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DTSTART;TZID=Europe/Stockholm:20221010T090000
DTEND;TZID=Europe/Stockholm:20221014T170000
DTSTAMP:20260409T005624
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:20260409T005624
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:20260409T005624
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:20260409T005624
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
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