle cryo-EM analysis that will take place at Aarhus University on 5-9 June 2023. Aim of the course is to provide training in cryo-EM image processing including the latest developments of the field. \n\n\n\nParticipants will receive hands-on training in state-of-the-art techniques for single particle cryo-EM image processing\, model building and validation from a range of international specialist guest lecturers. The course also includes theoretical talks and discussions on the use of cryo-EM to address difficult biological questions\, which can help the participants address their own research problems. \n\n\n\nParticipation in the entire course is mandatory and an attendance certificate will be given at the end of the course. \n\n\n\n \n\n\n\nCourse Objectives\n\n\n\n\nTo provide training in state-of-the-art techniques for structure determination using cryo-EM\n\n\n\nDiscuss data collection strategies\n\n\n\nTraining in basic principles of structure determination using cryo-EM\n\n\n\nHands-on practical training in the latest software suites for image processing of electron micrographs for high resolution structure determination\n\n\n\nDevelop problem solving skills through discussions and practical sessions in the presence of international experts in the field\n\n\n\nNetworking with experts\, software developers\, and researchers in cryo-EM and learn of not only the latest but also upcoming developments\n\n\n\nApplication and selection\n\n\n\n\nCourse fee payment deadline: 2 May 2023 \n\n\n\nThe registration fee: 1000 DKK and includes \n\n\n\n\nAttendance in the course 5-9 June 2023\n\n\n\nLunches\, coffee and refreshments on the course dates\n\n\n\nCourse materials\n\n\n\nCertificate of attendance\n\n\n\nCourse dinner on second night of the course (arranged by the course hosts in Aarhus city)\n\n\n\n\nPlease note\, the registration fee does not cover hotel\, travel expenses\, breakfasts\, and dinners (expect the course dinner second night) \n\n\n\nProgram\n\n\n\nProgram_1st-CryoNET-course-5-9-June-2023Download\n\n\n\nSupported by\n\n\n\n\nKnut & Alice Wallenberg Foundation\n\n\n\nNovo Nordisk Foundation\n\n\n\nNordforsk\n\n\n\nThermo Fisher Scientific\n\n\n\n\nOrganising committee\n\n\n\nThomas Boesen\, Aarhus University \n\n\n\nKarin Walldén\, Stockholm University \n\n\n\nMarta Carroni\, Stockholm University \n\n\n\nKaren Bech-Pedersen\, Aarhus University \n\n\n\nJesper Lykkegaard Karlsen\, Aarhus University \n\n\n\nAndreas Bøggild\, Aarhus University
URL:https://www.scilifelab.se/event/1stfirst-cryonet-course-on-advanced-single-particle-cryo-em-analysis/
LOCATION:Aarhus University\, Department of Molecular Biology and Genetics\, Universitetsbyen 81\, Århus\, Denmark
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/cover3.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230611T090000
DTEND;TZID=Europe/Stockholm:20230622T170000
DTSTAMP:20260408T234602
CREATED:20230216T102719Z
LAST-MODIFIED:20230216T130225Z
UID:10000812-1686474000-1687453200@www.scilifelab.se
SUMMARY:RaukR\, Advanced R for Bioinformatics workshop
DESCRIPTION:International course. The course is open for researchers at university or in industry such as PhD students\, postdocs\, group leaders\, core facility staff and analysts. \n\n\n\n\n\n\n\nCourse description\n\n\n\nJoin us this June in beautiful and historic Visby to improve your R skills and have a nice time!In Life Science and Bioinformatics\, R is increasingly being used to transform and analyse data\, perform statistical analysis and produce publication-ready visualisations. This workshop will focus on advanced R functionality\, to increase the participants skillset and understanding of what is possible to do today. \n\n\n\nYou are very welcome to apply or see the website for more information. Please\, help us spread the word to interested participants! \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication deadline: Fri\, 14.04.2023\, 24:00GMT \n\n\n\nNotification of acceptance/decline: Fri\, 21.04.2023 \n\n\n\nResponsible teachers: Marcin Kierczak\, Sebastian DiLorenzo\, Roy FrancisContact: RaukR@NBIS.se \n\n\n\n\n\n\n\n\n\nCourse website\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nAcademic: 10 000 SEK (Includes participation in all official activities and events\, course materials\, breakfast\, lunch and accommodations). \n\n\n\nParticipants from outside of academia should contact us for a fee quote. \n\n\n\nThe fee does not include travel costs. \n\n\n\n\n\n\n\nGuest speakers\n\n\n\nJenny Bryan (software engineer at RStudio\, Data science professor at UBC) (link to https://jennybryan.org/about/)Yihui Xie (software engineer at RStudio) (link to https://yihui.org/en/)Max Kuhn (software engineer at RStudio) (link to https://www.rstudio.com/authors/max-kuhn/)Christophe Dervieux (software engineer at RStudio) (link to https://cderv.rbind.io/about/) \n\n\n\n\n\n\n\nCourse content\n\n\n\n\nReproducible research in R (Quarto\, Rmarkdown\, Knitr)\n\n\n\nCollaborative work using Git and GitHub\, CD/CI\n\n\n\nR code style guide & best practices\n\n\n\nCode debugging\, optimization and profiling\n\n\n\nParallelisation and vectorization in R\n\n\n\nWriting own functions\n\n\n\nUnderstanding and using the system of R classes: S3\, S4\, R6 and RC\n\n\n\nAnatomy of an R package: writing your own package from scratch\n\n\n\nTidy data flow with tidyverse\n\n\n\nUsing the language of graphics\, ggplot2\n\n\n\nDeveloping simple web applications using shiny\n\n\n\nR and Python integration using reticulate\n\n\n\nStreamlined modelling using tidymodels\n\n\n\nTeam project work – developing data analyses workflow in R using acquired skills\n\n\n\n\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 is a number of places reserved for participants from Sweden. \n\n\n\n\n\n\n\nSelection criteria\n\n\n\nThis year\, the school can accommodate ~42 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/raukr-advanced-r-for-bioinformatics-workshop-2/
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/02/Visby-1.jpg
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230913T080000
DTEND;TZID=Europe/Stockholm:20230915T170000
DTSTAMP:20260408T234602
CREATED:20230421T112659Z
LAST-MODIFIED:20230421T112843Z
UID:10000866-1694592000-1694797200@www.scilifelab.se
SUMMARY:ELIXIR-GOBLET Train-the-Trainer
DESCRIPTION:Course Content\n\n\n\nThis course offers guidance\, ideas and tips for designing training/teaching\, development and delivery on training activities\, all based on research-driven educational principles. This course will cover 4 main topics: \n\n\n\n\nLearning principles and how they apply to training and teaching\n\n\n\nDesign and plan session\, course\, materials\n\n\n\nTeaching techniques to enhance learner engagement and participation\n\n\n\nAssessment and feedback in training and teaching\n\n\n\n\nThis course will be delivered through Canvas learning management system. You can find a link to the course pages here. \n\n\n\nNote! The course is highly interactive and hence it is important that you\, as a participant\, actively contribute to all sessions and elements of the course. \n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-04-21 \n\n\n\nApplication closes: 2023-08-21 \n\n\n\nConfirmation to accepted students: 2023-08-25 \n\n\n\nCourse Leaders and teachers: Jessica Lindvall and Nina Norgren \n\n\n\nIn case you miss information on any of the above dates\, please contact: Nina Norgren (traininghub@scilifelab.se) \n\n\n\n\nCOURSE WEBSITE AND PROGRAM\n\n\n\nREGISTRATION\n\n\n\n\nLearning Objectives\n\n\n\n\nTo get acquainted with Learning principles and how they apply to training\n\n\n\nTo be able to select and use training techniques that can help enhance learner engagement and participation\n\n\n\nTo learn how to use assessment and feedback in training\n\n\n\nTo learn about session\, course\, and materials design\n\n\n\n\nLearning Outcomes\n\n\n\nBy the end of this course\, learners will be able to: \n\n\n\n\nName learning principles that a good teacher/instructor should have in mind\n\n\n\nDescribe at least three training techniques\, drawing on learning principles\n\n\n\nDesign a training session and a course\n\n\n\nDevelop assessment questionnaires\n\n\n\nEnumerate types of materials needed for each part of a training session or course\n\n\n\n\nEntry requirements\n\n\n\nWhoever is interested in becoming a trainer/instructor\, or improving your training skills. If you have questions like the following ones\, this course may be very helpful to you. \n\n\n\n\nHow learning works?\n\n\n\nHow do I use learning principles and theories to improve my teaching/training?\n\n\n\nHow do I make my teaching/training more engaging and effective?\n\n\n\nHow should I adjust my teaching/training to different types of learners?\n\n\n\nHow do I ensure learning progress?\n\n\n\nHow can I assess whether my students are actually understanding my lessons? Are they actually learning?\n\n\n\nWhat is the best balance between theory and practice?\n\n\n\nHow can I best assess whether learning is occurring and/or has occurred?\n\n\n\nWhat works in a classroom and what doesn’t?\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: Priority will be given to applicants from SciLifeLab infrastructures\, institutes and organisations across the Nordic research community\, and to participants from Nordic ELIXIR nodes. \n\n\n\nCourse fee \n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and fikas\, and a course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nNote! If you are accepted and decide not to attend without communicating the reason for the no-show with us latest on the 8th of September\, we will invoice a no-show-fee of 2000 SEK. \n\n\n\nThe invoicing information needs to be included in the registration in order to guarantee your spot in the training event\, if you are to be accepted. By giving the invoice information you hereby confirm that the group leader/PI/manager has given a consent regarding your possible participation in the Training event.
URL:https://www.scilifelab.se/event/elixir-goblet-train-the-trainer/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS & Training Hub":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230918T080000
DTEND;TZID=Europe/Stockholm:20230922T170000
DTSTAMP:20260408T234602
CREATED:20230510T125126Z
LAST-MODIFIED:20230510T131009Z
UID:10000883-1695024000-1695402000@www.scilifelab.se
SUMMARY:Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)
DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS). \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  now \n\n\n\nApplication closes: 2023-09-04 \n\n\n\nConfirmation to accepted students: 2023-09-08 \n\n\n\n\n\n\n\nResponsible teachers\n\n\n\nAgata Smialowska\, Jakub Orzechowski Westholm\, Vincent van Hoef  \n\n\n\nPlease contact edu.epigenomics@nbis.se for course specific questions \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\n\n\n\n\nWorkshop 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\n*Please note that NBIS cannot invoice individuals. \n\n\n\n\n\n\n\nWorkshop content\n\n\n\nThis workshop aims to introduce the best practice bioinformatics methods for processing\, analyses\, visualisation and integration of epigenomics and functional genomics data. \n\n\n\nTopics covered include: \n\n\n\n\nData processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;\n\n\n\nChIP-seq: peak calling\, peak independent / dependent quality metrics\, differential binding analysis; DNA motif enrichment;\n\n\n\nATAC-seq: peak calling\, peak independent / dependent quality metrics\, differential accessibility analysis;\n\n\n\nQuantitative ChIP-seq using spike-ins;\n\n\n\nCUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;\n\n\n\nFunctional analysis\, including finding nearest genes and custom features\, GO terms and Reactome pathways enrichment;\n\n\n\nBasic multi-omics exploration and integration;\n\n\n\nVisualisations of epigenomics datasets;\n\n\n\nIntroduction to analysis of single cell functional genomics data (scATAC-seq);\n\n\n\nIntroduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq\, ChIP-seq\, ATAC-seq.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the workshop and complete the computer exercises: \n\n\n\n\nBYOL\, bring your own laptop with R and RStudio installed;\n\n\n\nBasic knowledge in Linux;\n\n\n\nBasic programming experience\, preferably in R.\n\n\n\n\n\n\n\n\nDesirable \n\n\n\n\nExperience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;\n\n\n\nPrevious experience with NGS data analyses;\n\n\n\nCompleting NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.\n\n\n\n\n\n\n\n\nDue to limited capacity the workshop can accommodate 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 workshop as well as gender and geographical balance. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. \n\n\n\nThis training content is estimated to correspond to a 1.5 HPs\, however the estimated credits are just guidelines. If formal credits are crucial\, participants need to confer with the home department whether the course is valid for formal credits.
URL:https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-online-3/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230926T080000
DTEND;TZID=Europe/Stockholm:20230928T170000
DTSTAMP:20260408T234602
CREATED:20230411T092804Z
LAST-MODIFIED:20230912T113701Z
UID:10000851-1695715200-1695920400@www.scilifelab.se
SUMMARY:Basic Course in Scanning and Transmission Electron Microscopy for Life Sciences
DESCRIPTION:This course covers lectures and practical demonstrations in SEM and TEM techniques\, specifically for life science applications. The contents include principles of electron microscopy\, specimen preparation\, cryo-electron microscopy and correlative light-electron microscopy. For electron microscopy in physical science applications\, there will be a similar-content basic course in early 2024. \n\n\n\nRead more\n\n\n\nApplication deadline: The registration closes on September 15 2023. \n\n\n\nLocation: Lectures at KBC Building and laboratory demonstrations at UCEM. \n\n\n\nParticipants: 18 persons \n\n\n\nInstructors: UCEM staff \n\n\n\nDuration: 3 days \n\n\n\nBreaks/Refreshments: Coffee\, cookies and fruit. \n\n\n\nCosts: No course fee\, but full attendance is required! \n\n\n\nExamination/Credits\n\n\n\nOral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.
URL:https://www.scilifelab.se/event/basic-course-in-scanning-and-transmission-electron-microscopy-for-life-sciences/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231009T090000
DTEND;TZID=Europe/Stockholm:20231013T170000
DTSTAMP:20260408T234602
CREATED:20230614T070145Z
LAST-MODIFIED:20230615T091559Z
UID:10000913-1696842000-1697216400@www.scilifelab.se
SUMMARY:Python programming with applications to bioinformatics
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of fundamental Python skills within all Swedish universities \n\n\n\nResponsible teachers: Nina Norgren\, Dimitris Bampalikis\, Jeanette Tångrot \n\n\n\nContact information: edu.intro-python@nbis.se \n\n\n\nVenues: SciLifeLab Uppsala\, Trippelrummet\, BMC & Umeå University\, Naturvetarhuset\, room NAT.D.370 \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\n\n\n\n\nImportant dates\n\n\n\nApplication open: June 15 \n\n\n\nApplication deadline: September 8 \n\n\n\nConfirmation to accepted participants: September 15 \n\n\n\n\n\n\n\nCourse fee\n\n\n\n A course fee* of 3000 SEK will be invoiced to accepted participants. This includes lunches\, coffee and snacks\, and course dinner \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse description\n\n\n\nThis course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course\, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. \n\n\n\nFormat \n\n\n\nThis course runs in parallel both on-site in Uppsala and in Umeå. Lectures will be streamed online from our Uppsala site to the Umeå site. Several teaching assistants will be present both in the Umeå and Uppsala classroom all week to help with exercises and questions. When registering you will be asked to which site you apply. \n\n\n\nThe course consists of a mix of presentations\, demonstrations\, and practical exercises (either in the lab with assistants or on your own). Prior to the course\, you can read a companion book “Programming Python”\, or “Learning Python”. Such a book will also prove useful for your programming tasks\, after the course is over. It is however not required\, and material will be presented in class. \n\n\n\n\n\n\n\nCourse content\n\n\n\n\nCore concepts about Python syntax: Data types\, blocks and indentation\, variable scoping\, iteration\, functions\, methods and arguments\n\n\n\nDifferent ways to control program flow using loops and conditional tests\n\n\n\nRegular expressions and pattern matching\n\n\n\nWriting functions and best-practice ways of making them usable\n\n\n\nReading from and writing to files\n\n\n\nCode packaging and Python libraries\n\n\n\nHow to work with biological data using external libraries.\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\n\nDescribe and apply basic concepts in Python\, such as:LoopsIf/else statementsFunctions\n\nReading/writing to files\n\n\n\n\n\nBeing able to edit and run Python code\n\n\n\nWrite file-processing Python programs that produce output to the terminal and/or external files\n\n\n\nCreate stand-alone python programs to process biological data\n\n\n\nKnow how to develop your skills in Python after the course (including debugging)\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage\, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises. \n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants in Uppsala and 15 in Umeå. 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\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to 1.5 hp credits\, however the estimated credits are just recommendations. 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/python-programming-with-applications-to-bioinformatics-2/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231017T080000
DTEND;TZID=Europe/Stockholm:20231019T170000
DTSTAMP:20260408T234602
CREATED:20230411T092159Z
LAST-MODIFIED:20230411T092229Z
UID:10000850-1697529600-1697734800@www.scilifelab.se
SUMMARY:Cryo-EM sample preparation and data collection
DESCRIPTION:The purpose of the course is to prepare and train Cryo-EM facility users in sample preparation methods\, introduce users to the image data acquisition workflow\, expand knowledge about cryo-EM methods among researchers and show that everyone can learn how to use cryo-EM for structure and cell biology. \n\n\n\nThe course is open for facility users or potential facility users\, such as PhD students\, postdocs\, and researchers within the life sciences who are curious and will profit from cryo-EM skills. Swedish and international course participants are welcome. To attend\, the course participants must have experience in basic electron microscopy and be familiar with structure or cell biology. \n\n\n\nThis course is supported by SciLifeLab\, CryoNET and Umeå University and organized by the SciLifeLab Cryo-EM facility\, both UmU and SU nodes together. \n\n\n\nRead more\n\n\n\nApplication deadline\n\n\n\nApplication should be submitted before September 29\, 2023 \n\n\n\nCourse organizers\n\n\n\nMichael Hall \n\n\n\nLocation\n\n\n\nUCEM and Chemical Biological Centre (KBC) BuildingUmeå University\, Linnaeus väg 6 \n\n\n\nTeachers and course instructors\n\n\n\n\n    Linda Sandblad\n\n\n\n    Michael Hall\n\n\n\n    Lars-Anders Carlson\n\n\n\n    Additional teachers t.b.a\n\n\n\n\nSocial program\n\n\n\nA social program depending on the current corona restriction will be communicated to the participants after acceptance. \n\n\n\nCourse content\n\n\n\nThis course will cover practical aspects of cryo-EM sample preparation and data acquisition. \n\n\n\nTopics covered\n\n\n\n\n    Basic theory of vitreous water\, how to handle a cryo sample and consequences\n\n\n\n    Plunge freezing methods\, tools and cryo-transfer\n\n\n\n    Sample and instrument requirements for single particle and tomography methods\n\n\n\n    Image data acquisition\, concept of low dose and the cryo-specific workflow\n\n\n\n    Introduction to automatic data acqui­sition software\, EPU\, Tomography\n\n\n\n    Introduction to cryo-EM image processing methods\n\n\n\n\nThe course consists of lectures\, cryo lab work\, demonstrations and practical exercises for all participants\, hands-on experiences of microscopy operation and discussions. A detailed schedule will be provided to accepted participant. \n\n\n\nCourse literature\n\n\n\nHandouts and material online. \n\n\n\nEntry requirements\n\n\n\nPriority will be given to researchers involved in project where the use of cryo-EM is needed\, which are to be briefly described upon application. \n\n\n\nThe course will be held at an advanced level\, assuming that participants have a master’s degree or equivalent in a technical life science discipline. It aims to be relevant for a broad research community\, also to participants not working in research environments using cryo-EM today. \n\n\n\nA maximum of 15 participants will be admitted. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender balance. \n\n\n\nExamination\n\n\n\nParticipation in all parts of the course\, lectures\, lab\, microscopy demonstrations and evaluation are mandatory. SciLifeLab and Umeå University will provide successful participants with a course certificate and a recommendation for 1 ECTS
URL:https://www.scilifelab.se/event/cryo-em-sample-preparation-and-data-collection-2/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231017T080000
DTEND;TZID=Europe/Stockholm:20231019T170000
DTSTAMP:20260408T234602
CREATED:20230810T125629Z
LAST-MODIFIED:20231013T081404Z
UID:10000946-1697529600-1697734800@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices - Cancelled
DESCRIPTION:This national workshop in Data Management is a co-arranged event between Uppsala University and Chalmers University\, and provides an introduction for PhD students\, postdocs\, researchers\, and other employees within all Swedish universities. The workshop will introduce important aspects of research data management through a series of lectures\, demonstrations\, 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. CANCELLED – next time (preliminary) in Stockholm\, April 2024 \n\n\n\nTopics covered will include: \n\n\n\n\nOpen Science and FAIR in practice\n\n\n\nOrganising data\, files and folders in research projects\n\n\n\nDescribing data with metadata\n\n\n\nPublishing data to public data repositories\n\n\n\nCleaning tabular data and metadata with OpenRefine\n\n\n\nWriting basic recipes for data analysis and visualisation with R\n\n\n\nVersioning data\, documents and scripts\n\n\n\nWriting Data Management Plans\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: now \n\n\n\nApplication closes: 2023-09-27 \n\n\n\nInformation to accepted students will be sent:  2023-09-29 \n\n\n\n\n\n\n\nContact\n\n\n\nedu.intro-dm@nbis.se \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\nFormat\n\n\n\nThis workshop runs in parallel on-site in Uppsala\, and Göteborg. Lectures will be streamed online from our Uppsala site (mainly) to the Gothenburg classrooms\, and vice versa. Teachers and teaching assistants will be present at both locations all week to help with exercises and questions. When registering you will be asked to select a preferred site. \n\n\n\n\n\n\n\nVenues\n\n\n\nUppsala \n\n\n\nTrippelrummet (E10:1307-1309)\, SciLifeLab Navet\, Entrance C11\, Biomedical Centre (BMC) \n\n\n\nHusargatan 3\, 752 37 Uppsala \n\n\n\nGothenburg \n\n\n\nCLS Room Scrum 1\, University library\, 2nd floor  \n\n\n\nHörsalsvägen 2 (entrance)\, 412 96 Gothenburg \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. \n\n\n\n\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. Installation instructions will be provided before the course starts\, and the course organisers arrange a pre-course event approximately one week prior to first course day. \n\n\n\n\n\n\n\nCredits & Certificate\n\n\n\nPlease note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. \n\n\n\nDue to limitations in space and capacity the course can accommodate a maximum of 25 participants per site.  If we receive more applications\, participants will be selected based on several criteria\, including correct entry information\, motivation to attend the course\, as well as gender and geographical balance. \n\n\n\nFor more detailed information about the workshop\, please visit the workshop website.
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-5/
LOCATION:Uppsala University\, Uppsala and Chalmers University\, Gothenburg
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231023T090000
DTEND;TZID=Europe/Stockholm:20231027T170000
DTSTAMP:20260408T234602
CREATED:20230811T112638Z
LAST-MODIFIED:20230811T120144Z
UID:10000948-1698051600-1698426000@www.scilifelab.se
SUMMARY:R Foundations for Life Scientists
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of  programming in R. \n\n\n\n\n\n\n\nImportant dates & Information\n\n\n\nApplication opens: 2023-08-20 \n\n\n\nApplication closes: 2023-09-20 \n\n\n\nConfirmation to accepted students: 2023-09-27 \n\n\n\nCourse Leader and teachers: Nima Rafati (CL)\, Prasoon Argawal (CL)\, Marcin Kierczak (CT)\, Sebastian DiLorenzo (CT) \n\n\n\nIn case you miss information on any of the above dates\, please contact us via edu.r@nbis.se \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 fee\n\n\n\nA course fee* of 2000 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\nCourse content\n\n\n\nThe course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting emphasizing the parts useful for life scientists. After introductory lectures on good programming practices\, basic software design theory and a brief overview of R\, we will delve into programming. \n\n\n\nTopics covered will include: \n\n\n\n\nVariables and Operators\n\n\n\nMatrices\, lists\, and dataframes\n\n\n\nData manipulation\n\n\n\nVisualization\n\n\n\nR packages\n\n\n\nBioconductor\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 different data structures commonly used in R.\n\n\n\nWork with different data types.\n\n\n\nImport and export data from and to R environment. \n\n\n\nManipulate data.\n\n\n\nWork with dataframes and lists.\n\n\n\nVisualize the data.\n\n\n\nExplain about R packages and steps to create them.\n\n\n\nInstall R packages from Bioconductor. \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\nGood general computer literacy\n\n\n\nBasic knowledge in mathematics and statistics\n\n\n\n\nDue to limited space the 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.
URL:https://www.scilifelab.se/event/r-foundations-for-life-scientists/
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:20231025T080000
DTEND;TZID=Europe/Stockholm:20231027T130000
DTSTAMP:20260408T234602
CREATED:20230814T082817Z
LAST-MODIFIED:20231019T092918Z
UID:10000950-1698220800-1698411600@www.scilifelab.se
SUMMARY:Subtomogram averaging workshop for cryo electron tomography
DESCRIPTION:Cryoelectron tomography is anemerging field in structural biology. We are happy to announce that we are hosting a Subtomogram averaging workshop for cryo electron tomography\, taking place on 25-27 October 2023 at Stockholm University.  \n\n\n\nThe aim of the course is to provide training in Subtomogram averagingusing e.g. Dynamo and Relion4 including the latest developments of the field. \n\n\n\nRegistration is now closed \n\n\n\nThe workshop provides hands-on training in all practical aspects of tomography and sub-tomogram averaging using the Dynamo software\, encompassing all stages of the pipeline: alignment and reconstruction of tilt series\, tomogram visualization and archiving\, particle selection and extraction\, and subtomogram alignment\, averaging\, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place\, and we welcome participants to bring their own data sets to work on them during this two-day course. \n\n\n\n\n\n\n\nParticipants will be selected on the basis of applications that describe their current research projects and plans. Priority will be given to participants that are currently processing their own cryo-ET data and are users of the SciLifeLab cryo-EM facilities. \n\n\n\nDeadline for application:  15 September 2023  \n\n\n\nNotification: Applicants will be notified of the outcome of their application by 20 September 2023 \n\n\n\nCourse fee payment deadline: 30 September 2023 \n\n\n\nThe registration fee: 1000 SEK and includes \n\n\n\n\nAttendance in the course 25-27 October 2023\n\n\n\nLunches\, coffee and refreshments on the course dates\n\n\n\nCourse materials\n\n\n\nCertificate of attendance\n\n\n\nCourse dinner on first night of the course\n\n\n\n\nPlease note\, the registration fee does not cover hotel\, travel expenses\, breakfasts\, and dinners (expect the course dinner second night) \n\n\n\nCourse Content\n\n\n\nThe course content can be found here \n\n\n\nRead more\n\n\n\nAs a general guideline\, we will cover: \n\n\n\n\nAlignment and reconstruction of tilt series.\n\n\n\nManual and automated particle picking in different geometries (filaments\, membranes\, isolated particles…).\n\n\n\nArchiving and cataloguing of tilt series\, tomograms and annotations.\n\n\n\nCreation of subtomogram averaging projects.\n\n\n\nAdvanced tools in subtomogram averaging.\n\n\n\nClassification methods.\n\n\n\nCreation of 3d scenes.\n\n\n\nScripting in Dynamo: gentle introduction to programming.\n\n\n\n\nComputing facilities\n\n\n\nComputer room at KÖL\, Stockholm University \n\n\n\nVenues \n\n\n\n25-26/10-23 \n\n\n\nDepartment of Biochemistry and BiophysicsComputer room at KÖL\, K343Stockholm University\, Svante Arrhenius väg 16CStockholm \n\n\n\n27/10-23 \n\n\n\nSciLifeLab Seminar room in building gamma 2\, Air&Fire Tomtebodavägen 23ASolna \n\n\n\n \n\n\n\nProgram\n\n\n\nProgram_231018_1Download
URL:https://www.scilifelab.se/event/subtomogram-averaging-workshop-for-cryo-electron-tomography/
LOCATION:Arrhenius Laboratory\, Stockholm University\, Svante Arrhenius väg 16C\, Stockholm
CATEGORIES:Course
ORGANIZER;CN="Cryo-EM Infrastructure Unit":MAILTO:cryoem_stockholm_lab@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231106T090000
DTEND;TZID=Europe/Stockholm:20231110T170000
DTSTAMP:20260408T234602
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
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231113T090000
DTEND;TZID=Europe/Stockholm:20231117T170000
DTSTAMP:20260408T234602
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:20260408T234602
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
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231204T090000
DTEND;TZID=Europe/Stockholm:20231206T170000
DTSTAMP:20260408T234602
CREATED:20230906T082705Z
LAST-MODIFIED:20231106T132742Z
UID:10000967-1701680400-1701882000@www.scilifelab.se
SUMMARY:Snakemake “bring-your-own-code” (BYOC) workshop - Cancelled
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. CANCELLED! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-09-11 \n\n\n\nApplication closes: 2023-10-29 \n\n\n\nConfirmation to accepted students: 2023-11-06 \n\n\n\nCourse Leader and teachers: Verena Kutschera (CL)\, Marcel Martin\, John Sundh. In case you have any workshop-specific questions\, please contact: edu.byoc-snakemake@nbis.se \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 fee\n\n\n\nThis online training event has no fee. However\, if you confirm your participation but do not do so (no-show) you will be invoiced 2\,000 SEK*.*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\nAs data analysis projects grow and change over time\, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up\, perform and monitor defined sequences of computational tasks (“workflows”)\, thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. \n\n\n\nThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. \n\n\n\nThis Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \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\nBe able to create Snakemake workflows for bioinformatics data analysis\n\n\n\nDemonstrate knowledge of the structure and syntax of different types of Snakemake workflows\n\n\n\nDemonstrate knowledge of advanced features of the Snakemake workflow language\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: \n\n\n\n\nPrevious participation in the NBIS Tools for reproducible research course. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.).\n\n\n\nYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improve. \n\n\n\nA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required).\n\n\n\n\nDue to limited space the course can accommodate a maximum of 12 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/snakemake-bring-your-own-code-byoc-workshop-online/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231206T080000
DTEND;TZID=Europe/Stockholm:20231208T170000
DTSTAMP:20260408T234602
CREATED:20231002T115541Z
LAST-MODIFIED:20231002T115646Z
UID:10000980-1701849600-1702054800@www.scilifelab.se
SUMMARY:DDLS Biomarker Discovery: from theory to real world examples
DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of understanding biomarker research and methods. \n\n\n\nWorkshop location:  SciLifeLab\, Tomtebodavägen 23A\, Solna \n\n\n\nVenue:  Air&Fire (G2690) and Milky Way (A2631) \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-10-01 \n\n\n\nApplication closes: 2023-10-30 \n\n\n\nConfirmation to accepted students: 2023-11-15 \n\n\n\n \n\n\n\nCourse Leaders and teachers: Animesh Acharjee\, Clemens Wittenbecher\, Markus Mayrhofer\, Mun-Gwan Hong\, Paul Pyl\, Prasoon Agarwal \n\n\n\nplease contact edu.biomarkers@nbis.se for course-specific questions \n\n\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\nWorkshop fee\n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunch and coffee. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nWorkshop content\n\n\n\nThe main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research\, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery. \n\n\n\nTopics covered will include: \n\n\n\n\nBiomarker study design for “context of use”\n\n\n\nTypes of biomarkers\, diagnostic\, prognostic\, and wellness\n\n\n\nBiomarkers are in use for various diseases such as cancer\, cardiovascular diseases\n\n\n\nBiomarker discovery from various omics data including proteome\, microbiome\n\n\n\nBiomarker and multi-omics data integration\n\n\n\nMachine learning methods\, lasso logistic regression and random forest\, to identify biomarkers\n\n\n\nPerformance indicators\, e.g. sensitivity and specificity\n\n\n\nInternal/external validation\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required to be able to follow the workshop and complete the exercises: \n\n\n\n\nAbility to bring your own laptop with R installed for the practical exercises\n\n\n\nBasic Programming/scripting experience in R\n\n\n\nor took an R course NBIS prepared.\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nSome basic knowledge of biostatistics\n\n\n\nPrevious experience in biomarker-related studies\n\n\n\n\nDue to limited space\, the 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.
URL:https://www.scilifelab.se/event/ddls-biomarker-discovery-from-theory-to-real-world-examples/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240212T090000
DTEND;TZID=Europe/Stockholm:20240216T170000
DTSTAMP:20260408T234602
CREATED:20231113T100039Z
LAST-MODIFIED:20231113T125832Z
UID:10001025-1707728400-1708102800@www.scilifelab.se
SUMMARY:Single Cell RNA-Seq Data Analyses Workshop
DESCRIPTION:This 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” day where you get to practice your skills on a dataset of your choosing. \n\n\n\n\n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) \n\n\n\nResponsible teachers: Åsa Björklund\, Susanne Reinsbach\, Roy Francis \n\n\n\nContact information: edu.sc@nbis.se    \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: 13 Nov 2023 \n\n\n\nApplication closes: 17 Jan 2024 \n\n\n\nConfirmation to accepted participants: Weeks 3-4\, 2024 \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 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 content\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\nCelltype prediction\n\n\n\nTrajectory inference analysis\n\n\n\nComparison of analysis toolkits: Seurat\, Scran and Scanpy\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\n\nYou are used to program in either R and/or Python\n\n\n\nYou already understand the basis of NGS technologies\n\n\n\nYou are able to analyse bulk RNA-sequencing data\n\n\n\nYou are used to navigate and use UNIX command line (bash)\n\n\n\nHave full access to your computer (admin permissions). Instructions on installation will be sent by email to accepted participants.\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space\, the course accommodates a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria such as correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/single-cell-rna-seq-data-analyses-workshop/
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:20240214T120000
DTEND;TZID=Europe/Stockholm:20240215T140000
DTSTAMP:20260408T234602
CREATED:20240205T143352Z
LAST-MODIFIED:20240205T143719Z
UID:10001143-1707912000-1708005600@www.scilifelab.se
SUMMARY:Epigenetics Workshop
DESCRIPTION:Join us for our free Epigenetics workshop\, where we will delve into pressing questions about epigenetic information\, with a focus on DNA methylation. This translational technology is gaining ground in clinical practice\, but there is room for improvement in Sweden. From methylation sequencing panels to bioinformatic analysis\, we will explore it all. Long-read sequencing platforms also hold promise for future clinical applications. \n\n\n\nDon’t miss out on interactive discussions and expert presentations\, all for free!  \n\n\n\nRegistration\n\n\n\nLooking forward to your participation!
URL:https://www.scilifelab.se/event/epigenetics-workshop/
LOCATION:Birgittasalen\, Hus 240\, Hälsovägen\, US\, Linköping
CATEGORIES:Course
ORGANIZER;CN="Clinical Genomics Link%C3%B6ping":MAILTO:tobias.strid@liu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240220T080000
DTEND;TZID=Europe/Stockholm:20240222T170000
DTSTAMP:20260408T234602
CREATED:20231215T082629Z
LAST-MODIFIED:20231215T082631Z
UID:10001070-1708416000-1708621200@www.scilifelab.se
SUMMARY:Basic Course in Scanning and Transmission Electron Microscopy for Life Sciences
DESCRIPTION:This course covers lectures and practical demonstrations in SEM and TEM techniques\, specifically for life science applications. The contents include principles of electron microscopy\, specimen preparation\, cryo-electron microscopy and correlative light-electron microscopy. For electron microscopy in physical science applications\, there will be a similar-content basic course organised later. \n\n\n\nRead more and register\n\n\n\nApplication deadline: The registration closes on 26 January 2024. \n\n\n\nLocation: Lectures at KBC Building and laboratory demonstrations at UCEM facility\, Umeå University \n\n\n\nParticipants: 18 persons \n\n\n\nInstructors: UCEM staff \n\n\n\nDuration: 3 days \n\n\n\nBreaks/Refreshments: Coffee\, cookies and fruit. \n\n\n\nCosts: No course fee\, but full attendance is required! \n\n\n\nExamination/Credits: Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.
URL:https://www.scilifelab.se/event/basic-course-in-scanning-and-transmission-electron-microscopy-for-life-sciences-2/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/12/Bild1.jpg
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240311T080000
DTEND;TZID=Europe/Stockholm:20240315T170000
DTSTAMP:20260408T234602
CREATED:20231220T151424Z
LAST-MODIFIED:20240213T125934Z
UID:10001073-1710144000-1710522000@www.scilifelab.se
SUMMARY:RNA-seq data analysis
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of  lectures and computer practicals. \n\n\n\nTopics covered will include: \n\n\n\n\nRNAseq quality control analysis\n\n\n\nMapping of short reads\n\n\n\nQuantification of gene expression\n\n\n\nExploratory data analysis\n\n\n\nDifferential gene expression\n\n\n\nGene set enrichment analysis\n\n\n\n\nMore details about the course can be found at the previous year webpage: RNAseq course 2023 \n\n\n\nThe course will follow similar structure and topics. \n\n\n\nNOTE: in March 2024\, the course will be a 5-day-course on-site in Uppsala. \n\n\n\nRegister here\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\n\nBasic knowledge in Linux and R\n\n\n\nYour own laptop with the following specs:At least 6 GB of RAM.Operating system Win10\, OS X or Linux\n\nAt least 30 GB of free storage\n\n\n\n\n\n\nDesirable: \n\n\n\n\nExperience working with NGS data analysis or completed the NBIS workshop “Introduction to Bioinformatics using NGS data”\n\n\n\nExperience working in R or completed the NBIS course “R Programming Foundations for Life Scientists”\n\n\n\n\nDue to our best practice 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\nCourse fee\n\n\n\nA course fee* of 3000 SEK for non-profit organisations will be invoiced to accepted participants. This includes lunches\, coffee\, snacks\, and one course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nImportant dates:\n\n\n\n\nApplication open: December 19\, 2023\n\n\n\nApplication deadline: February 19\, 2024\n\n\n\n\nResponsible teacher/s:Johan Reimegård\, Julie Lorent\, Nima Rafati \n\n\n\nContact information for questions regarding the courseedu.rnaseq@nbis.se
URL:https://www.scilifelab.se/event/rna-seq-data-analysis-2/
LOCATION:Uppsala University\, Uppsala\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240318T090000
DTEND;TZID=Europe/Stockholm:20240322T170000
DTSTAMP:20260408T234602
CREATED:20231214T083927Z
LAST-MODIFIED:20231214T083931Z
UID:10001069-1710752400-1711126800@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\, 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\n\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\nImportant dates\n\n\n\nApplication opens: 13-December-2023 \n\n\n\nApplication closes: 05-February-2024 \n\n\n\nConfirmation to accepted students: Week 6\, 2024 \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 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 3000 SEK. Please note that NBIS cannot invoice individuals. \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 outcome\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\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\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-online-4/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240321T080000
DTEND;TZID=Europe/Stockholm:20240322T170000
DTSTAMP:20260408T234602
CREATED:20240125T130718Z
LAST-MODIFIED:20240223T112954Z
UID:10001125-1711008000-1711126800@www.scilifelab.se
SUMMARY:Introductory Course in Organisational learning
DESCRIPTION:How do we build a collaborative and innovative workplace? \n\n\n\nIn the first offering of this two-day course in Organizational Learning\, learn how we can adapt and improve as an organization through gathering\, sharing\, and applying knowledge. This course goes beyond individual skill development to building organizational culture and structure. Through creating and utilizing organizational processes that foster collective learning and development\, we can achieve the workplace we want. \n\n\n\nThe lectures\, discussions\, and exercises of this course will teach foundational principles and theories of Organizational Learning\, including concepts on organizational knowledge\, knowledge management\, and workplace training.We will also give you practical tools and sustainable strategies you can apply beyond the course—such as how to enhance learning at all levels\, from the individual (micro level)\, to group/team (meso level) and organization (macro level). \n\n\n\nWe welcome managers\, coordinators\, and leaders from all career stages to learn how to build a workplace culture of continuous learning in a resource-friendly way using organizational knowledge and collective intelligence! \n\n\n\nRegistration Deadline\n\n\n\nThere is no deadline for application. Applications will be accepted on a rolling basis\, and applicants will be confirmed their enrollment within 5 business days.  \n\n\n\nRegistration\n\n\n\nTargeted level of the training event:\n\n\n\nIntroductory level \n\n\n\nTarget Audience:\n\n\n\nInfrastructure managers\, SciLifeLab affiliated group leaders\, and other staff with managerial roles. \n\n\n\nPrerequisites:\n\n\n\nNo prior knowledge of organisational learning\, management or individual learning is required\, but experience from management is beneficial.  \n\n\n\nLearning Outcomes: \n\n\n\nBy the end of this course\, participants should be able to: \n\n\n\n– explain key concepts in Organisational Learning\, and how these relate to culture\, leadership and organisational processes. \n\n\n\n– identify similarities and differences between individual learning\, group learning and organisational learning \n\n\n\n– identify workplace learning activities\, and recognize how these can be designed to create additional organisational value \n\n\n\n–  identify barriers and promoters for knowledge dissemination and organisational learning \n\n\n\nSyllabus:\n\n\n\nDay 1 (Thursday 21.3.2024):                                          \n\n\n\nModule 1 – Introduction to Organisational Learning \n\n\n\nModule 2 – Basic concepts of Individual learning \n\n\n\nDay 2 (Friday 22.3.2024):                        \n\n\n\nModule 3 – Concepts of Organisational Learning \n\n\n\nModule 4 – How we promote organisational learning \n\n\n\nSpring 2024: \n\n\n\nAfter the course an optional follow-up session will be held online. Exact date will be decided by the participants. \n\n\n\nCourse fee:\n\n\n\nThere is no course attendance fee. Please note that the course does not include any meals or accommodation. \n\n\n\nSelection criteria:\n\n\n\nDue to limited space\, the course accommodates a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria such as correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nImportant dates\n\n\n\nApplication open: Jan 25\, 2024 \n\n\n\nApplication closes: Feb 20\, 2024 \n\n\n\nConfirmation to applicants Feb 23\, 2024 \n\n\n\nFor further questions\, please contact us at traininghub@scilifelab.se.
URL:https://www.scilifelab.se/event/organisational-learning/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Training Hub":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240410T123000
DTEND;TZID=Europe/Stockholm:20240410T163000
DTSTAMP:20260408T234602
CREATED:20240125T103059Z
LAST-MODIFIED:20240223T112828Z
UID:10001122-1712752200-1712766600@www.scilifelab.se
SUMMARY:SciLifeLab Train the Trainer Course
DESCRIPTION:This course offers guidance\, ideas and tips for designing training/teaching\, development and delivery on training activities\, all based on research-driven educational principles. This course will cover the following topics: \n\n\n\n\nLearning principles and how they apply to training and teaching\n\n\n\nDesign and plan session\, course\, materials\n\n\n\nTeaching techniques to enhance learner engagement and participation\n\n\n\nAssessment and feedback in training and teaching\n\n\n\nCreating and maintaining engagement\n\n\n\n\nCourse dates are: April 10\, April 17\, April 24 and May 2\, held from 12:30-16:30 each day \n\n\n\nRegistration Deadline: \n\n\n\nThe registration deadline is March 22\, 2024.  \n\n\n\nConfirmation to applicants 27-March-2024 \n\n\n\nThis course will be delivered through Zoom. You can find a link to the course pages below. \n\n\n\nRegistration\n\n\n\nNotes: \n\n\n\n\nThe course is highly interactive and hence it is important that you\, as a participant\, actively contribute to all sessions and elements of the course.\n\n\n\nThere are no fees for this course.\n\n\n\n\nAll are welcome to participate. \n\n\n\nLearning Objectives and Learning Outcomes\n\n\n\nLearning Objectives \n\n\n\n\nTo get acquainted with Learning principles and how they apply to training\n\n\n\nTo be able to select and use training techniques that can help enhance learner engagement and participation\n\n\n\nTo learn how to use assessment and feedback in training\n\n\n\nTo learn about session\, course\, and materials design as well as strategies for making learning engaging\n\n\n\n\nLearning Outcomes \n\n\n\nBy the end of this course\, learners will be able to: \n\n\n\n\nName learning principles that a good teacher/instructor should have in mind\n\n\n\nDescribe at least three training techniques\, drawing on learning principles\n\n\n\nDesign a training session and a course\n\n\n\nDevelop assessment questionnaires\n\n\n\nEnumerate types of materials needed for each part of a training session or course\n\n\n\n\nDescribe strategies to promote engagement amongst learners \n\n\n\nTarget Audience \n\n\n\nThis course is directed towards anyone who is interested in becoming a trainer/instructor\, or improving your training skills. \n\n\n\nPrerequisites\n\n\n\nEntry requirements \n\n\n\nThis course is directed towards anyone who is interested in becoming a trainer/instructor\, or improving your training skills. If you have questions like the following ones\, this course may be very helpful to you. \n\n\n\n\nHow learning works?\n\n\n\nHow do I use learning principles and theories to improve my teaching/training?\n\n\n\nHow do I make my teaching/training more engaging and effective?\n\n\n\nHow should I adjust my teaching/training to different types of learners?\n\n\n\nHow do I ensure learning progress?\n\n\n\nHow can I assess whether my students are actually understanding my lessons? Are they actually learning?\n\n\n\nWhat is the best balance between theory and practice?\n\n\n\nHow can I best assess whether learning is occurring and/or has occurred?\n\n\n\nWhat works in a classroom and what doesn’t?\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: Priority will be given to applicants from SciLifeLab infrastructures\, institutes and organizations across the Nordic research community\, and to participants from Nordic ELIXIR nodes. \n\n\n\nSyllabus\n\n\n\nPlease see the course website\, which will be updated regularly\, for more information: https://scilifelab-training.github.io/train-the-trainer/2403/
URL:https://www.scilifelab.se/event/scilifelab-train-the-trainer-course/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="Training Hub":MAILTO:traininghub@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240415T080000
DTEND;TZID=Europe/Stockholm:20240416T170000
DTSTAMP:20260408T234602
CREATED:20240318T115849Z
LAST-MODIFIED:20240318T120120Z
UID:10001209-1713168000-1713286800@www.scilifelab.se
SUMMARY:A primer on cryo-EM data processing using cryoSPARC on BerzeLiUs
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of cryo-EM data processing using national supercomputing resources. \n\n\n\nApplication\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-03-18Application closes: 2024-04-07Confirmation to accepted students: 2024-04-08 \n\n\n\nCourse Leader and teachers: Tim Schulte \, Piotr Draczkowski \n\n\n\nIn case you miss information on any of the above dates\, please contact: Tim Schulte \, Piotr Draczkowski \n\n\n\nCourse fee\n\n\n\nThe course is free of charge. \n\n\n\nCourse content\n\n\n\nWhat is this about? \n\n\n\nHow to use Berzelius compute cluster for cryo-EM data processing. We will process the beta- galactosidase dataset\, known from the Relion tutorials\, but applying cryoSPARC on BerzeLiUs\, as implemented by the PReSTO team. \n\n\n\nThe main purpose of this training is to learn how to: \n\n\n\n● access and use BerzeLiUs● apply Presto\, especially cryoSPARC on BerzeLiUs to process cryo-EM data \n\n\n\nWho should apply?\n\n\n\nAnyone interested in processing cryo-EM data using national supercomputing resources\, especially BerzeLiUs cluster. This is a primer for data processing on Berzelius\, not an introduction to cryo-EM. We expect applicants to be familiar with the general concepts of cryo-EM and data processing. Participants need to have a computer to access Berzelius remotely. \n\n\n\nLearning outcomes\n\n\n\nUpon completion of this course\, you will be able to:’ \n\n\n\n● apply for the allocation of computational resources on BerzeLiUs cluster● set up and start your cryoSPARC instance on BerzeLiUs● submit jobs to the cluster using the predefined submission lines● manage the jobs● process cryo-EM data on BezleLIUs using a standard data processing pipeline in CryoSPARC \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● Basic knowledge of Linux● Ability to bring your own laptop● Set up an account in NAISS SUPR (supr.naiss.se) \n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n● Experience in processing cryo-EM data using any of the available software packages \n\n\n\nDue to limited space the course can accommodate a maximum of 15 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/a-primer-on-cryo-em-data-processing-using-cryosparc-on-berzelius/
LOCATION:Online event via Zoom
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240416T090000
DTEND;TZID=Europe/Stockholm:20240418T170000
DTSTAMP:20260408T234602
CREATED:20240103T100130Z
LAST-MODIFIED:20240103T100350Z
UID:10001098-1713258000-1713459600@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R
DESCRIPTION:A national course open for PhD students (prioritized)\, postdocs\, researchers and other employees within Swedish universities who are interested in learning to produce publication quality plots using different packages in R. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Markus Ringner\, Louella Vasquez\, Katja Kozjek \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: January 8\, 2024 \n\n\n\nApplication deadline: March 22\, 2024 \n\n\n\nConfirmation to accepted participants: March 25\, 2024 \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website (2023 version)\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThe fee for this on-site workshop is 2000 SEK to be paid by invoice to NBIS. Please note that NBIS cannot invoice individuals so we need your institutional invoicing address. The fee covers lunches\, coffee and a course dinner. Those who accept the spot and then do not attend without prior notification will also be invoiced. \n\n\n\nNote that travel and accommodation is not included in the fee and must be arranged by the participants. \n\n\n\n\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 teach how to produce 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 their data. \n\n\n\n\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 how to: \n\n\n\n\nformat the data necessary for ggplot\n\n\n\nmake bar-charts\, box-plots and others using ggplot\n\n\n\nmake PCA plots in ggplot\n\n\n\nuse R packages for heatmaps\n\n\n\nplot data on maps using R (optional)\n\n\n\nplot and handle phylogenetic trees in R (optional)\n\n\n\nmake interactive plots in R using Rshiny\n\n\n\nhost a Rshiny app in one of the available servers\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nBy the end of the course the participant will be able to: \n\n\n\n\nhandle data in R for visualizations\n\n\n\napply the grammar efficiently in ggplot to obtain the desired plot\n\n\n\ncombine different data and/or different plots that are of publication-grade\n\n\n\nwrite your own simple Rshiny app\n\n\n\ndeploy Rshiny apps in public servers. \n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete the plotting exercises: \n\n\n\n\nfamiliarity with using R and Rstudio\n\n\n\na computer with R and Rstudio installed\n\n\n\ninstallation of necessary R packages prior to the start of the course\n\n\n\n\n\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/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240422T080000
DTEND;TZID=Europe/Stockholm:20240426T170000
DTSTAMP:20260408T234602
CREATED:20240124T152112Z
LAST-MODIFIED:20240422T093632Z
UID:10001121-1713772800-1714150800@www.scilifelab.se
SUMMARY:TEM sample preparation practical course
DESCRIPTION:This is a practical course on sample preparation for TEM and includes: \n\n\n\n\nUltra-microtome sectioning\n\n\n\nChemical fixation\n\n\n\nPlastic embedding\n\n\n\nTEM imaging\n\n\n\nHigh-pressure freezing & freeze substitution\n\n\n\nImmunolabeling techniques (Immunogold\, CLEM)\n\n\n\nVolume EM (FIB-SEM & Tomography)\n\n\n\n\nParticipants will practice TEM sample preparation and TEM imaging with a sample from their own project. Lab space limits the number of participants to 8\, chosen by motivation and project aim. Write a short project description\, motivation for participating and what sample you would like to bring for the course. Fixation and plastic embedding take time\, therefore one test-sample should be brought to be prepared before the course\, and a new test-sample is brought for the first day. \n\n\n\nIn addition\, a small presentation about an EM-project idea of your own should be prepared and presented on the last day. \n\n\n\nParticipants should attend all theoretical and practical parts of the course to receive a certificate of 1\,5 hp. \n\n\n\nPre-requisite criterion: Basic EM course at UCEM or previous equal experiences with EM methods. \n\n\n\nTeachers: Sara Henriksson\, Agnieszka Ziolkowska\, Narin Mohamad and Linda Sandblad \n\n\n\nContact: linda.sandblad@umu.se \n\n\n\nApplication deadline: 27 March 2024. \n\n\n\nMore Information and registration
URL:https://www.scilifelab.se/event/tem-sample-preparation-practical-course/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/01/UCEM_logo_pos.png
ORGANIZER;CN="UCEM Ume%C3%A5":MAILTO:hussein.haggag@umu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240422T080000
DTEND;TZID=Europe/Stockholm:20240426T170000
DTSTAMP:20260408T234602
CREATED:20240131T120230Z
LAST-MODIFIED:20240314T093013Z
UID:10001134-1713772800-1714150800@www.scilifelab.se
SUMMARY:Introduction to Biostatistics and Machine Learning
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of biostatistical and machine learning skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts\, such as the commonly misinterpreted p-value. \n\n\n\nImportant dates\n\n\n\nApplication open: now \n\n\n\nApplication closes: 2024-03-24 \n\n\n\nConfirmation to accepted students:  2024-03-28 \n\n\n\nResponsible teachers:  Olga Dethlefsen\, Eva Freyhult \n\n\n\nIf you do not receive information according to the above dates\, please contact edu.ml-biostats@nbis.se \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\nCourse content\n\n\n\n\nProbability theory\n\n\n\nHypothesis testing and confidence intervals\n\n\n\nResampling\n\n\n\nLinear regression methods\n\n\n\nIntroduction to generalized linear models\n\n\n\nModel evaluation\n\n\n\nUnsupervised learning incl. clustering and dimension reduction methods\n\n\n\nSupervised learning incl. classification\n\n\n\n\nEducation\n\n\n\nIn this course we focus on an active learning approach. The course participants are expected to do some pre-course reading and exercises\, corresponding up to 40h studying. The education consists of teaching blocks alternating between lectures\, group discussions\, live coding sessions etc. \n\n\n\nEntry requirements\n\n\n\n\nBasic R programming skills (check your R skills by taking our self-assessment test)\n\n\n\nBYOL (bring your own laptop) with R and RStudio installed\n\n\n\nNo prior biostatistical knowledge is assumed\, only basic math skills (pre-course studying materials will be available upon course acceptance)\n\n\n\n\nThe 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\nRegistration
URL:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning-3/
LOCATION:BMC Trippelrummet\, Husargatan 3\, entrance C11\, Uppsala\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/01/course-image.png
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240422T080000
DTEND;TZID=Europe/Stockholm:20240426T170000
DTSTAMP:20260408T234602
CREATED:20240219T105136Z
LAST-MODIFIED:20240220T100128Z
UID:10001162-1713772800-1714150800@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research
DESCRIPTION:NBIS / ELIXIR-SE course open for PhD students\, postdocs\, group leaders and core facility staff at all Swedish universities interested in making their computational analysis more reproducible. \n\n\n\nCourse Website\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-02-19 \n\n\n\nApplication closes: 2024-03-18 \n\n\n\nConfirmation to accepted students: 2024-03-22 \n\n\n\nCourse Leader and teachers: \n\n\n\n\nJohn Sundh (CL)\n\n\n\nErik Fasterius (CL)\n\n\n\nEstelle Proux-Wéra\n\n\n\nLokeshwaran Manoharan\n\n\n\nTomas Larsson\n\n\n\nCormac Kinsella\n\n\n\nMahesh Binzer-Panchal\n\n\n\n\nIn case you miss information on any of the above dates\, please contact:  edu.trr@nbis.se \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/tea and snacks as well as a course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nThis course will introduce best practices in making research reproducible – from code tracking to software packaging and documentation – via short lectures and hands-on tutorials. \n\n\n\nTopics covered will include: \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\nUpon completion of this course\, you 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 Quarto and Jupyter\n\n\n\nPackage and distribute computational environments using Docker and Singularity\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 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\nDue to limited space the 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\nContact information: edu.trr@nbis.se
URL:https://www.scilifelab.se/event/nbis-elixir-se-tools-for-reproducible-research-2/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240423T080000
DTEND;TZID=Europe/Stockholm:20240425T170000
DTSTAMP:20260408T234602
CREATED:20231114T122916Z
LAST-MODIFIED:20231115T133031Z
UID:10001032-1713859200-1714064400@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National Bioinformatics Infrastructure Sweden (NBIS) gives a course in research data management practices. This workshop in Data Management is a unique event to provide an introduction to practices for better management of data for PhD students\, postdocs\, researchers\, and other employees within all Swedish universities. The workshop will introduce important aspects of research data management through a series of lectures\, demonstrations\, and hands-on computer exercises. The course is intended for researchers who want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication closes: 2024-03-22 \n\n\n\nInformation to accepted students will be sent: 2024-04-02 \n\n\n\nContact: edu.intro-dm@nbis.se  \n\n\n\n\n\n\n\nApplication\n\n\n\nWorkshop Website\n\n\n\n\n\n\n\n\n\n\n\nFormat & Content\n\n\n\nThis workshop runs on-site in Solna\, Stockholm. Teachers and teaching assistants will be present all week to help with exercises and questions. \n\n\n\nTopics covered will include: \n\n\n\n\nOpen Science and FAIR in practice\n\n\n\nOrganising data\, files and folders in research projects\n\n\n\nDescribing data with metadata\n\n\n\nPublishing data to public data repositories\n\n\n\nCleaning tabular data and metadata with OpenRefine\n\n\n\nWriting basic recipes for data analysis and visualisation with R\n\n\n\nVersioning data\, documents and scripts (e.g. by using Git & GitHub)\n\n\n\nWriting Data Management Plans\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show)\, you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. \n\n\n\n\n\n\n\nCredits & Certificate\n\n\n\nPlease note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating the topics covered and the duration of the workshop. \n\n\n\nDue to limitations in space and capacity\, the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria\, including correct entry information\, motivation to attend the course\, as well as gender and geographical balance. \n\n\n\nFor more detailed information about the workshop\, please visit the workshop website \n\n\n\n\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. The course organisers arrange a pre-course event approximately one week prior to the first-course day.
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-6/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240520T080000
DTEND;TZID=Europe/Stockholm:20240524T170000
DTSTAMP:20260408T234602
CREATED:20240219T094821Z
LAST-MODIFIED:20240515T124935Z
UID:10001161-1716192000-1716570000@www.scilifelab.se
SUMMARY:2nd CryoNET course on advanced single particle cryo-EM analysis
DESCRIPTION:CryoNet is a Nordic network in cryogenic electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryogenic electron microscopy as a strong pillar of Nordic life science research. \n\n\n\nThe core of the network is constituted by the cryo-EM facilities at University of Copenhagen\, Aarhus University\, Stockholm University and Umeå University. \n\n\n\nWe are happy to announce the 2nd CryoNET course on advanced single particle cryo-EM analysis that will take place in Stockholm on 20-24 May 2024. Aim of the course is to provide training in cryo-EM image processing including latest developments of the field. \n\n\n\nParticipants will receive hands-on training in state-of-the-art techniques for single particle cryo-EM image processing\, model building and validation from a range of international specialist guest lecturers. The course also includes theoretical talks and discussions on the use of cryo-EM to address difficult biological questions\, which can help the participants address their own research problems. New for this year is to include Micro-ED and basic processing of Micro-ED data. \n\n\n\nParticipation in the entire course is mandatory and an attendance certificate will be given at the end of the course. \n\n\n\nCourse Objectives\n\n\n\n\nTo provide training in state-of-the-art techniques for high resolution structure determination by cryo-EM\, including hands-on practical training in latest software suites for image processing\n\n\n\nDiscuss data collection strategies\n\n\n\nTraining in basic principles of structure determination using cryo-EM\n\n\n\nGet an introduction to Micro-ED and softwares used for processing of Micro-ED data\n\n\n\nDevelop problem solving skills through discussions and practical sessions in the presence of international experts in the field\n\n\n\nNetworking with experts\, software developers\, and researchers in cryo-EM and learn of not only the latest but also upcoming developments\n\n\n\n\n\n\n\n\nCourse fee covers \n\n\n\n\nAttendance in the course 20-24 May 2024\n\n\n\nLunches\, coffee and refreshments on the course dates\n\n\n\nCourse materials\n\n\n\nCertificate of attendance\n\n\n\nCourse dinner\n\n\n\n\nPlease note\, the registration fee does not cover hotel\, travel expenses\, breakfasts\, and dinners (expect the course dinner) \n\n\n\nCourse fee payment: The course fee of 2\,500 SEK should be paid either by bank transfer (latest 30th of April)\, or via invoice that has been sent out to those that have selected this option.  \n\n\n\nProgram\n\n\n\nProgram_2nd-CryoNET-course-20-24-may-2024_240515Download\n\n\n\nSupported by\n\n\n\n\nKnut & Alice Wallenberg Foundation\n\n\n\nNovo Nordisk Foundation\n\n\n\nThermo Fisher Scientific\n\n\n\nMiTeGen\n\n\n\n\nOrganising committee\n\n\n\n\nKarin Walldén\, Stockholm University\n\n\n\nMarta Carroni\, Stockholm University\n\n\n\nThomas Boesen\, Aarhus University\n\n\n\nJesper Lykkegaard Karlsen\, Aarhus University\n\n\n\nAndreas Bøggild\, Aarhus University\n\n\n\nTillmann Pape\, University of Copenhagen
URL:https://www.scilifelab.se/event/2nd-cryonet-course-on-advanced-single-particle-cryo-em-analysis/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/02/CryoEM-bild.png
END:VEVENT
END:VCALENDAR