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DTSTART;TZID=Europe/Stockholm:20240410T123000
DTEND;TZID=Europe/Stockholm:20240410T163000
DTSTAMP:20260506T235247
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:20260506T235247
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:20260506T235247
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:20260506T235247
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:20260506T235247
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:20260506T235247
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:20260506T235247
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
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