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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210929T090000
DTEND;TZID=Europe/Stockholm:20211001T130000
DTSTAMP:20260413T205221
CREATED:20210615T081112Z
LAST-MODIFIED:20210615T090743Z
UID:10000401-1632906000-1633093200@www.scilifelab.se
SUMMARY:Snakemake BYOC (bring-your-own-code) workshop (ONLINE)
DESCRIPTION:National workshop open for PhD students (prioritized)\, postdocs\, researchers and others from all Swedish universities who have previously participated in the NBIS Tools for reproducible research course or with demonstrated experience in writing Snakemake workflows. \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nCourse application\n\n\n\n\n\n\n\n\nImportant dates \n\n\n\nApplication opens:  June 15 \n\n\n\nApplication closes: August 31 \n\n\n\nConfirmation to accepted students:  September 3 \n\n\n\nResponsible teachers:  Verena Kutschera\, John Sundh\, Per Unneberg \n\n\n\nContact information: edu.byoc-snakemake@nbis.se \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 1\,700 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nWorkshop content \n\n\n\nAs data analysis projects grow and change over time\, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up\, perform and monitor defined sequences of computational tasks (“workflows”)\, thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. \n\n\n\nThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. \n\n\n\nThis Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \n\n\n\nLearning outcomes \n\n\n\nAfter participation in the BYOC workshop\, participants will: \n\n\n\nBe able to create Snakemake workflows for bioinformatics data analysisDemonstrate knowledge of the structure and syntax of different types of Snakemake workflowsDemonstrate knowledge of advanced features of the Snakemake workflow language\n\n\n\n\n\n\n\nEntry requirements \n\n\n\nPrevious participation in the NBIS Tools for reproducible research workshop. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflowsYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improveA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required). You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the workshop.\n\n\n\nThe workshop can accommodate a maximum of 16 participants. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.
URL:https://www.scilifelab.se/event/snakemake-byoc-bring-your-own-code-workshop-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211004T080000
DTEND;TZID=Europe/Stockholm:20211008T170000
DTSTAMP:20260413T205221
CREATED:20210603T125859Z
LAST-MODIFIED:20210603T130143Z
UID:10000397-1633334400-1633712400@www.scilifelab.se
SUMMARY:Introduction to biostatistics and machine learning - Online
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts\, such as the commonly misinterpreted p-value. \n\n\n\nImportant date \n\n\n\nApplication open: nowApplication closes: 2021-08-21Confirmation to accepted students:  2021-09-01Responsible 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\nCourse website\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\nCourse content \n\n\n\nProbability theoryHypothesis testing and confidence intervalsResamplingLinear regression methodsIntroduction to generalized linear modelsModel evaluationUnsupervised learning incl. clustering and dimension reduction methodsSupervised learning incl. classification\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 mini-lectures\, group discussions\, live coding sessions etc. \n\n\n\nEntry requirements \n\n\n\nBasic R programming skillsBYOL (bring your own laptop) with R and RStudio installedNo prior biostatistical knowledge is assumed\n\n\n\nThe course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\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. \n\n\n\n*Please note that NBIS cannot invoice individuals
URL:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211006T000100
DTEND;TZID=Europe/Stockholm:20211006T230000
DTSTAMP:20260413T205221
CREATED:20210914T123507Z
LAST-MODIFIED:20211006T084940Z
UID:10000446-1633478460-1633561200@www.scilifelab.se
SUMMARY:Application Open: Publishing workshop for junior researchers
DESCRIPTION:Applications are open to take part in this 3-part workshop series by Science and SciLifeLab for early career researchers (PhD students and postdocs) in SciLifeLab affiliated groups.  \n\n\n\nWorkshop leaders: \n\n\n\nValda Vinson (Editor\, Science Magazine)Sacha Vignieri (Deputy Editor for research\, Science Magazine)\n\n\n\nThis series is limited to a maximum 30 participants. Participants will be selected after applications close\, and selected participants will be notified shortly thereafter. The workshop is free of charge. \n\n\n\nRegistered participants must attend all three sessions of the workshop. The topics covered all relate to publishing\, in particular: “Before you submit”\, “Life of the paper”\, and “the publishing landscape”. \n\n\n\nWorkshop 1 – Thursday\, 4th of November\, 16:00-17:30 CETWorkshop 2 – Thursday\, 11th of November\, 16:00-17:30 CETWorkshop 3 – Thursday\, 18th of November\, 16-17:30 CET\n\n\n\nDeadline for application: October 6\, 2021. Selected participants will be notified shortly thereafter. \n\n\n\napply here\n\n\n\nPlease note that this workshop series is only open to SciLifeLab affiliated groups.  \n\n\n\n\n\n\n\nContent\n\n\n\n\n\nBefore you submit\n\n\n\n\n\nLife of the paper\n\n\n\n\n\nThe publishing landscape\n\n\n\n\n\n\n\nPart A \n\n\n\nQuick background      Authorship      Picking a journal       Planning ahead  \n\n\n\n\n\nPart A \n\n\n\nCover Letter     Title/Abstract     Process at Science\n\n\n\n\n\nPart A – Within Science \n\n\n\nWhat happens after acceptance     Promoting your paper\n\n\n\n\n\n\n\nPart B \n\n\n\nStructure your paper Dos and Don’ts Data presentation/visualization/statistics Data accessibility\n\n\n\n\n\nPart B \n\n\n\nReview process     Writing a review     Responding to reviews\n\n\n\n\n\nPart B – More Broadly \n\n\n\nTowards reproducibilityOpen access and preprintsMeasuring Impact\n\n\n\n\n\n\n\n\n\n\n\n\n\nEach session will be 1 hour 25 minutes long with the following structure: \n\n\n\n25 minute talk + 10 minute Q&A25 minute talk + 10 minute Q&A15 minute wrap up + general questions\n\n\n\nAll workshop sessions will take place virtually on the Zoom platform.
URL:https://www.scilifelab.se/event/publishing-workshop-for-junior-researchers/
LOCATION:Online event via Zoom
CATEGORIES:Community,Course
ORGANIZER;CN="Science/AAAS and SciLifeLab":MAILTO:events@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211012T080000
DTEND;TZID=Europe/Stockholm:20211014T170000
DTSTAMP:20260413T205221
CREATED:20210901T133811Z
LAST-MODIFIED:20211011T141253Z
UID:10000422-1634025600-1634230800@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\nImportant dates\n\n\n\nApplication opens: 2021-09-01Application closes: 2021-09-29Confirmation to accepted students: 2021-09-30 \n\n\n\nContact\n\n\n\nedu.intro-dm@nbis.se \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nApplication form\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\n1700 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 15 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\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. \n\n\n\nCourse content\n\n\n\nTopics covered will include: \n\n\n\nOpen Science and FAIR in practiceOrganising data\, files and folders in research projectsVersioning data\, documents and scripts with GitDescribing data with metadataCleaning tabular data and metadata with OpenRefineSubmitting data to public data repositoriesWriting basic recipes for data analysis and visualisation with R (Links to an external site.)\n\n\n\n\n\n\n\nLearning objectives: \n\n\n\nTo get acquainted with\, and reflect upon\, the principles of Open Science and FAIRTo understand the importance of metadata\, and how it affects “FAIRness”To learn how to organise files to make project work more efficientTo learn to clean up messy tabular data and metadataTo learn how to find\, and submit to\, relevant public repositories for data publicationTo learn to apply simple version control practices on filesTo learn to start using R to analyse data
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices/
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:20211018T080000
DTEND;TZID=Europe/Stockholm:20211022T170000
DTSTAMP:20260413T205221
CREATED:20210602T093819Z
LAST-MODIFIED:20210602T094321Z
UID:10000395-1634544000-1634922000@www.scilifelab.se
SUMMARY:Python programming with applications to bioinformatics - ONLINE
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\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\nImportant dates \n\n\n\nApplication opens: June 21Application closes: September 4Confirmation to accepted students: September 8Responsible teachers: Nina Norgren\, Dimitris Bampalikis \n\n\n\nIf you do not receive information according to the above dates please contact: Nina Norgren (edu.intro-python@nbis.se) \n\n\n\nCourse fee \n\n\n\nNo course fee will be invoiced for online courses. However\, if you accept a position at the course and do not participate (no-show) you will be invoiced 2000 SEK.*Please note that NBIS cannot invoice individuals \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\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\nFormat \n\n\n\nPresentations and demonstrations. Practical exercises (either in the lab with assistants or on your own). Presentations will be given online\, mixed with exercises where teaching assistants will be available online to help with the exercises. \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\nDue to limited space the course can accommodate a maximum of 30 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the 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 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/python-programming-with-applications-to-bioinformatics-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211020T080000
DTEND;TZID=Europe/Stockholm:20211022T170000
DTSTAMP:20260413T205221
CREATED:20210714T131729Z
LAST-MODIFIED:20210714T133644Z
UID:10000405-1634716800-1634922000@www.scilifelab.se
SUMMARY:Cryo-EM sample preparation and data collection
DESCRIPTION:The purpose of the course is to prepare and train Cryo-EM unit 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 unit users or potential unit 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 unit\, both UmU and SU nodes together. \n\n\n\nImportant dates\n\n\n\nApplication should be submitted before September 17\, 2021 \n\n\n\nConfirmation to accepted participants: September 22\, 2021(If you don’t receive information about your application before September 27\, please contact hussein.haggag@umu.se \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nApplication\n\n\n\n\n\n\n\n\nCourse organizers\n\n\n\nCamilla Holmlund and Michael Hall \n\n\n\nTeachers and course instructors\n\n\n\nLinda SandbladMichael HallLars-Anders CarlsonCamilla HolmlundAdditional teachers t.b.a\n\n\n\nSocial program\n\n\n\nA social program depending on the current corona restrictions will be communicated to the participants after acceptance.  \n\n\n\nCourse fee\n\n\n\nA course fee of 800 SEK\, including coffee and lunches\, will be invoiced to accepted 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\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 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 \n\n\n\nPlease note that SciLifeLab training courses do not provide any formal university credits.The course 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 course application\, whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/cryo-em-sample-preparation-and-data-collection/
CATEGORIES:Course
ORGANIZER;CN="UCEM Ume%C3%A5":MAILTO:hussein.haggag@umu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211025T080000
DTEND;TZID=Europe/Stockholm:20211029T170000
DTSTAMP:20260413T205221
CREATED:20210524T095145Z
LAST-MODIFIED:20211027T085846Z
UID:10000391-1635148800-1635526800@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\n\nCourse website\n\n\n\nApplication\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  nowApplication closes: 2021-10-10Confirmation to accepted students:  2021-10-14 \n\n\n\nResponsible teachers\n\n\n\nAgata Smialowska\, Olga Dethlefsen\, Jakub WestholmPlease contact edu.epigenomics@nbis.se for course specific questions. \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 and integration of epigenomics and functional genomics data. \n\n\n\nTopics covered include\n\n\n\nData processing and analyses for differential methylation with Illumina EPIC arrays and Bisulfite-seq;ChIP-seq and ATAC-seq: peak calling\, peak independent/dependent quality metrics\, differential binding and differential accessibility analysis; motif enrichment;Functional analysis\, including finding nearest genes and custom features\, over-represented GO terms and Reactome pathways;Advanced ChIP methods: CUT&RUN\, CUT&Tag\, use of spike-ins in ChIP-seq;Integrative visualisations of epigenomics datasets;Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data.Basic multi-omics exploration and integration;Introduction to analysis of single cell functional genomics data (scATAC-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\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\nThe 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 course application\, whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
LOCATION:
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