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DTSTART;TZID=Europe/Stockholm:20230918T080000
DTEND;TZID=Europe/Stockholm:20230922T170000
DTSTAMP:20260624T081214
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:20230611T090000
DTEND;TZID=Europe/Stockholm:20230622T170000
DTSTAMP:20260624T081214
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:20230424T090000
DTEND;TZID=Europe/Stockholm:20230428T170000
DTSTAMP:20260624T081214
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:20230424T090000
DTEND;TZID=Europe/Stockholm:20230428T153000
DTSTAMP:20260624T081214
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:20230418T090000
DTEND;TZID=Europe/Stockholm:20230420T170000
DTSTAMP:20260624T081214
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:20230417T090000
DTEND;TZID=Europe/Stockholm:20230419T170000
DTSTAMP:20260624T081214
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:20230320T090000
DTEND;TZID=Europe/Stockholm:20230324T170000
DTSTAMP:20260624T081214
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:20230313T080000
DTEND;TZID=Europe/Stockholm:20230316T170000
DTSTAMP:20260624T081214
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:20230208T090000
DTEND;TZID=Europe/Stockholm:20230210T170000
DTSTAMP:20260624T081214
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:20230130T080000
DTEND;TZID=Europe/Stockholm:20230203T140000
DTSTAMP:20260624T081214
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:20221121T090000
DTEND;TZID=Europe/Stockholm:20221125T153000
DTSTAMP:20260624T081214
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:20221028T102000
DTEND;TZID=Europe/Stockholm:20221028T110000
DTSTAMP:20260624T081214
CREATED:20221020T111054Z
LAST-MODIFIED:20221020T111433Z
UID:10000719-1666952400-1666954800@www.scilifelab.se
SUMMARY:Seminar: Single cell and spatially resolved epigenomics
DESCRIPTION:Spatial omics has emerged as a new frontier of biological and biomedical research. In particular\, spatial transcriptomics has enabled genome-scale gene expression mapping with spatial resolution in tissue sections. So far\, the ability to capture spatial epigenetic information at the cellular level and genome scale has been lacking. This talk will describe recent advances in spatial epigenomics (ATAC-seq\, CUT&Tag)\, single cell epigenomics\, and how they can be applied to study multiple sclerosis. \n\n\n\n\n\n\n\nSpeaker\n\n\n\nProf. Gonçalo Castelo-Branco is the Professor of Glial Cell Biology at the Department of Medical Biochemistry and Biophysics at Karolinska Institutet\, Stockholm\, Sweden. Prof. Castelo-Branco received his PhD in Medical Biochemistry in 2005\, working on development of dopaminergic neurons and neural stem differentiation. He completed post-doctoral fellowships first at the Karolinska Institutet and then at the University of Cambridge\, United Kingdom\, working in neural and pluripotent stem cells and chromatin. Prof. Castelo-Branco started his research group in 2012\, focusing on the molecular mechanisms defining the epigenetic state of cells of the oligodendrocyte lineage. The main focus of Prof. Castelo-Branco’s research group is to investigate how distinct epigenetic states within the oligodendrocyte lineage are established\, by identifying key transcription factors\, chromatin modifying complexes and non-coding RNAs that are involved in epigenetic transitions\, using technologies such as RNA-Seq (single-cell and bulk)\, quantitative proteomics and epigenomics\, among others. The long term aim of this research group to design epigenetic based-therapies to induce regeneration (remyelination) in demyelinating diseases\, such as multiple sclerosis. \n\n\n\nLab website \n\n\n\n\n\n\n\n\n\nZOOM link\n\n\n\n\n\nContact: Jakub Westholm\, SciLifeLab Bioinformatics Long-term Support
URL:https://www.scilifelab.se/event/seminar-single-cell-and-spatially-resolved-epigenomics/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20221027T080000
DTEND;TZID=Europe/Stockholm:20221028T170000
DTSTAMP:20260624T081214
CREATED:20220920T125029Z
LAST-MODIFIED:20220920T125030Z
UID:10000685-1666857600-1666976400@www.scilifelab.se
SUMMARY:Swedish Bioinformatics Workshop
DESCRIPTION:This year SBW will take place at Umeå University\, October 27-28. The two days will be filled with inspiring talks\, including keynote talks by Kerstin Lindblad-Toh (Uppsala University/Broad Institute)\, Debora S. Marks (Harvard University)\, and Simon Anders (Heidelberg University). There will also be three parallel hands-on workshops\, a poster session\, and a social event.  \n\n\n\nThe target group is traditionally PhD students and postdocs working with any kind of bioinformatics and computational biology. This workshop aims to bring together talented students and young researchers across faculties and universities from throughout the country.  \n\n\n\nVisit sbw2022.com to register and view the programme. Registration will be open until 23rd September. \n\n\n\nRead more
URL:https://www.scilifelab.se/event/swedish-bioinformatics-workshop/
LOCATION:Naturvetarhuset\, Umeå University\, Umeå
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/09/Skärmavbild-2022-09-20-kl.-14.49.52.png
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:20260624T081214
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:20221011T090000
DTEND;TZID=Europe/Stockholm:20221013T170000
DTSTAMP:20260624T081214
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:20221010T090000
DTEND;TZID=Europe/Stockholm:20221014T170000
DTSTAMP:20260624T081214
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:20220926T080000
DTEND;TZID=Europe/Stockholm:20220930T170000
DTSTAMP:20260624T081214
CREATED:20220523T075158Z
LAST-MODIFIED:20220523T100120Z
UID:10000614-1664179200-1664557200@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data
DESCRIPTION:This is a national workshop open to PhD students\, post-docs\, and other researchers affiliated to Swedish academia and healthcare. The workshop is organised by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures. \n\n\n\nNBIS 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. For more detailed information about workshop syllabus\, learning outcomes and entry requirements\, please visit the workshop website. \n\n\n\nImportant dates\n\n\n\nWorkshop: 26-Sep-2022 – 30-Sep-2022 \n\n\n\nApplication opens: 23-May-2022 \n\n\n\nApplication closes: 19-Aug-2022 \n\n\n\nConfirmation to accepted students: 26-Aug-2022 \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\nContact\n\n\n\nnbis.se \n\n\n\nMalin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\n\n\n\n\n\nWorkshop Website\n\n\n\nApplication
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data/
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:20220912T080000
DTEND;TZID=Europe/Stockholm:20220916T170000
DTSTAMP:20260624T081214
CREATED:20220511T090525Z
LAST-MODIFIED:20220511T110221Z
UID:10000605-1662969600-1663347600@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 skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts\, such as the commonly misinterpreted p-value. \n\n\n\nImportant dates\n\n\n\nApplication open: now \n\n\n\nApplication closes: 2022-08-14 \n\n\n\nConfirmation to accepted students:  2022-08-19 \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 \n\n\n\nedu.ml-biostats@nbis.se\, olga.dethlefsen@nbis.se\, eva.freyhult@nbis.se \n\n\n\n\n\n\n\n\nCOURSE WEBSITE\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\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 mini-lectures\, group discussions\, live coding sessions etc. \n\n\n\n\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 24 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\n2000 SEK (includes lunches and coffee) \n\n\n\n*Please note that NBIS cannot invoice individuals
URL:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning/
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:20220907T080000
DTEND;TZID=Europe/Stockholm:20220909T170000
DTSTAMP:20260624T081214
CREATED:20220811T104626Z
LAST-MODIFIED:20220822T124149Z
UID:10000642-1662537600-1662742800@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R - Lund - CANCELLED
DESCRIPTION:National course open for PhD students (prioritized)\, postdocs\, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R – CANCELLED \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus Ringner \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jul 28\, 2022 \n\n\n\nApplication deadline: Aug 21\, 2022 \n\n\n\nConfirmation to accepted participants: Aug 25\, 2022 \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website (previous version)\n\n\n\n\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis 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\nA course fee* of 1300 SEK will be invoiced to accepted participants. This includes 3 lunches\, 1 dinner\, coffee and cakes. \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 aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make 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 the 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: \n\n\n\n·          how to format the data necessary for ggplot \n\n\n\n·          how to make bar-charts\, box-plots and others using ggplot \n\n\n\n·          how to make PCA plots in ggplot \n\n\n\n·          how to use R packages for heatmaps \n\n\n\n·          how to plot data on maps using R (optional) \n\n\n\n·          how to plot and handle phylogenetic trees in R (optional) \n\n\n\n·          how to make interactive plots in R using Rshiny \n\n\n\n·          how to host a Rshiny app in one of the available servers \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·          handle data in R for visualizations \n\n\n\n·          apply the grammar efficiently in ggplot to get the desired plot \n\n\n\n·          combine different data and/or different plots that are of publication-grade \n\n\n\n·          write your own simple Rshiny app \n\n\n\n·          deploy Rshiny apps in public servers.  \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 R and Rstudioa computer with R and Rstudioyou will be asked to install different R packages necessary for the course prior to the course. \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-2/
LOCATION:Biologihuset\, Sölvegatan 35\, Lund\, 223 62\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220831T090000
DTEND;TZID=Europe/Stockholm:20220902T130000
DTSTAMP:20260624T081214
CREATED:20220511T071103Z
LAST-MODIFIED:20220511T071340Z
UID:10000604-1661936400-1662123600@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\nCOURSE WEBSITE\n\n\n\nREGISTRATION\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  May 15 \n\n\n\nApplication closes: June 17 \n\n\n\nConfirmation to accepted students:  June 28 \n\n\n\nResponsible teachers:  Verena Kutschera\, John Sundh\, Per Unneberg\, Marcel Martin \n\n\n\nContact information: edu.byoc-snakemake@nbis.se \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 1\,700 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\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.This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \n\n\n\n\n\n\n\nLearning outcomes\n\n\n\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-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:20220829T080000
DTEND;TZID=Europe/Stockholm:20220902T170000
DTSTAMP:20260624T081214
CREATED:20220524T092955Z
LAST-MODIFIED:20220714T084938Z
UID:10000616-1661760000-1662138000@www.scilifelab.se
SUMMARY:Spatial omics data analysis
DESCRIPTION:This workshop provides resources to advanced tools for analysis of spatial datasets via a series of online lectures and computer practicals. The total course duration is 40 hours\, including the online lectures and practical coding workshop that will be held online. \n\n\n\nImportant dates\n\n\n\nApplication open: 2022-05-20 \n\n\n\nApplication deadline: 2022-07-31 \n\n\n\n\n\n\n\nCourse Leaders\n\n\n\nPaulo CzarnewskiChristophe Avenel\n\n\n\n\n\n\n\nLecturers and content creators\n\n\n\nLars BormCarolina WählbyGiovanni PallaNaveed IshaqueAnna SchaarDavid FischerHanna SpitzerSergio SallasÅsa BjörklundSebastian TiesmeyerLudvig BergenstråleEduard Chelebian\n\n\n\n\n\n\n\nContact information and Application\n\n\n\n\n\n\n\n\nCourse website\n\n\n\nEmail\n\n\n\nApplication\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis workshop is free of charge. \n\n\n\n\n\n\n\nCourse content\n\n\n\nTopics covered will include \n\n\n\nHands-on experience with ST (Visium)\, ISS\, scRNAseq data analysisFluorescence-based image formats\, standards and quality controlImage alignment\, registration and ISS decodingNuclei-based and segmentation-free cell identificationData imputation using ISS and single cell datasetsAnalysis of Spatial Transcriptomics datasetCell-type deconvolution (ST and single cell)Cell-cell and ligand-receptor interaction analysisMapping of multiple spatial data to a common referenceHigh-resolution projection of gene expression to H&E imagesInteractive visualisation of spatial omics data\n\n\n\n\n\n\n\nWho can apply?\n\n\n\nThis is an international course hosted by the National Bioinformatics Infrastructure Sweden (ELIXIR-SE) in collaboration with the Human Developmental Cell Atlas (HDCA)\, the Royal Institute of Technology\, Stockholm University\, Karolinska Institutet\, Uppsala University\, Charité Clinical University (ELIXIR-DE)\, Helmholtz Munich (Germany) and the European Molecular Biology Organisation. The course is open for PhD students\, postdocs\, group leaders and core facility staff working on spatial omics technologies. \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. \n\n\n\nPractical exercises will be performed in Python\, so we only accept students that fulfill the entry requirements (see below). \n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the practical exercises: \n\n\n\nBasic knowledge in PythonBe able to use your own computer with a web cameraHave miniconda3 installed in your computerDesirable: Previous experience with single cell RNA-seq analysis is an advantage.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\nDue to limited space the course can accommodate a maximum of 32 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/spatial-omics-data-analysis/
LOCATION:Online event via Zoom
CATEGORIES:Course
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/03/AdobeStock_218922152_front-scaled.jpg
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220613T080000
DTEND;TZID=Europe/Stockholm:20220617T170000
DTSTAMP:20260624T081214
CREATED:20220413T114236Z
LAST-MODIFIED:20220413T135107Z
UID:10000583-1655107200-1655485200@www.scilifelab.se
SUMMARY:RaukR\, Advanced R for Bioinformatics - Online workshop
DESCRIPTION:International workshop. The workshop is open for researchers at university or in industry such as PhD students\, postdocs\, group leaders\, core facility staff and analysts. \n\n\n\nJoin us online this June 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\nWhile we still cannot gather in Visby due variability of pandemic restrictions internationally\, we will have the workshop online! We hope that\, like last year\, we will learn a lot and have fun coding together! See you there! \n\n\n\nThe workshop is organised by NBIS.  \n\n\n\nResponsible teachers: Marcin Kierczak\, Sebastian DiLorenzo\, Roy FrancisContact: RaukR@NBIS.se \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\n\nAPPLICATION\n\n\n\nWEBSITE\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication deadline: Fri\, 13.05.2022\, 24:00GMT \n\n\n\nNotification of acceptance/decline: Fri\, 20.05.2022 \n\n\n\nWorkshop fee\n\n\n\nAcademic: no fee this year. However\, if you register and will be admitted but you will not attend the event without a valid reason\, you will be charged a no-show fee (4000 SEK). \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\nGuest speakers\n\n\n\nJenny Bryan (software engineer at RStudio\, Data science professor at UBC) Yihui Xie (software engineer at RStudio) Christophe Dervieux (software engineer at RStudio)  \n\n\n\nContent\n\n\n\nreproducible research in R (rmarkdown\, knitr)\,collaborative work using git and GitHub\, CD/CI\,R code style guidelines\,code debugging\, optimization and profiling\,parallelization and vectorization in R\,writing own functions – best practices\,understanding and using the system of R classes: S3\, S4\, R6 and RC\,anatomy of an R package: writing your own package from scratch\,code debugging\, profiling and optimization\,tidy data flow with tidyverse\,using the language of graphics\, ggplot2\,developing simple web applications using shiny\,R and Python integration using reticulate\n\n\n\nEntry requirements\n\n\n\nThe workshop 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\nSelection criteria\n\n\n\nThis year\, we can accommodate ~30 participants. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/raukr-advanced-r-for-bioinformatics-workshop/
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:20220510T120000
DTEND;TZID=Europe/Stockholm:20220513T160000
DTSTAMP:20260624T081214
CREATED:20220224T125406Z
LAST-MODIFIED:20220302T073938Z
UID:10000536-1652184000-1652457600@www.scilifelab.se
SUMMARY:Nordic ELIXIR-GOBLET Train-the-Trainer - Online
DESCRIPTION:This course offers guidance\, ideas and tips for designing training/teaching\, development and delivery on training activities\, all based on research-driven educational principles. This course will cover 4 main topics: \n\n\n\nLearning principles and how they apply to training and teachingDesign and plan session\, course\, materialsTeaching techniques to enhance learner engagement and participationAssessment and feedback in training and teaching\n\n\n\n\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\nThis course will be delivered through Canvas learning management system.  \n\n\n\nCourse Time: 12:00 – 16:00 CETCourse Format: Online via Zoom and it will include breakout sessions \n\n\n\n\n\n\n\nContact\n\n\n\nFor queries\, please don’t hesitate to contact us at education@nbis.se \n\n\n\n\n\n\n\n\nCOURSE WEBSITE AND PROGRAM\n\n\n\nREGISTRATION\n\n\n\n\n\n\n\n\nDeadline for applying to the course is 3rd of April. You will receive notification regarding acceptance to the course or if you are on the reserve list no later than one week after the closing of the registration. \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThere is no course attendance fee. \n\n\n\nNote! If you are accepted and decide not to attend without communicating the reason for the no-show with us\, we will invoice a no-show-fee of 200 Euros. \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. NOTE – Uppsala University cannot invoice individuals. \n\n\n\n\n\n\n\nCourse content\n\n\n\nLearning Objectives: \n\n\n\nTo get acquainted with Learning principles and how they apply to trainingTo be able to select and use training techniques that can help enhance learner engagement and participationTo learn how to use assessment and feedback in trainingTo learn about session\, course\, and materials design\n\n\n\nLearning Outcome: \n\n\n\nBy the end of this course\, learners will be able to: \n\n\n\nName learning principles that a good teacher/instructor should have in mindDescribe at least three training techniques\, drawing on learning principlesDesign a training session and a courseDevelop assessment questionnairesEnumerate types of materials needed for each part of a training session or course\n\n\n\n\n\n\n\nTarget audience\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\nHow learning works?How do I use learning principles and theories to improve my teaching/training?How do I make my teaching/training more engaging and effective?How should I adjust my teaching/training to different types of learners?How do I ensure learning progress?How can I assess whether my students are actually understanding my lessons? Are they actually learning?What is the best balance between theory and practice?How can I best assess whether learning is occurring and/or has occurred?What works in a classroom and what doesn’t?\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nWe will accept a maximum of 20 participants. Priority will be given to applicants from institutes and organisations across the Nordic research community and to participants from Nordic ELIXIR nodes. \n\n\n\n\n\n\n\nCourse team\n\n\n\nInstructors: \n\n\n\nJessica Lindvall (ELIXIR-SE Training Coordinator\, NBIS\, Sweden \n\n\n\nNina Norgren (ELIXIR-SE\, Training Coordinator\, NBIS\, Sweden) \n\n\n\nNazeefa Fatima (ELIXIR-NO\, Data Steward\, UiO\, Norway) \n\n\n\nErik Hjerde (ELIXIR-NO\, Training Coordinator\, UiT\, Norway) \n\n\n\nPriit Adler (ELIXIR-EE\, Trainer\, UT\, Estonia) \n\n\n\nAllegra Via (ELIXIR-IT\, Training Coordinator\, IBPM-CNR\, IT) \n\n\n\nPatricia Palagi (ELIXIR-CH\, Training coordinator\, SIB) \n\n\n\nOrganisers: \n\n\n\nELIXIR-SE \n\n\n\nELIXIR-NO \n\n\n\nELIXIR-FI \n\n\n\nELIXIR-EE
URL:https://www.scilifelab.se/event/nordic-elixir-goblet-train-the-trainer-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:20220427T080000
DTEND;TZID=Europe/Stockholm:20220429T170000
DTSTAMP:20260624T081214
CREATED:20220125T121449Z
LAST-MODIFIED:20220128T090507Z
UID:10000517-1651046400-1651251600@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R - Lund
DESCRIPTION:National course open for PhD students (prioritized)\, postdocs\, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus Ringner \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\naPPLY HERE\n\n\n\n\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jan 31\, 2022 \n\n\n\nApplication deadline: Mar 18\, 2022 \n\n\n\nConfirmation to accepted participants: Mar 25\, 2022 \n\n\n\nCourse fee\n\n\n\nThis 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\nCourse description\n\n\n\nThis course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make 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 the data. \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: \n\n\n\n·          how to format the data necessary for ggplot \n\n\n\n·          how to make bar-charts\, box-plots and others using ggplot \n\n\n\n·          how to make PCA plots in ggplot \n\n\n\n·          how to use R packages for heatmaps \n\n\n\n·          how to plot data on maps using R (optional) \n\n\n\n·          how to plot and handle phylogenetic trees in R (optional) \n\n\n\n·          how to make interactive plots in R using Rshiny \n\n\n\n·          how to host a Rshiny app in one of the available servers \n\n\n\nLearning outcomes\n\n\n\nBy the end of the course the participant will be able to: \n\n\n\n·          handle data in R for visualizations \n\n\n\n·          apply the grammar efficiently in ggplot to get the desired plot \n\n\n\n·          combine different data and/or different plots that are of publication-grade \n\n\n\n·          write your own simple Rshiny app \n\n\n\n·          deploy Rshiny apps in public servers.  \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 R and Rstudioa computer with R and Rstudioyou will be asked to install different R packages necessary for the course prior to the course. \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/
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:20220425T090000
DTEND;TZID=Europe/Stockholm:20220429T153000
DTSTAMP:20260624T081214
CREATED:20220131T095506Z
LAST-MODIFIED:20220201T080802Z
UID:10000518-1650877200-1651246200@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\nAPPLICATION\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Feb 1\, 2022 \n\n\n\nApplication deadline: Mar 25\, 2022 \n\n\n\nConfirmation to accepted participants: Apr 1\, 2022 \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\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\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 outcomesBy 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\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\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/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T080000
DTEND;TZID=Europe/Stockholm:20220407T170000
DTSTAMP:20260624T081214
CREATED:20211202T132557Z
LAST-MODIFIED:20211202T132705Z
UID:10000497-1649145600-1649350800@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\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\nAPPLICATION\n\n\n\n\n\n\n\n\nContact: edu.intro-dm@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication is open now \n\n\n\nApplication closes: 2022-03-15 \n\n\n\nConfirmation to accepted students: 2022-03-21 \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\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. \n\n\n\nInstallation instructions will be provided before the course starts. \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(Links to an external site.) \n\n\n\n\n\n\n\nLearning objectives: \n\n\n\n  • To get acquainted with\, and reflect upon\, the principles of Open \n\n\n\nScience and FAIR \n\n\n\n  • To understand the importance of metadata\, and how it affects \n\n\n\n“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 \n\n\n\ndata 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
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-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:20220328T090000
DTEND;TZID=Europe/Stockholm:20220401T170000
DTSTAMP:20260624T081214
CREATED:20211216T145021Z
LAST-MODIFIED:20220110T113421Z
UID:10000502-1648458000-1648832400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data - ONLINE
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within or affiliated to Swedish academia. This workshop is organized by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nDue to the Covid-19 situation\, this workshop will be held online. \n\n\n\nIf you have questions regarding the workshop\, please email: edu.intro-ngs@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication opens:  10 January 2022 \n\n\n\nApplication closes: 27 February 2022 \n\n\n\nConfirmation to accepted students:  Week 9\, 2022 \n\n\n\nResponsible teachers:  Malin Larsson\, Martin Dahlö\, Roy Francis \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 workshop fee* \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nThis is an intense one-week beginner level workshop that introduces the analysis of next generation sequencing (NGS) data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures. \n\n\n\nAfter this workshop you should be able to: \n\n\n\n●      Use the Linux command line interface to manage simple file processing operations and organize directory structures. \n\n\n\n●      Connect to and work on a remote high performance compute cluster. \n\n\n\n●      Apply programs in Linux for analysis of NGS data. \n\n\n\n●      Describe the basic principles of NGS. \n\n\n\n●      Summarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them. \n\n\n\n●      Explain common NGS file formats. \n\n\n\n●      Interpret quality control of NGS reads. \n\n\n\n●      Explain the steps involved in variant calling using whole genome sequencing data. \n\n\n\n●      Independently perform a basic variant calling workflow on example data. \n\n\n\n●      Explain the steps involved in differential gene expression using RNA seq data. \n\n\n\n●      Independently perform differential gene expression analysis on example data. \n\n\n\nEntry requirements\n\n\n\nA background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to: \n\n\n\n●      Have relevant previous experience in sequencing or analysis. \n\n\n\n●      Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing. \n\n\n\n●      It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others. \n\n\n\n\n\n\n\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\nDue to the high volume of applications from Swedish institutions\, we currently do not accept international applicants. \n\n\n\n\n\n\n\n\nAPPLICATION
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online-3/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220202T090000
DTEND;TZID=Europe/Stockholm:20220204T170000
DTSTAMP:20260624T081214
CREATED:20211109T084020Z
LAST-MODIFIED:20211111T104547Z
UID:10000482-1643792400-1643994000@www.scilifelab.se
SUMMARY:Single Cell RNA-seq data analysis
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours\, including the online lectures (15 hours) to be watched in advance and practical workshop that will be held on site in Stockholm (30 hours). The practical session is divided into both analysis overview and a Bring-Your-Own-Data (BYOD) day. \n\n\n\nDates \n\n\n\n2022-02-02 to 2022-02-04 on site (9:00 – 17:00) \n\n\n\nVenue \n\n\n\nRooms Air & Fire \n\n\n\nTomtebodavägen 23b\, SciLifeLab Solna\, Stockholm\, Sweden \n\n\n\nImportant dates \n\n\n\nApplication open: 2021-11-05 \n\n\n\nApplication deadline: 2021-12-16 \n\n\n\nCourse Leaders \n\n\n\nPaulo Czarnewski & Åsa Björklund \n\n\n\nContact information for questions regarding the course \n\n\n\nCourse Website\n\n\n\nEmail: edu.sc@nbis.se \n\n\n\nCourse feeThis workshop has a fee of 1700kr and will be invoiced to the selected participants *. Applications without complete invoice information will not be considered. Course fees cover all coffee breaks\, all lunches and 1 course dinner. \n\n\n\n* Please note that NBIS cannot invoice individuals. \n\n\n\nTopics covered will include \n\n\n\nOverview of the current scRNAseq technologiesBasic overview of pipelines for processing raw reads into expression valuesQuality control and normalizationDimensionality reduction techniquesData integration and batch correctionDifferential gene expressionClustering techniquesCelltype predictionTrajectory inference analysisAnalysis of spatial transcriptomics datasetsComparison of different analysis pipelines such as Seurat\, Scran and Scanpy\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. We do accept application from other countries\, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries. \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. \n\n\n\nPractical exercises will be performed using either R or Python\, so we only accept students that fulfill the entry requirements (see below). NBIS offers \n\n\n\nEntry requirements \n\n\n\nRequired for being able to follow the course and complete the practial exercises: \n\n\n\nYour own laptop with the following specs:\n\nOperating system Win10\, OS X or Linux\nAt least 8 GB of RAM.\nOperating system Win10\, OS X or Linux\nAt least 30 GB of free storage\nHave full access to your computer (admin permissions).\n\nYou are used to scripting in:\n\nUNIX command line (bash)\nEither R and/or Python\n\nYou already understand the basis of NGS technologiesYou are able to analyze bulk RNA-sequencing dataInstructions on installation will be sent by email to accepted participants.\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. \n\n\n\nLink to application \n\n\n\nRead more and register
URL:https://www.scilifelab.se/event/single-cell-rna-seq-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:20220117T080000
DTEND;TZID=Europe/Stockholm:20220121T170000
DTSTAMP:20260624T081214
CREATED:20211022T070851Z
LAST-MODIFIED:20211022T071315Z
UID:10000473-1642406400-1642784400@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\nImportant dates\n\n\n\nApplication opens: 2021-11-01 \n\n\n\nApplication closes: 2021-12-05 \n\n\n\nConfirmation to accepted students:  2021-12-19 \n\n\n\nResponsible teachers:  Claudio Mirabello\, Bengt Sennblad \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 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\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\nNN building blocks\, including concepts such as neurons\, activation functions\, loss functions\, gradient descent and back-propagationConvolutional Neural NetworksRecursive Neural NetworksAutoencodersBest practices when designing NNs\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\nDistinguish the concepts of “Artificial Intelligence”\, “Machine Learning”\, “Neural Networks”\, “Deep Learning”Distinguish between different types of learning (e.g. supervised\, unsupervised\, reinforcement) and recognise which applies to their own problemDistinguish between linear and non-linear approaches and recognise which is best suited for application to their own problemDescribe what a feed-forward neural network (FFNN) is\, along with its components (neurons\, layers\, weights\, bias\, activation functions\, cost functions)Explain how training of a FFNN works from a mathematical point of view (gradient descent\, learning rate\, backpropagation)Execute with pen and paper a few steps of training of a very simple FFNN modelTell the difference between a shallow and a deep networkExplain broadly how different NN architectures are wired and how they workImplement and apply the most appropriate architecture to a given problem/datasetAnalyze training curves and prediction outputs to evaluate if the training has been successfulDebug possible issues with the training and suggest changes to fix themExplain the difference between training\, validation and testingDefine what overfitting is from a mathematical point of view\, and what issues it causesIdentify 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\nCOURSE INFORMATION\n\n\n\nAPPLICATION\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\nFamiliarity with Unix/LinuxAbility to bring your own laptop with Python and Jupyter Notebooks  installed for the practical exercisesProgramming/scripting experience in Python (e.g. having attended the NBIS workshop in basic Python or equivalent)Basic experience of statistics and mathematics (e.g. having attended the NBIS workshop Introduction to Biostatistics and Machine Learning or equivalent)\n\n\n\nDesired \n\n\n\nYou have experience of working with Jupyter NotebooksYou have a necessity  to work with large datasets (e.g. thousands of samples)\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/
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
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DTSTART;TZID=Europe/Stockholm:20211122T080000
DTEND;TZID=Europe/Stockholm:20211126T170000
DTSTAMP:20260624T081214
CREATED:20210706T071301Z
LAST-MODIFIED:20210706T071802Z
UID:10000404-1637568000-1637946000@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data - ONLINE
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within Swedish academia. This workshop is organized by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nDue to the Covid-19 situation\, this workshop will be held online. \n\n\n\nIf you have questions regarding the workshop\, please email: edu.intro-ngs@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication opens:  August 16\, 2021  \n\n\n\nApplication closes: October 10\, 2021 \n\n\n\nConfirmation to accepted students:  October 15\, 2021 \n\n\n\nResponsible teachers  \n\n\n\nMalin Larsson\, Martin Dahlö\, Roy Francis \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\nPlease note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures. \n\n\n\nAfter this workshop you should be able to: \n\n\n\nDescribe the basic principles of next generation sequencing.Use the Linux command line interface to manage simple file processing operations\, and organize directory structures.Connect to and work on a remote high performance compute cluster.Apply programs in Linux for analysis of NGS data.Summarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.Explain common NGS file formats.Interpret quality control of NGS reads.Explain the steps involved in variant calling using whole genome sequencing data.Independently perform a basic variant calling workflow on example data.Explain the steps involved in differential gene expression using RNA seq data.Independently perform differential gene expression analysis on example data.\n\n\n\nEntry requirements\n\n\n\nA background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to \n\n\n\nHave relevant previous experience in sequencing or analysis.Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.\n\n\n\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\n\n\n\n\n\nLink to application\n\n\n\n\nThe application opens on August 16\, 2021.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online-2/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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