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DTSTART;TZID=Europe/Stockholm:20221010T090000
DTEND;TZID=Europe/Stockholm:20221014T170000
DTSTAMP:20260409T123419
CREATED:20220621T081729Z
LAST-MODIFIED:20220621T081841Z
UID:10000631-1665392400-1665766800@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\n\n\n\n\nVenue\n\n\n\nSciLifeLab Uppsala\, BMC\, Navet (Trippelrummet) \n\n\n\nUmeå University\, KBC building\, room KBG201 \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: June 21 \n\n\n\nApplication deadline: September 4 \n\n\n\nConfirmation to accepted participants: September 8 \n\n\n\n\n\n\n\nCourse fee\n\n\n\n A course fee* of 2000 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\n\n\nCourse website\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\n\n\n\n\n\nCourse description\n\n\n\n This 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\nCore concepts about Python syntax: Data types\, blocks and indentation\, variable scoping\, iteration\, functions\, methods and argumentsDifferent ways to control program flow using loops and conditional testsRegular expressions and pattern matchingWriting functions and best-practice ways of making them usableReading from and writing to filesCode packaging and Python librariesHow to work with biological data using external libraries.\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nDescribe and apply basic concepts in Python\, such as:LoopsIf/else statementsFunctionsReading/writing to filesBeing able to edit and run Python codeWrite file-processing Python programs that produce output to the terminal and/or external filesCreate stand-alone python programs to process biological dataKnow how to develop your skills in Python after the course (including debugging)\n\n\n\n\n\n\n\nEntry requirements\n\n\n\n The 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. Please 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/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20221011T080000
DTEND;TZID=Europe/Stockholm:20221013T170000
DTSTAMP:20260409T123419
CREATED:20220912T161617Z
LAST-MODIFIED:20220912T161619Z
UID:10000680-1665475200-1665680400@www.scilifelab.se
SUMMARY:Cryo-EM sample preparation and data collection course
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\nApplication deadlineApplication should be submitted before September 16\, 2022 \n\n\n\nRead more\n\n\n\nCourse organizersCamilla Holmlund and Michael Hall \n\n\n\nLocationUCEM and Chemical Biological Centre (KBC) BuildingUmeå UniversityLinnaeus väg 6 \n\n\n\nTeachers and course instructors \n\n\n\nLinda SandbladMichael HallLars-Anders CarlsonCamilla HolmlundAdditional teachers t.b.a\n\n\n\nSocial programA social program depending on the current corona restriction will be communicated to the participants after acceptance. \n\n\n\nCourse feeA course fee of 800 SEK\, including coffee and lunches\, will be invoiced to accepted participants after acceptance. \n\n\n\nCourse contentThis course will cover practical aspects of cryo-EM sample preparation and data acquisition.Topics covered: \n\n\n\nBasic theory of vitreous water\, how to handle a cryo sample and consequencesPlunge freezing methods\, tools and cryo-transferSample and instrument requirements for single particle and tomography methodsImage data acquisition\, concept of low dose and the cryo-specific workflowIntroduction to automatic data acqui­sition software\, EPU\, TomographyIntroduction to cryo-EM image processing methods\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 literatureHandouts and material online. \n\n\n\nEntry requirementsPriority 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 Participation 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-course/
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20221011T090000
DTEND;TZID=Europe/Stockholm:20221013T170000
DTSTAMP:20260409T123419
CREATED:20220621T074909Z
LAST-MODIFIED:20220831T075512Z
UID:10000630-1665478800-1665680400@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures 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. \n\n\n\nNote: We follow the recommendations and guidelines from Swedish authorities and Folkhälsomyndigheten. The course is designed to be an interactive face-to-face event. However\, we follow the situation carefully and will deliver the course online if needed. \n\n\n\nContact: edu.intro-dm@nbis.se \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  open now \n\n\n\nApplication closes:  2022-09-09 \n\n\n\nConfirmation to accepted students:  2022-09-13 \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\n1500 SEK paid by invoice to NBIS. This includes lunches\, coffee and snacks. Please note that NBIS cannot invoice individuals. \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 several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\n\n\n\n\nCourse content\n\n\n\nTopics covered will include \n\n\n\n• Open Science and FAIR in practice \n\n\n\n• Organising data\, files and folders in research projects \n\n\n\n• Versioning data\, documents and scripts with Git \n\n\n\n• Describing data with metadata \n\n\n\n• Cleaning tabular data and metadata with OpenRefine \n\n\n\n• Submitting data to public data repositories \n\n\n\n• Writing basic recipes for data analysis and visualisation with R \n\n\n\n\n\n\n\nLearning objectives \n\n\n\n• To get acquainted with\, and reflect upon\, the principles of Open Science and FAIR \n\n\n\n• To understand the importance of metadata\, and how it affects “FAIRness” \n\n\n\n• To learn how to organise files to make project work more efficient \n\n\n\n• To learn to clean up messy tabular data and metadata \n\n\n\n• To learn how to find\, and submit to\, relevant public repositories for data publication \n\n\n\n• To learn to apply simple version control practices on files \n\n\n\n• To learn to start using R to analyse data \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.
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-3/
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:20221024T090000
DTEND;TZID=Europe/Stockholm:20221028T170000
DTSTAMP:20260409T123419
CREATED:20220516T122403Z
LAST-MODIFIED:20220516T122509Z
UID:10000607-1666602000-1666976400@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: 2022-09-23 \n\n\n\nConfirmation to accepted students: 2022-09-30 \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\nCOURSE WEBSITE\n\n\n\nAPPLICATION\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\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\nData processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;ChIP-seq: peak calling\, peak independent / dependent quality metrics\, differential binding analysis; DNA motif enrichment;ATAC-seq: peak calling\, peak independent / dependent quality metrics\, differential accessibility analysis;Quantitative ChIP-seq using spike-ins;CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;Functional analysis\, including finding nearest genes and custom features\, GO terms and Reactome pathways enrichment;Basic multi-omics exploration and integration;Visualisations of epigenomics datasets;Introduction to analysis of single cell functional genomics data (scATAC-seq);Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq\, ChIP-seq\, ATAC-seq.\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the workshop and complete the computer exercises: \n\n\n\nBYOL\, bring your own laptop with R and RStudio installed;Basic knowledge in Linux;Basic programming experience\, preferably in R.\n\n\n\n\n\n\n\nDesirable \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;Previous experience with NGS data analyses;Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.\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-2/
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:20221114T080000
DTEND;TZID=Europe/Stockholm:20221118T170000
DTSTAMP:20260409T123419
CREATED:20221031T165001Z
LAST-MODIFIED:20221031T165003Z
UID:10000725-1668412800-1668790800@www.scilifelab.se
SUMMARY:TEM sample preparation practical course part II
DESCRIPTION:TEM sample preparation course – Chemical fixation\, high pressure freezing\, plastic embedding and staining methods including practice on ultra-microtome sectioning\, TEM imaging and an introduction to CLEM (Correlative Light and Electron Microscopy)\, FIB-SEM (Focused Ion Beam) and electron tomography. \n\n\n\nRead more\n\n\n\nPre-requisite criterion: Basic EM course at UCEM or equal previous experiences of EM methods. \n\n\n\nParticipants will practice EM sample preparation and EM imaging with one sample from their own project. Our lab space limits the number of participants to 8 so we will select participants based on your motivation and how your project aims fits to the course content. Please write a short project description\, a motivation for participating and what sample you would like to process during the course. \n\n\n\nPlease\, look at the program and the methods that are covered in this course. Make sure you have time to participate full days and the entire week. Since the fixation and plastic embedding takes time\, you should bring one test-sample to Agnieszka on Monday 7 of November\, and a new test-sample on the first course day\, 14 November. \n\n\n\nPreliminary Program:The course preliminary program will be announced here once it is organised. \n\n\n\nLocation:Lectures at KBC and laboratory demonstrations at UCEM – Level 5\, 6 + new EM building (Level 1)\, Umeå University. \n\n\n\nParticipants:8 persons. Open to all research students\, postdocs and staff. \n\n\n\nInstructors: \n\n\n\nSara Henriksson – EM research engineerGayathri Vegesna – EM research engineerAgnieszka Ziolkowska – EM research engineerCamilla Holmlund – EM research engineerLinda Sandblad – EM facility director\n\n\n\nDuration:5 days \n\n\n\nBreaks/Refreshments:Coffee\, cookies and fruit will be served. \n\n\n\nCosts:No course fee\, but full attendance is required! \n\n\n\nCredits:Students that attend all theoretical and practical parts of the course\, will receive a certificate for 1\,5 hp.
URL:https://www.scilifelab.se/event/tem-sample-preparation-practical-course-part-ii/
LOCATION:Kemiskt Biologiskt Centrum\, Umeå University\, Linnaeus väg 6\, Umeå\, 90736
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20221121T090000
DTEND;TZID=Europe/Stockholm:20221125T153000
DTSTAMP:20260409T123419
CREATED:20220906T074137Z
LAST-MODIFIED:20220907T061609Z
UID:10000670-1669021200-1669390200@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
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: John Sundh\, Erik Fasterius \n\n\n\nContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse webpage\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Sep 5\, 2022 \n\n\n\nApplication deadline: Oct 21\, 2022 \n\n\n\nConfirmation to accepted participants: Oct 28\, 2022 \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 2\,000 SEK. \n\n\n\n*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\nGood practices for data analysisVersion control and collaborative code developmentPackage and environment managementWorkflow managementDocumentation and reportingContainerized computational environments\n\n\n\n\n\n\n\nLearning outcomes \n\n\n\nBy the end of the course the student will be able to: \n\n\n\nOrganize and structure computational projectsTrack changes and collaborate on code using GitInstall packages and manage software environments using CondaStructure computational steps into workflows with Snakemake and NextflowCreate automated reports and document their analyses with RMarkdown and JupyterPackage and distribute computational environments using Docker and Singularity\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\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)A computer with a webcamYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseSome knowledge in R and/or python is beneficial but not strictly required\n\n\n\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-online-2/
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:20221205T080000
DTEND;TZID=Europe/Stockholm:20221208T170000
DTSTAMP:20260409T123419
CREATED:20221031T164615Z
LAST-MODIFIED:20221031T164743Z
UID:10000724-1670227200-1670518800@www.scilifelab.se
SUMMARY:Workshop on Advanced Correlative Light and Electron Microscopy (CLEM) methods
DESCRIPTION:This 4-day workshop aims to highlight the advanced correlative light and electron microscopy (CLEM) techniques. Participants will learn the latest workflows on how to correlate fluorescence microscopy images with high resolution EM images obtained from state-of-the-art equipment. \n\n\n\nRead more\n\n\n\nWorkshop Content:The workshop includes both theory lectures and practical sessions on In-resin preserved florescence for CLEM\, Tokuyasu ultramicrotome sectioning combined with staining techniques on sections\, Cryo-CLEM and cryo-FIB milling\, as well as opportunities to discuss specific research projects and receive practical advice. Technical challenges and new ideas will be discussed\, and the participants are welcome to contribute with their experiences.  \n\n\n\nTarget Audience:This workshop is supported by the Nordic EMBL partnership for Molecular Medicine and welcomes applications from its members and other institutions. Participants are required to have practical experience in both light and electron microscopy. Due to limited number of places\, registration is based on a selection process. Selected lectures will be open to a larger range of participants and can be registered for under a ‘lecture only’ registration.Certificate/Credits:A course certificate will be provided to successful participants and a recommendation for 1\,5 ECTS.
URL:https://www.scilifelab.se/event/workshop-on-advanced-correlative-light-and-electron-microscopy-clem-methods/
LOCATION:Kemiskt Biologiskt Centrum\, Umeå University\, Linnaeus väg 6\, Umeå\, 90736
CATEGORIES:Course
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230130T080000
DTEND;TZID=Europe/Stockholm:20230203T140000
DTSTAMP:20260409T123419
CREATED:20221130T151251Z
LAST-MODIFIED:20230124T084743Z
UID:10000740-1675065600-1675432800@www.scilifelab.se
SUMMARY:Single cell RNAseq data analysis
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data. The total course duration is 5 days\, including the lectures and practical exercises that will be held on site in Stockholm. \n\n\n\nApplication\n\n\n\nApplication open: 2022-11-25 \n\n\n\nApplication deadline: 2022-12-21 \n\n\n\napplication form\n\n\n\nCourse Leaders\n\n\n\nPaulo Czarnewski \n\n\n\nÅsa Björklund \n\n\n\nContact: edu.sc@nbis.se \n\n\n\nCourse fee\n\n\n\nThis workshop has a fee of 2000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks\, all lunches and 1 course dinner. \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\nAnalysis of spatial transcriptomics datasets\n\n\n\nComparison of different analysis pipelines such as Seurat\, Scran and Scanpy\n\n\n\n\nWho can apply?\n\n\n\nThis is a national course. The course is open for PhD students\, postdocs\, group leaders and core facility staff within all Swedish universities. Even if we do accept application from other countries\, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. \n\n\n\nPractical exercises will be performed using either R or Python\, so we only accept students that fulfil the entry requirements below. \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\nDue to limited space the course 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 course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/single-cell-rnaseq-data-analysis/
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:20230206T090000
DTEND;TZID=Europe/Stockholm:20230210T170000
DTSTAMP:20260409T123419
CREATED:20221124T091335Z
LAST-MODIFIED:20221214T103757Z
UID:10000738-1675674000-1676048400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data - Lund\, Umeå and Uppsala
DESCRIPTION:This intense one-week workshop provides an introduction to the analysis of next generation sequencing data. The workshop is open to PhD students\, post-docs\, and other researchers affiliated to Swedish academia and healthcare. It is organised by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: 21-Nov-2022Application closes: 31-Dec-2022Information to accepted students will be sent:  Week 2\, 2023 \n\n\n\n\n\n\n\nVenues\n\n\n\nThis workshop runs in parallel on-site in Uppsala\, Umeå and Lund. Lectures will be streamed online from our Uppsala site (mainly) to the other classrooms. Several teaching assistants will be present in the Umeå\, Lund and Uppsala classrooms all week to help with exercises and questions. When registering you will be asked to select a preferred site. \n\n\n\nUppsalaTrippelrummet (E10:1307-1309)Entrance C11Biomedical Centre (BMC) / SciLifeLab / Uppsala UniversityHusargatan 3752 37 Uppsala \n\n\n\nUmeåUB341Universitetsbibioteket plan 3Umeå University901 87 Umeå \n\n\n\nLundSölvegatan 35Lund University223 62 Lund \n\n\n\n\n\n\n\nFor more detailed information about workshop syllabus\, learning outcomes and entry requirements\, please visit the workshop website. \n\n\n\nwebsite & Application\n\n\n\n\n\n\n\nContact\n\n\n\nEmail: edu.intro-ngsMalin Larsson\, Martin Dahlö\, Roy Francis \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\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\nLectures 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\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. 
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-2/
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230208T090000
DTEND;TZID=Europe/Stockholm:20230210T170000
DTSTAMP:20260409T123419
CREATED:20221214T102444Z
LAST-MODIFIED:20221214T102750Z
UID:10000751-1675846800-1676048400@www.scilifelab.se
SUMMARY:Omics Integration and Systems Biology - Online
DESCRIPTION:The National Bioinformatics Infrastructure Sweden (NBIS) is pleased to announce the workshop in Omics Integration and Systems Biology. This workshop is open for PhD students\, postdocs\, group leaders and core facility staff from Swedish academic institutions looking for an introduction to multi-omics data analysis and integration of biological data. This course will include lectures and hands-on exercises from NBIS / Scilifelab experts from Stockholm\, Lund and Gothenburg. \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\nImportant dates\n\n\n\n\nApplication opens: 15 December 2022\n\n\n\nApplication closes: 25 January 2023\n\n\n\nConfirmation to accepted applicants: 1 February 2023\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 2000 SEK. * Please note that NBIS cannot invoice individuals. \n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this course is to provide an integrated view of data-driven hypothesis generation through machine learning integration methods\, biological graph / network analysis and genome-scale metabolic models. A general description of different methods for analyzing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods and pitfalls in their integration. The techniques will be discussed in terms of their rationale and applicability. The course will also include hands-on sessions and seminars by invited speakers.Some of the covered topics include: \n\n\n\n\nData pre-processing and cleaning prior to integration;\n\n\n\nApplication of machine learning for multi-omics analysis including deep learning;\n\n\n\nMulti-omics integration\, clustering and dimensionality reduction;\n\n\n\nBiological network inference\, community and topology analysis and visualization;\n\n\n\nCondition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic\, proteomic\, metabolomic and fluxomig data;\n\n\n\nIdentification of key biological functions and pathways;\n\n\n\nIdentification of potential biomarkers and targetable genes through modeling and biological network analysis;\n\n\n\nApplication of network approaches in meta-analyses;\n\n\n\nSimilarity network fusion and matrix factorization techniques;\n\n\n\nIntegrated data visualization techniques\n\n\n\n\nFurther details about the course content may be found on the course website. \n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThis course is open for PhD students\, postdocs\, group leaders and core facility staff from Swedish academic institutions. Please note that NBIS training events do not provide any formal university credits. 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. \n\n\n\nPractical exercises can be performed using R or Python\, so we only accept students with previous experience in one of those programming languages. We will not discuss how to process specific omics\, and the students are referred to other NBIS courses for this matter. \n\n\n\nRequired \n\n\n\n\nBasic knowledge in R or Python;\n\n\n\nBasic understanding of frequentist statistics;\n\n\n\nA computer with a web camera\, Zoom\, and permissions for installing software.\n\n\n\n\nDesired \n\n\n\n\nExperience with analysis of NGS and other omic data;\n\n\n\nCompleting NBIS courses “Introduction to Bioinformatics using NGS data” and “Introduction to biostatistics and machine learning”\n\n\n\nBasic conda and git knowledge\n\n\n\n\nThis workshop can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria including entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nContact information\n\n\n\nFor questions about this workshop please contact: edu.omics-integration@nbis.se
URL:https://www.scilifelab.se/event/omics-integration-and-systems-biology-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:20230214T120000
DTEND;TZID=Europe/Stockholm:20230214T130000
DTSTAMP:20260409T123419
CREATED:20230120T101420Z
LAST-MODIFIED:20230207T103736Z
UID:10000793-1676376000-1676379600@www.scilifelab.se
SUMMARY:FunCoup network analysis workshop
DESCRIPTION:Network biology is a new paradigm to understand the complex interactions of the molecules in an organism using an integrative and systems approach. This workshop is intended for scientists interested in learning more about and applying network analysis in their research. We will describe and demonstrate the comprehensive network database FunCoup (https://funcoup.sbc.su.se/) and show how it can be used to answer various research questions at the systems biology level.  \n\n\n\n\n\n\n\n \n\n\n\nPROGRAM: \n\n\n\n1. Introduction to FunCoup and its unique features for analyzing functional coupling between genes/proteins\, as well as accompanying analysis tools such as PathBIX and MaxLink. \n\n\n\n2. Demonstration of FunCoup and accompanying tools\, as well as programmatic usage of FunCoup in an R notebook. \n\n\n\n\n\nRegistration\n\n\n\nLink to zoom
URL:https://www.scilifelab.se/event/funcoup-network-analysis-workshop/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230313T080000
DTEND;TZID=Europe/Stockholm:20230316T170000
DTSTAMP:20260409T123419
CREATED:20221212T141504Z
LAST-MODIFIED:20221212T142110Z
UID:10000747-1678694400-1678986000@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\nImportant dates\n\n\n\nApplication open: December 15\, 2022  \n\n\n\nApplication deadline: February 12\, 2023 \n\n\n\nResponsible teacher/s\n\n\n\nJohan Reimegård\, Julie Lorent\, Nima Rafati \n\n\n\nContact information for questions regarding the course\n\n\n\nedu.rnaseq@nbis.se \n\n\n\nCourse fee\n\n\n\nA course fee* of 1800 SEK will be invoiced to accepted participants. This includes lunches\, coffee\, snacks\, and one course dinner. *Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\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\n\n\n\n\nMore details about the course can be found at: \n\n\n\nThe previous year website\n\n\n\n\n\n\n\nThe course will follow similar structure and topics. NOTE: In March 2023\, the course will be a 4-day-course on-site in Uppsala. \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: \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nAt least 6 GB of RAM. \n\n\n\n\n\nOperating system Win10\, OS X or Linux \n\n\n\n\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\n\n\n\n\nApplication
URL:https://www.scilifelab.se/event/rna-seq-data-analysis/
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:20230320T090000
DTEND;TZID=Europe/Stockholm:20230324T170000
DTSTAMP:20260409T123419
CREATED:20221026T132922Z
LAST-MODIFIED:20230306T114543Z
UID:10000723-1679302800-1679677200@www.scilifelab.se
SUMMARY:NBIS workshop in Neural Nets and Deep Learning
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of Neural networks and Deep Learning skills within all Swedish universities. \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: 2022-10-25 \n\n\n\nApplication closes: 2023-02-10 \n\n\n\nConfirmation to accepted students:  2023-02-17 \n\n\n\nResponsible teachers:  Claudio Mirabello\, Christophe Avenel \n\n\n\nIf you do not receive information according to the above dates please contact: edu.neural-nets-deep-learning@nbis.se \n\n\n\nCourse webpage\n\n\n\nApplication\n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 2200 SEK will be invoiced to accepted participants. This 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\nThis course will give an introduction to the concept of Neural Networks (NN) and Deep Learning. \n\n\n\nTopics covered will include: \n\n\n\n\nNN building blocks\, including concepts such as neurons\, activation functions\, loss functions\, gradient descent and back-propagation\n\n\n\nConvolutional Neural Networks\n\n\n\nRecursive Neural Networks\n\n\n\nAutoencoders\n\n\n\nBest practices when designing NNs\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\nDistinguish the concepts of “Artificial Intelligence”\, “Machine Learning”\, “Neural Networks”\, “Deep Learning”\n\n\n\nDistinguish between different types of learning (e.g. supervised\, unsupervised\, reinforcement) and recognise which applies to their own problem\n\n\n\nDistinguish between linear and non-linear approaches and recognise which is best suited for application to their own problem\n\n\n\nDescribe what a feed-forward neural network (FFNN) is\, along with its components (neurons\, layers\, weights\, bias\, activation functions\, cost functions)\n\n\n\nExplain how training of a FFNN works from a mathematical point of view (gradient descent\, learning rate\, backpropagation)\n\n\n\nExecute with pen and paper a few steps of training of a very simple FFNN model\n\n\n\nTell the difference between a shallow and a deep network\n\n\n\nExplain broadly how different NN architectures are wired and how they work\n\n\n\nImplement and apply the most appropriate architecture to a given problem/dataset\n\n\n\nAnalyze training curves and prediction outputs to evaluate if the training has been successful\n\n\n\nDebug possible issues with the training and suggest changes to fix them\n\n\n\nExplain the difference between training\, validation and testing\n\n\n\nDefine what overfitting is from a mathematical point of view\, and what issues it causes\n\n\n\nIdentify what constitutes good practices of dataset design and how to avoid introducing information leakage or other biases when building their own datasets\n\n\n\n\n\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\nFamiliarity with Unix/Linux\n\n\n\nAbility to bring your own laptop with Python and Jupyter Notebooks  installed for the practical exercises\n\n\n\nProgramming/scripting experience in Python (e.g. having attended the NBIS workshop in basic Python or equivalent)\n\n\n\nBasic experience of statistics and mathematics (e.g. having attended the NBIS workshop Introduction to Biostatistics and Machine Learning or equivalent)\n\n\n\n\nDesirable: \n\n\n\n\nYou have experience of working with Jupyter Notebooks\n\n\n\nYou have a necessity  to work with large datasets (e.g. thousands of samples)\n\n\n\n\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 several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/nbis-workshop-in-neural-nets-and-deep-learning-2/
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:20230327T090000
DTEND;TZID=Europe/Stockholm:20230329T170000
DTSTAMP:20260409T123419
CREATED:20230202T135124Z
LAST-MODIFIED:20230203T094025Z
UID:10000802-1679907600-1680109200@www.scilifelab.se
SUMMARY:Regional Mass Spectrometry Imaging Spring Workshop
DESCRIPTION:The scientific program will aim to reflect cutting edge innovations and current developments in mass spectrometry imaging (MSI)\, alongside new applications in various areas. The goal for this workshop is to promote and educate academic\, industry and government scientists on the latest applications and innovations in MSI applied to biomedical\, biological and data science research areas. \n\n\n\nA three-day scientific agenda with oral presentations\, workshop discussions\, and poster presentations covering the latest developments and applications of MSI by leading and upcoming scientists from academic\, government\, and industry labs \n\n\n\n\n\n\n\nWebsite\, program & Registration\n\n\n\n\n\n\n\nImportant dates\n\n\n\nFebruary 10\, 2023              Deadline for regular fee and abstracts submission \n\n\n\n\n\n\n\nOrganizers & Contacts for questions\n\n\n\nPer Andrén\, Spatial Mass Spectrometry\, SciLifeLab\, per.andren@farmbio.uu.se \n\n\n\nJeanette Jansson\, Apotekarsocieteten\, jeanette.jansson@lakemedelsakademin.se
URL:https://www.scilifelab.se/event/regional-mass-spectrometry-imaging-spring-workshop/
LOCATION:Uppsala Konsert & Kongress\, Vaksala torg 1\, Uppsala\, 75331\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/02/Mass-Spectrometry-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230404T080000
DTEND;TZID=Europe/Stockholm:20230509T170000
DTSTAMP:20260409T123419
CREATED:20230307T080222Z
LAST-MODIFIED:20230307T091417Z
UID:10000828-1680595200-1683651600@www.scilifelab.se
SUMMARY:Digital image analysis for scientific applications
DESCRIPTION:Language of instruction: EnglishCourse period: 2023-04-11– 2023-05-09Course structure: The course will be hybrid on site and via zoom to facilitate remote participation. For computer exercises we encourage on-site participation for best possible support\, but will do our best to also support those participating remotely. \n\n\n\nRECOMMENDED PREREQUISITES\n\n\n\nThe target group is PhD students from all subjects where digital image analysis (IA)  is used as a research tool. No previous experience in IA is required from the course participants\, but an interest in its potential as a tool in their own research is important. The course can be followed with a basic knowledge of mathematics (corresponding to upper‐ secondary level entry requirements) and basic computer skills. \n\n\n\nLEARNING OUTCOMES\n\n\n\n\nexplain fundamental notions of IA\, such as digitization\, image enhancement\, segmentation\, and feature extraction and classification;\n\n\n\ncritically evaluate several different methods for image segmentation\, compression\, distance computation\, frequency analysis\, etc.\n\n\n\nuse software to apply and evaluate algorithms for solving image analysis problems;\n\n\n\nanalyze and plan the steps necessary to solve a realistic image analysis problem;\n\n\n\ngive examples of applications in research and industry where image analysis is used.\n\n\n\n\nLEARNING OUTCOMES FOR DOCTORAL DEGREE \n\n\n\nThe course participants will practice their ability to perform scientific analyses\, find and test appropriate IA methods\, and present and discuss their scientific results. \n\n\n\nCOURSE CONTENTS\n\n\n\nThe focus of the course is on reaching a broad understanding of IA and a basic understanding of the theory and algorithms behind the IA methods. The course starts with basic IA methods and computer exercises\, including IA research methodology and IA research ethics. Modern techniques based on Artificial Intelligence will also be discussed in relation to the classical approaches.  \n\n\n\nINSTRUCTION\n\n\n\nThe pedagogical approach will combine traditional lectures\, examples of real life applications and hands-on exercises. We also use a flipped classroom approach based on our pre-recorded course material which enables participants to prepare for discussions and exercises. \n\n\n\nASSESSMENT\n\n\n\nThe examination will be divided into two parts: \n\n\n\n\ncompleted four computer exercises\, which enable the course participants to both get familiar with the interfaces of common software and to solve realistic image processing problems\,\n\n\n\na written exam\n\n\n\n\nCompleted exercises and passing written exam gives 5hp.  \n\n\n\nCOURSE EXAMINER\n\n\n\nCarolina Wählby\, carolina.wahlby@it.uu.se together with other seniors involved in the BioImage Informatics Unit of SciLifeLab (https://www.scilifelab.se/units/bioimage-informatics/)\, the Image analysis node of the National Microscopy Infrastructure (http://www.nmisweden.se/)\, and the Centre for Image Analysis (https://www.cb.uu.se/) hosted at the Dept. of Information Technology. \n\n\n\nDEPARTMENT WITH MAIN RESPONSIBILITY\n\n\n\nDept. of Information Technology \n\n\n\nCONTACT PERSON/S \n\n\n\nCarolina Wählby\, carolina.wahlby@it.uu.se \n\n\n\nAPPLICATION\n\n\n\nSubmit the application for admission to: carolina.wahlby@it.uu.seSubmit the application not later than: March 25\, 2023
URL:https://www.scilifelab.se/event/digital-image-analysis-for-scientific-applications/
LOCATION:Uppsala University\, Uppsala\, Sweden
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/03/Course.jpg
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230417T090000
DTEND;TZID=Europe/Stockholm:20230419T170000
DTSTAMP:20260409T123419
CREATED:20230223T124619Z
LAST-MODIFIED:20230223T125220Z
UID:10000819-1681722000-1681923600@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R - Lund
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\n \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Markus Ringner\, Juliana Assis   \n\n\n\nContact information: edu.plotting.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\nImportant dates\n\n\n\nApplication open: February 23\, 2023 \n\n\n\nApplication deadline: March 31\, 2023 \n\n\n\nConfirmation to accepted participants: April 3\, 2023 \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\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-lund-3/
LOCATION:Retina D227\, Biologihuset\, Sölvegatan 35\, Lund\, 223 62
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230418T090000
DTEND;TZID=Europe/Stockholm:20230420T170000
DTSTAMP:20260409T123419
CREATED:20230119T131036Z
LAST-MODIFIED:20230314T102233Z
UID:10000791-1681808400-1682010000@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures 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. \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  open now \n\n\n\nApplication closes:  2023-03-28 \n\n\n\nConfirmation to accepted students:  2023-03-17 and 2023-03-31 \n\n\n\nContact: edu.intro-dm@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\nCourse fee\n\n\n\n1500 SEK paid by invoice to NBIS. This includes lunches\, coffee and snacks. Please note that NBIS cannot invoice individuals. \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 several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\n\n\n\n\nCourse content\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\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.
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-4/
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:20230424T090000
DTEND;TZID=Europe/Stockholm:20230428T153000
DTSTAMP:20260409T123419
CREATED:20230223T130931Z
LAST-MODIFIED:20230223T131154Z
UID:10000820-1682326800-1682695800@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
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\nResponsible teachers: Erik Fasterius\, John Sundh \n\n\n\nContact information: edu.trr@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\nImportant dates\n\n\n\nApplication open: Feb 27\, 2023 \n\n\n\nApplication deadline: Mar 31\, 2023 \n\n\n\nConfirmation to accepted participants: Apr 7\, 2023 \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 2\,000 SEK.*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\n\n\n\n\nLearning outcomesBy 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\nA computer with a webcam\n\n\n\nYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the course\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-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:20230424T090000
DTEND;TZID=Europe/Stockholm:20230428T170000
DTSTAMP:20260409T123419
CREATED:20230118T132842Z
LAST-MODIFIED:20230118T133136Z
UID:10000790-1682326800-1682701200@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\n \n\n\n\nImportant dates\n\n\n\nApplication open: now \n\n\n\nApplication closes: 2023-02-24 \n\n\n\nConfirmation to accepted students:  2023-03-10 \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 olga.dethlefsen@nbis.se\, eva.freyhult@nbis.se \n\n\n\n\n\n\n\n\n\nLink to Application\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\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\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\n\n\n\n\nEntry requirements\n\n\n\n\nBasic R programming skills (check your 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\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.
URL:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning-2/
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:20230508T090000
DTEND;TZID=Europe/Stockholm:20230512T170000
DTSTAMP:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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:20260409T123419
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
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