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DTSTART;TZID=Europe/Stockholm:20220202T090000
DTEND;TZID=Europe/Stockholm:20220204T170000
DTSTAMP:20260614T004234
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:20220118T100000
DTEND;TZID=Europe/Stockholm:20220223T160000
DTSTAMP:20260614T004235
CREATED:20211101T090147Z
LAST-MODIFIED:20211101T090730Z
UID:10000477-1642500000-1645632000@www.scilifelab.se
SUMMARY:Digital image analysis for scientific applications – focus MAX IV\, 5-8 ECTS credits
DESCRIPTION:The course aims at giving doctoral students and researchers from different disciplines a sufficient understanding of digital image processing and analysis techniques to solve basic image analysis problems. The content of the course includes methods especially suitable for MAX IV data. The course will also offer an introduction to several freely available software tools (e.g. CellProfiler\, ImageJ\, and ilastik)\, preparing the participants to start using computerized image analysis in their research. By inviting researchers interested in using MAX IV and image analysis\, and allowing them to work on data of similar type but produced elsewhere\, the course has the added value of attracting more researchers to MAX IV and also increasing the awareness of future possibilities giving a head-start in defining and planning MAX IV projects. The basics of image analysis are general\, but by designing examples and hands-on computer exercises based on published data from other world-leading X-ray facilities\, we can prepare participants for the future. After the course\, the participants will not only have a better understanding of the underlying theory and possibilities of image analysis but also be better at designing their experiments in the MAX IV environment. \n\n\n\nCourse Period\n\n\n\nJanuary-February 2022 \n\n\n\nCourse information\n\n\n\nLectures and computer exercises will be given online in English on Tuesdays and Wednesdays\, starting from January 18 to February 23 (weeks 3-8)\, from 10 am to 4 pm.The course will be given remotely via Zoom and Studium \n\n\n\nMore information can be found here \n\n\n\n \n\n\n\nECTS credits\n\n\n\n8 ECTS for the whole course (including a short project)\, 5 ECTS for a shorter version \n\n\n\nApplication\n\n\n\nApplication from course participants should be sent to Damian Matuszewski\, damian.matuszewski@it.uu.se\, not later than 15 December 2021.
URL:https://www.scilifelab.se/event/digital-image-analysis-for-scientific-applications-focus-max-iv-5-8-ects-credits/
LOCATION:Online event via Zoom
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220117T080000
DTEND;TZID=Europe/Stockholm:20220121T170000
DTSTAMP:20260614T004235
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
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211122T080000
DTEND;TZID=Europe/Stockholm:20211126T170000
DTSTAMP:20260614T004235
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
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211115T090000
DTEND;TZID=Europe/Stockholm:20211119T143000
DTSTAMP:20260614T004235
CREATED:20210909T083631Z
LAST-MODIFIED:20210909T084003Z
UID:10000443-1636966800-1637332200@www.scilifelab.se
SUMMARY:ELIXIR Tools for Reproducible Research - ONLINE
DESCRIPTION:Elixir / NBIS course 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\, Verena Kutschera \n\n\n\nContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\nApplication\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: September 1 \n\n\n\nApplication deadline: October 15 \n\n\n\nConfirmation to accepted participants: October 22 \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\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\nIn this course you will learn how to make your data analyses reproducible. In particular\, you will learn: \n\n\n\ngood practices for data analysishow to use the version control system git to track edits and collaborate on codinghow to use the package and environment manager Condahow to use the workflow managers Snakemake and Nextflowhow to use R Markdown to generate automated reportshow to use Jupyter notebooks to document your ongoing analysishow to use Docker and Singularity to distribute containerized computational environments\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/elixir-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:20211115T080000
DTEND;TZID=Europe/Stockholm:20211119T170000
DTSTAMP:20260614T004235
CREATED:20210706T064513Z
LAST-MODIFIED:20210706T065837Z
UID:10000403-1636963200-1637341200@www.scilifelab.se
SUMMARY:RNA-seq data analysis ONLINE
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for processing and analyses of RNA-seq data via a series of  online lectures and computer practicals. The workshop will be held online. \n\n\n\nImportant dates\n\n\n\nApplication open: August 27\, 2021Application deadline: October 15\, 2021 \n\n\n\nResponsible teacher/s \n\n\n\nJohan Reimegård\, Julie Lorent \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\nThis online workshop has no fee. However\, if you accept a position and do not participate you will be invoiced* 1300 kr \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse content\n\n\n\nTopics covered will include: \n\n\n\nRNA seq introductionRNA seq read mapping programsRNA seq QC analysisDifferential expression analysisGene set enrichment analysis\n\n\n\nMore details about the course can be found at the previous year’s webpage \n\n\n\nThe course will follow similar structure and topics.  \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\nBasic knowledge in Linux and RSteady and fast internet connection to be able to follow the workshop.Your own laptop with the following specs:At least 6 GB of RAM. Operating system Win10\, OS X or LinuxAt least 30 GB of free storage\n\n\n\nDesirable: \n\n\n\nExperience working with NGS data analysis or completed the NBIS workshop “Introduction to Bioinformatics using NGS data”Experience working in R or completed the NBIS course “R Programming Foundations for Life Scientists”\n\n\n\nDue to our best practise 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\n\nLink to application
URL:https://www.scilifelab.se/event/rna-seq-data-analysis-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211025T080000
DTEND;TZID=Europe/Stockholm:20211029T170000
DTSTAMP:20260614T004235
CREATED:20210524T095145Z
LAST-MODIFIED:20211027T085846Z
UID:10000391-1635148800-1635526800@www.scilifelab.se
SUMMARY:Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)
DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS) \n\n\n\n \n\n\n\n\nCourse website\n\n\n\nApplication\n\n\n\n\nImportant dates\n\n\n\nApplication opens:  nowApplication closes: 2021-10-10Confirmation to accepted students:  2021-10-14 \n\n\n\nResponsible teachers\n\n\n\nAgata Smialowska\, Olga Dethlefsen\, Jakub WestholmPlease contact edu.epigenomics@nbis.se for course specific questions. \n\n\n\nWorkshop fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK.  \n\n\n\n*Please note that NBIS cannot invoice individuals. \n\n\n\nWorkshop content\n\n\n\nThis workshop aims to introduce the best practice bioinformatics methods for processing\, analyses and integration of epigenomics and functional genomics data. \n\n\n\nTopics covered include\n\n\n\nData processing and analyses for differential methylation with Illumina EPIC arrays and Bisulfite-seq;ChIP-seq and ATAC-seq: peak calling\, peak independent/dependent quality metrics\, differential binding and differential accessibility analysis; motif enrichment;Functional analysis\, including finding nearest genes and custom features\, over-represented GO terms and Reactome pathways;Advanced ChIP methods: CUT&RUN\, CUT&Tag\, use of spike-ins in ChIP-seq;Integrative visualisations of epigenomics datasets;Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data.Basic multi-omics exploration and integration;Introduction to analysis of single cell functional genomics data (scATAC-seq). \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the workshop and complete the computer exercises: \n\n\n\nBYOL\, bring your own laptop with R and RStudio installed;Basic knowledge in Linux;Basic programming experience\, preferably in R.\n\n\n\nDesirable \n\n\n\nExperience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;Previous experience with NGS data analyses;Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.\n\n\n\nDue to limited capacity the workshop can accommodate maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. \n\n\n\nThe training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines.If formal credits are crucial\, the student needs to confer with the home department before course application\, whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/epigenomics-data-analysis-from-bulk-to-single-cell-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211020T080000
DTEND;TZID=Europe/Stockholm:20211022T170000
DTSTAMP:20260614T004235
CREATED:20210714T131729Z
LAST-MODIFIED:20210714T133644Z
UID:10000405-1634716800-1634922000@www.scilifelab.se
SUMMARY:Cryo-EM sample preparation and data collection
DESCRIPTION:The purpose of the course is to prepare and train Cryo-EM unit users in sample preparation methods\, introduce users to the image data acquisition workflow\, expand knowledge about cryo-EM methods among researchers and show that everyone can learn how to use cryo-EM for structure and cell biology. \n\n\n\nThe course is open for unit users or potential unit users\, such as PhD students\, postdocs\, and researchers within the life sciences who are curious and will profit from cryo-EM skills. Swedish and international course participants are welcome. To attend\, the course participants must have experience in basic electron microscopy and be familiar with structure or cell biology. \n\n\n\nThis course is supported by SciLifeLab\, CryoNET and Umeå University and organized by the SciLifeLab Cryo-EM unit\, both UmU and SU nodes together. \n\n\n\nImportant dates\n\n\n\nApplication should be submitted before September 17\, 2021 \n\n\n\nConfirmation to accepted participants: September 22\, 2021(If you don’t receive information about your application before September 27\, please contact hussein.haggag@umu.se \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nApplication\n\n\n\n\n\n\n\n\nCourse organizers\n\n\n\nCamilla Holmlund and Michael Hall \n\n\n\nTeachers and course instructors\n\n\n\nLinda SandbladMichael HallLars-Anders CarlsonCamilla HolmlundAdditional teachers t.b.a\n\n\n\nSocial program\n\n\n\nA social program depending on the current corona restrictions will be communicated to the participants after acceptance.  \n\n\n\nCourse fee\n\n\n\nA course fee of 800 SEK\, including coffee and lunches\, will be invoiced to accepted participants after acceptance. \n\n\n\nCourse content\n\n\n\nThis course will cover practical aspects of cryo-EM sample preparation and data acquisition. \n\n\n\nTopics covered: \n\n\n\nBasic theory of vitreous water\, how to handle a cryo sample and consequencesPlunge freezing methods\, tools and cryo-transferSample and instrument requirements for single particle and tomography methodsImage data acquisition\, concept of low dose and the cryo-specific workflowIntroduction to automatic data acqui­sition software\, EPU\, TomographyIntroduction to cryo-EM image processing methods\n\n\n\nThe course consists of lectures\, cryo lab work\, demonstrations and practical exercises for all participants\, hands-on experiences of microscopy operation and discussions. A detailed schedule will be provided to accepted participant. \n\n\n\nCourse literature\n\n\n\nHandouts and material online. \n\n\n\nEntry requirements\n\n\n\nPriority will be given to researchers involved in project where the use of cryo-EM is needed\, which are to be briefly described upon application. \n\n\n\nThe course will be held at an advanced level\, assuming that participants have a master’s degree or equivalent in a technical life science discipline. It aims to be relevant for a broad research community\, also to participants not working in research environments using cryo-EM today. \n\n\n\nA maximum of 15 participants will be admitted. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender balance. \n\n\n\nExamination \n\n\n\nParticipation in all parts of the course\, lectures\, lab\, microscopy demonstrations and evaluation are mandatory. SciLifeLab and Umeå University will provide successful participants with a course certificate and a recommendation for 1 ECTS \n\n\n\nPlease note that SciLifeLab training courses do not provide any formal university credits.The course content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines.If formal credits are crucial\, the student needs to confer with the home department before course application\, whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/cryo-em-sample-preparation-and-data-collection/
CATEGORIES:Course
ORGANIZER;CN="UCEM Ume%C3%A5":MAILTO:hussein.haggag@umu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211018T080000
DTEND;TZID=Europe/Stockholm:20211022T170000
DTSTAMP:20260614T004235
CREATED:20210602T093819Z
LAST-MODIFIED:20210602T094321Z
UID:10000395-1634544000-1634922000@www.scilifelab.se
SUMMARY:Python programming with applications to bioinformatics - ONLINE
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of fundamental Python skills within all Swedish universities. \n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\nImportant dates \n\n\n\nApplication opens: June 21Application closes: September 4Confirmation to accepted students: September 8Responsible teachers: Nina Norgren\, Dimitris Bampalikis \n\n\n\nIf you do not receive information according to the above dates please contact: Nina Norgren (edu.intro-python@nbis.se) \n\n\n\nCourse fee \n\n\n\nNo course fee will be invoiced for online courses. However\, if you accept a position at the course and do not participate (no-show) you will be invoiced 2000 SEK.*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description \n\n\n\nThis course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course\, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. \n\n\n\nCourse content \n\n\n\nCore concepts about Python syntax: Data types\, blocks and indentation\, variable scoping\, iteration\, functions\, methods and argumentsDifferent ways to control program flow using loops and conditional testsRegular expressions and pattern matchingWriting functions and best-practice ways of making them usableReading from and writing to filesCode packaging and Python librariesHow to work with biological data using external libraries.\n\n\n\n\n\n\n\nLearning outcomes \n\n\n\nDescribe and apply basic concepts in Python\, such as:LoopsIf/else statementsFunctionsReading/writing to filesBeing able to edit and run Python codeWrite file-processing Python programs that produce output to the terminal and/or external filesCreate stand-alone python programs to process biological dataKnow how to develop your skills in Python after the course (including debugging)\n\n\n\nFormat \n\n\n\nPresentations and demonstrations. Practical exercises (either in the lab with assistants or on your own). Presentations will be given online\, mixed with exercises where teaching assistants will be available online to help with the exercises. \n\n\n\nEntry requirements \n\n\n\nThe course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage\, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises. \n\n\n\nDue to limited space the course can accommodate a maximum of 30 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/python-programming-with-applications-to-bioinformatics-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211012T080000
DTEND;TZID=Europe/Stockholm:20211014T170000
DTSTAMP:20260614T004235
CREATED:20210901T133811Z
LAST-MODIFIED:20211011T141253Z
UID:10000422-1634025600-1634230800@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. \n\n\n\nNote: We follow the recommendations and guidelines from Swedish authorities and Folkhälsomyndigheten. The course is designed to be an interactive face-to-face event. However\, we follow the situation carefully and will deliver the course online if needed. \n\n\n\nImportant dates\n\n\n\nApplication opens: 2021-09-01Application closes: 2021-09-29Confirmation to accepted students: 2021-09-30 \n\n\n\nContact\n\n\n\nedu.intro-dm@nbis.se \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nApplication form\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\n1700 SEK paid by invoice to NBIS. This includes lunches\, coffee and snacks. Please note that NBIS cannot invoice individuals. \n\n\n\nDue to limited space the course can accommodate a maximum of 15 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nEntry requirements\n\n\n\nNo previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. Installation instructions will be provided before the course starts. \n\n\n\nCourse content\n\n\n\nTopics covered will include: \n\n\n\nOpen Science and FAIR in practiceOrganising data\, files and folders in research projectsVersioning data\, documents and scripts with GitDescribing data with metadataCleaning tabular data and metadata with OpenRefineSubmitting data to public data repositoriesWriting basic recipes for data analysis and visualisation with R (Links to an external site.)\n\n\n\n\n\n\n\nLearning objectives: \n\n\n\nTo get acquainted with\, and reflect upon\, the principles of Open Science and FAIRTo understand the importance of metadata\, and how it affects “FAIRness”To learn how to organise files to make project work more efficientTo learn to clean up messy tabular data and metadataTo learn how to find\, and submit to\, relevant public repositories for data publicationTo learn to apply simple version control practices on filesTo learn to start using R to analyse data
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211006T000100
DTEND;TZID=Europe/Stockholm:20211006T230000
DTSTAMP:20260614T004235
CREATED:20210914T123507Z
LAST-MODIFIED:20211006T084940Z
UID:10000446-1633478460-1633561200@www.scilifelab.se
SUMMARY:Application Open: Publishing workshop for junior researchers
DESCRIPTION:Applications are open to take part in this 3-part workshop series by Science and SciLifeLab for early career researchers (PhD students and postdocs) in SciLifeLab affiliated groups.  \n\n\n\nWorkshop leaders: \n\n\n\nValda Vinson (Editor\, Science Magazine)Sacha Vignieri (Deputy Editor for research\, Science Magazine)\n\n\n\nThis series is limited to a maximum 30 participants. Participants will be selected after applications close\, and selected participants will be notified shortly thereafter. The workshop is free of charge. \n\n\n\nRegistered participants must attend all three sessions of the workshop. The topics covered all relate to publishing\, in particular: “Before you submit”\, “Life of the paper”\, and “the publishing landscape”. \n\n\n\nWorkshop 1 – Thursday\, 4th of November\, 16:00-17:30 CETWorkshop 2 – Thursday\, 11th of November\, 16:00-17:30 CETWorkshop 3 – Thursday\, 18th of November\, 16-17:30 CET\n\n\n\nDeadline for application: October 6\, 2021. Selected participants will be notified shortly thereafter. \n\n\n\napply here\n\n\n\nPlease note that this workshop series is only open to SciLifeLab affiliated groups.  \n\n\n\n\n\n\n\nContent\n\n\n\n\n\nBefore you submit\n\n\n\n\n\nLife of the paper\n\n\n\n\n\nThe publishing landscape\n\n\n\n\n\n\n\nPart A \n\n\n\nQuick background      Authorship      Picking a journal       Planning ahead  \n\n\n\n\n\nPart A \n\n\n\nCover Letter     Title/Abstract     Process at Science\n\n\n\n\n\nPart A – Within Science \n\n\n\nWhat happens after acceptance     Promoting your paper\n\n\n\n\n\n\n\nPart B \n\n\n\nStructure your paper Dos and Don’ts Data presentation/visualization/statistics Data accessibility\n\n\n\n\n\nPart B \n\n\n\nReview process     Writing a review     Responding to reviews\n\n\n\n\n\nPart B – More Broadly \n\n\n\nTowards reproducibilityOpen access and preprintsMeasuring Impact\n\n\n\n\n\n\n\n\n\n\n\n\n\nEach session will be 1 hour 25 minutes long with the following structure: \n\n\n\n25 minute talk + 10 minute Q&A25 minute talk + 10 minute Q&A15 minute wrap up + general questions\n\n\n\nAll workshop sessions will take place virtually on the Zoom platform.
URL:https://www.scilifelab.se/event/publishing-workshop-for-junior-researchers/
LOCATION:Online event via Zoom
CATEGORIES:Community,Course
ORGANIZER;CN="Science/AAAS and SciLifeLab":MAILTO:events@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20211004T080000
DTEND;TZID=Europe/Stockholm:20211008T170000
DTSTAMP:20260614T004235
CREATED:20210603T125859Z
LAST-MODIFIED:20210603T130143Z
UID:10000397-1633334400-1633712400@www.scilifelab.se
SUMMARY:Introduction to biostatistics and machine learning - Online
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts\, such as the commonly misinterpreted p-value. \n\n\n\nImportant date \n\n\n\nApplication open: nowApplication closes: 2021-08-21Confirmation to accepted students:  2021-09-01Responsible teachers:  Olga Dethlefsen\, Eva Freyhult \n\n\n\nIf you do not receive information according to the above dates please contact olga.dethlefsen@nbis.se\, eva.freyhult@nbis.se \n\n\n\n\n\n\n\n\nCourse website\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\n\nCourse content \n\n\n\nProbability theoryHypothesis testing and confidence intervalsResamplingLinear regression methodsIntroduction to generalized linear modelsModel evaluationUnsupervised learning incl. clustering and dimension reduction methodsSupervised learning incl. classification\n\n\n\nEducation \n\n\n\nIn this course we focus on an active learning approach. The course participants are expected to do some pre-course reading and exercises\, corresponding up to 40h studying. The education consists of teaching blocks alternating between mini-lectures\, group discussions\, live coding sessions etc. \n\n\n\nEntry requirements \n\n\n\nBasic R programming skillsBYOL (bring your own laptop) with R and RStudio installedNo prior biostatistical knowledge is assumed\n\n\n\nThe course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nCourse fee \n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals
URL:https://www.scilifelab.se/event/introduction-to-biostatistics-and-machine-learning-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210929T090000
DTEND;TZID=Europe/Stockholm:20211001T130000
DTSTAMP:20260614T004235
CREATED:20210615T081112Z
LAST-MODIFIED:20210615T090743Z
UID:10000401-1632906000-1633093200@www.scilifelab.se
SUMMARY:Snakemake BYOC (bring-your-own-code) workshop (ONLINE)
DESCRIPTION:National workshop open for PhD students (prioritized)\, postdocs\, researchers and others from all Swedish universities who have previously participated in the NBIS Tools for reproducible research course or with demonstrated experience in writing Snakemake workflows. \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nCourse application\n\n\n\n\n\n\n\n\nImportant dates \n\n\n\nApplication opens:  June 15 \n\n\n\nApplication closes: August 31 \n\n\n\nConfirmation to accepted students:  September 3 \n\n\n\nResponsible teachers:  Verena Kutschera\, John Sundh\, Per Unneberg \n\n\n\nContact information: edu.byoc-snakemake@nbis.se \n\n\n\nWorkshop fee \n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 1\,700 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nWorkshop content \n\n\n\nAs data analysis projects grow and change over time\, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up\, perform and monitor defined sequences of computational tasks (“workflows”)\, thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. \n\n\n\nThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. \n\n\n\nThis Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \n\n\n\nLearning outcomes \n\n\n\nAfter participation in the BYOC workshop\, participants will: \n\n\n\nBe able to create Snakemake workflows for bioinformatics data analysisDemonstrate knowledge of the structure and syntax of different types of Snakemake workflowsDemonstrate knowledge of advanced features of the Snakemake workflow language\n\n\n\n\n\n\n\nEntry requirements \n\n\n\nPrevious participation in the NBIS Tools for reproducible research workshop. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflowsYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improveA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required). You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the workshop.\n\n\n\nThe workshop can accommodate a maximum of 16 participants. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.
URL:https://www.scilifelab.se/event/snakemake-byoc-bring-your-own-code-workshop-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210908T080000
DTEND;TZID=Europe/Stockholm:20210910T170000
DTSTAMP:20260614T004235
CREATED:20210527T110708Z
LAST-MODIFIED:20210906T135301Z
UID:10000393-1631088000-1631293200@www.scilifelab.se
SUMMARY:Workshop on Plotting in R - ONLINE
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.The course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus RingnerContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\n\nApplication\n\n\n\nCourse website\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: June 01Application deadline: July 30Confirmation to accepted participants: August 06 \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 1700 SEK.*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.In particular\, you will learn: \n\n\n\n·          how to format the data necessary for ggplot·          how to make bar-charts\, box-plots and others using ggplot·          how to make PCA plots in ggplot·          how to use R packages for heatmaps·          how to plot data on maps using R (optional)·          how to plot and handle phylogenetic trees in R (optional)·          how to make interactive plots in R using Rshiny·          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·          apply the grammar efficiently in ggplot to get the desired plot·          combine different data and/or different plots that are of publication-grade·          write your own simple Rshiny app·          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 a webcam running R and Rstudio You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseyou 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-plotting-in-r-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210906T080000
DTEND;TZID=Europe/Stockholm:20210910T170000
DTSTAMP:20260614T004235
CREATED:20210603T124622Z
LAST-MODIFIED:20210615T135807Z
UID:10000396-1630915200-1631293200@www.scilifelab.se
SUMMARY:ELIXIR Omics Integration and Systems Biology - Online
DESCRIPTION:The National Bioinformatics Infrastructure Sweden (NBIS) / ELIXIR Sweden is pleased to announce the workshop in Omics Integration and Systems Biology. This workshop is open for PhD students\, postdocs\, group leaders and core unit staff from European institutions looking for an introduction to multi-omics integration and systems biology approaches. \n\n\n\nThis workshop will include lectures and hands-on exercises from NBIS / Scilifelab experts from Stockholm\, Lund and Gothenburg\, as well as guest sessions from: \n\n\n\nRicard Argelaguet\, PhD\, Babraham Institute\, United KingdomKim-Anh Lê Cao\, PhD\, Melbourne University\, AustraliaPedro Beltrao\, PhD\, EMBL-EBI\, United KingdomNikolaus Sonnenschein\, PhD\, DTU Technical University of Denmark\, Denmark\n\n\n\n More information to come on the course website. \n\n\n\nImportant Dates \n\n\n\n\nApplication opens: 3 JuneApplication closes: 9 AugustConfirmation to accepted students: 16 August\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\nFee \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\nContent \n\n\n\nThe aim of this workshop is to provide an integrated view of data-driven hypothesis generation through biological network analysis\, constraint-based modelling\, and supervised and unsupervised integration methods. A general description of different methods for analysing 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 several seminars by invited speakers. \n\n\n\nSome of the covered topics include: \n\n\n\nData pre-processing and cleaning prior to integration\n\n\n\nApplication of key machine learning methods 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\nFurther details about the course content may be found on the course website. \n\n\n\nEntry requirements \n\n\n\nThis is a course is open for PhD students\, postdocs\, group leaders and core unit staff from European 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\nBasic knowledge in R or Python;Basic understanding of frequentist statistics;A computer with web camera\, Zoom\, and permissions for installing software.\n\n\n\nDesirable: \n\n\n\nExperience with analysis of NGS and other omic data;Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “Introduction to biostatistics and machine learning”Basic conda and git knowledge\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/elixir-omics-integration-and-systems-biology-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210830T080000
DTEND;TZID=Europe/Stockholm:20210903T170000
DTSTAMP:20260614T004235
CREATED:20210607T141128Z
LAST-MODIFIED:20210608T125759Z
UID:10000398-1630310400-1630688400@www.scilifelab.se
SUMMARY:Summer School Advanced topics in single cell Transcriptomics - Online
DESCRIPTION:Overview\n\n\n\nNBIS (SciLifeLab Bioinformatics Platform) and SIB (Swiss Institute of Bioinformatics) are pleased to co-organize this online course in Advanced topics in single cell Transcriptomics. \n\n\n\nThis jointly collaborative effort between the SIB and NBIS (SciLifeLab Bioinformatics Platform) was launched in 2019 as an every-second-year seasonal school where the thematic topic mirrors the life science demand of knowledge up-skilling. In 2019 we did a seasonal school on the topic of single-cell omics analysis and this year we are repeating this theme as the demand is still extremely high. \n\n\n\nIn recent years\, single-cell transcriptomics has become a widely used technology to study heterogeneous and dynamic biological systems. A large number of new tools and approaches have been developed for analyzing this new type of data. The goal of this joint School is to provide PhD students and postdocs with theoretical and mostly hands-on knowledge on selected advanced topics in Single Cell analysis. In particular\, the participants will be split into small groups to develop mini projects (more details provided later to accepted students. \n\n\n\nFor this one week course in single-cell transcriptomic we are delighted to have several excellent researchers and experts from both the Swedish and the Swiss Life Science community such as teachers such as Alma Andersson\, Åsa Björklund\, Volker Bergen\, Paulo Czarnewski\, Emma Dann\, Charlotte Soneson\, Panagiotis Papasaikas\, Geert van Geest and others. \n\n\n\nTarget audience\n\n\n\nThis course is designed for intermediate users and we consider the knowledge of basic steps in single-cell analysis as a prerequisite. \n\n\n\nCourse and Application details\n\n\n\nApplication is now open at SIB announcement Summer School Advanced topics in single cell Transcriptomics. The SIB page will be regularly updated with more detailed information. \n\n\n\nAny questions please contact Jessica Lindvall (Training coordination\, NBIS)\, jessica.lindvall@nbis.se and Grégoire Rossier (Training coordination\, SIB)\, Gregoire.Rossier@sib.swiss        \n\n\n\nImportant dates\n\n\n\nDeadline for free-of-charge cancellation is set to 28/07/2021. Cancellation after this date will not be reimbursed. \n\n\n\nCourse fee\n\n\n\nThe registration fees for academics are 300 CHF (appriximately 270 Euro) and 1500 CHF (approximately 1370 Euro) for for-profit companies.
URL:https://www.scilifelab.se/event/summer-school-advanced-topics-in-single-cell-transcriptomics-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210614T080000
DTEND;TZID=Europe/Stockholm:20210624T170000
DTSTAMP:20260614T004235
CREATED:20210503T140254Z
LAST-MODIFIED:20210503T141941Z
UID:10000375-1623657600-1624554000@www.scilifelab.se
SUMMARY:RaukR\, Advanced R for Bioinformatics\, Summer course
DESCRIPTION:International course. The course is open for researchers at university or in industry such as PhD students\, postdocs\, group leaders\, core unit staff and analysts.Apply hereCourse website \n\n\n\ncourse website\n\n\n\nThe course is organised by NBIS \n\n\n\nResponsible teachers: Marcin Kierczak\, Sebastian DiLorenzoContact: RaukR@NBIS.se \n\n\n\nImportant dates\n\n\n\nApplication deadline: Friday\, 23.04.2021\, 24:00 GMTNotification of acceptance/decline: Friday\, 30.04.2021 \n\n\n\nCourse 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 (3000 SEK).Participants from outside of academia should contact us for a fee quote. \n\n\n\nCourse description\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 Summer course will focus on advanced R functionality\, to increase the participants skillset and understanding of what is possible to do today. \n\n\n\nBig part of RaukR experience was coding and exchanging knowledge in a unique environment provided by Campus Visby in Gotland. Sadly\, due to COVID-19 outbreak\, RaukR 2020 did not happen. This year\, we still have to obey a number of restrictions and guidelines due to the outbreak. While we still cannot gather in Visby\, we decided to go online and we hope this year we will also learn a lot and have fun coding together! We wish you all the best. See you online! Stay safe and healthy! \n\n\n\nYou are very welcome to apply or see the homepage for more information. Please\, help us spread the word to interested participants! \n\n\n\nGuest speaker\n\n\n\nMax Kuhn (software engineer at RStudio) \n\n\n\nCourse content\n\n\n\nreproducible research in R (rmarkdown\, knitr)\,collaborative work using git and GitHub\, CD/CI\,R code style guidelines\,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\,efficient use of magrittr pipes\,using the language of graphics\, ggplot2\,developing simple web applications using shiny\,efficient modelingthe second week will be devoted to collaborative project workthe last day\, all groups will present their project work\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\nSelection criteria\n\n\n\nThis year\, the school can accommodate ~30 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. This year\, we will also give priority to students who have already been admitted to RaukR 2020 (which had been cancelled).
URL:https://www.scilifelab.se/event/raukr-advanced-r-for-bioinformatics-summer-course/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
LOCATION:https://www.scilifelab.se/event/raukr-advanced-r-for-bioinformatics-summer-course/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210531T080000
DTEND;TZID=Europe/Stockholm:20210611T170000
DTSTAMP:20260614T004235
CREATED:20210413T071434Z
LAST-MODIFIED:20210526T120645Z
UID:10000355-1622448000-1623430800@www.scilifelab.se
SUMMARY:Super-Resolution\, Light-Sheet\, STED-FCS and FRET-FCS
DESCRIPTION:The Advanced Light Microscopy Unit\, ALM\, at Scilifelab gives a two-week course focusing on four new imaging and fluorescence spectroscopy techniques: \n\n\n\nLight-Sheet Imaging\n\n\n\nLong time-lapse imaging of live model organisms with low phototoxicityUltrafast volumetric imaging of cells with lattice light-sheet microscopy\n\n\n\nSuper-Resolution Imaging in Living Cells – MoNaLISA\n\n\n\nSmart probes. 50 nm resolution at 1-2 Hz. 100 x 100 mm field of view. Time lapse imaging\n\n\n\nSTED-FCS\n\n\n\nFluctuation spectroscopy with 30 nm resolutionSub-diffraction dynamics in living cells\n\n\n\nFRET-FCS\n\n\n\nEasy detection of protein-protein interactions in living cellsHighly sensitive detection of rare oligomers in living cells\n\n\n\nLecturers\n\n\n\nSteven EdwardsErdinc SezginIlaria TestaStefan Wennmalm\n\n\n\nCredits: 3 hp for PhD students\, but open for anyone \n\n\n\nLocation: Web-based \n\n\n\nRegistration: stewen@kth.se
URL:https://www.scilifelab.se/event/super-resolution-light-sheet-sted-fcs-and-fret-fcs/
CATEGORIES:Course
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2019/10/microscope.png
ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210517T080000
DTEND;TZID=Europe/Stockholm:20210521T170000
DTSTAMP:20260614T004235
CREATED:20210428T093317Z
LAST-MODIFIED:20210428T093423Z
UID:10000368-1621238400-1621616400@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 run 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:  February 01\, 2021 Application closes: April 11\, 2021Confirmation to accepted students:  April 16\, 2021\n\n\n\nResponsible teachers:  Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\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 a 2000 SEK workshop fee**Please 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.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online/
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260614T004235
CREATED:20210414T092540Z
LAST-MODIFIED:20210506T225135Z
UID:10000364-1620028800-1620406800@www.scilifelab.se
SUMMARY:Quick and clean: advanced Python for data science in biology - ONLINE
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of Advanced Python skills within all Swedish universities. \n\n\n\nImportant dates\n\n\n\nApplication is open!Application closes: April 15\, 2021Confirmation to accepted students: April 21\, 2021For questions about the course\, please contact Ashfaq Ali (ashfaq.ali@nbis.se)\, Sergiu Netotea (sergiu.netotea@nbis.se)\n\n\n\nCourse fee\n\n\n\nThe course is free of charge but a no show fee course fee of 2000 SEK will be invoiced to accepted participants who failed to attend the course after accepting to participate. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nThe main aim of this course is to introduce students to the so-called Zen of Python for quick and clean application of python in data science. The workshop is structured around  based on the industry way of classifying big data jobs: data analytics\, data science\, data engineering.  \n\n\n\nParticipants will have an opportunity to learn the following topics \n\n\n\nGeneral overview of computer choke points for various architectures together with a fast paced tutorial on advanced language concepts.Scientific computing\, statistics\, visualization and data mining\, via libraries such as numpy\, pandas\, statmodels and several other “science stack” libraries.Programming with focus on how to perform machine learning\, deep learning\, statistical learning and pattern recognition using python\, via scikit-learn\, tensorflow\, pymc3 and other more exotic libraries.Engineering the computing infrastructure and Python’s role in it. How to run Python on clouds and GPU machinesLearning how Python can be used to organize your workflow with efficiency and reproducibility in mind.Application to research themes where you will either pick one real ‘omics subject from a given task list or you will use Python in your project under our assistance. This is a great time to solidify your knowledge by applying it to your own research scope!\n\n\n\nLearning Outcomes\n\n\n\nAt the end of the course the course participants will have achieved following objectives \n\n\n\nGeneral knowledge about computational workflow using pythonHave knowledge about computer architecture and use of python for efficient computingKnowledge about python libraries for machine learning\, deep learning and statistical learning and their applicationsAbility to apply advanced python libraries in own research field\n\n\n\nWorkshop organization\n\n\n\nWe aim for a balance between lecturing and exercise in Jupyter notebooks (jupyter.org) which is used for taking notes\, self study\, hands on tasks and interaction. Considering that the course is online\, lectures will be delivered via zoom links and exercises will be carried out in zoom breakout rooms with the help of teaching assistants. Course session leaders will be available to answer theoretical and practical questions. Questions are welcome at any time. \n\n\n\nYou will be asked to prepare your laptop a week before the course starts. We will also use a slack channel for communication\, posting links or code tips. \n\n\n\nImportant to Know\n\n\n\nThe workshop covers some of the basic concepts of python programming and each session will have advanced material on the topic that may test the limits of the participant’s knowledge of python and computers. Difficulties during learning are expected and are part of the course design. \n\n\n\nFor the sessions on analyses of your own data\, students are encouraged to send their topic of interest before the start of the course.   \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises \n\n\n\nA computer with any OS.           Python\, R or any other computer language basic knowledge.Basic skills handling your own computer.For those interested in tasks involving cloud computing\, access to Amazon AWS is required. (user configuration)\n\n\n\nDesirable to have \n\n\n\nYou have bioinformatics or systems biology background\, statistical and machine learning skills.Have Linux on your laptop\, or access to a Linux server.You did programming before (not just courses) and can handle the command line.Have a good idea for a task you want to achieve on the fourth day.\n\n\n\nDue to limited space the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on several criteria including entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nGithub page (older version)
URL:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
CATEGORIES:Course
LOCATION:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260614T004235
CREATED:20210414T092106Z
LAST-MODIFIED:20210414T093012Z
UID:10000363-1620028800-1620406800@www.scilifelab.se
SUMMARY:Genome Assembly and Annotation 2021 – Online
DESCRIPTION:Elixir course open for PhD students\, postdocs\, researchers and other employees in need of Genome assembly and annotation skills. \n\n\n\nImportant dates\n\n\n\nApplication opens: 30th of March Application closes:19th of AprilConfirmation to accepted students: 26th of April \n\n\n\nResponsible teachers:  Christophe Klopp (FR)\, Lucile Soler (SE)\, Mahesh Binzer-Panchal (SE)\, Nima Rafati (SE)\, Tomas Larsson (SE)\, Henrik Lantz (SE)\, Brane Leskosek (SI)\, Marko Vidak (SI) and Erik Hjerde (NO) \n\n\n\nIf you do not receive information according to the above dates please contact:  Erik Hjerde \n\n\n\nCourse fee\n\n\n\nThe course is free of charge. \n\n\n\nCourse content\n\n\n\nThis course will introduce the best practice bioinformatics methods to assemble and annotate genomes via a series of lectures\, group work and computer practicals. Topics covered will include: \n\n\n\nQuality Assessment of sequencing dataLong read technologies and assemblies and assembly polishingAssembly ValidationHi-C sequencingMethod in Structural AnnotationAbinitio annotationAnnotation with makerAbinitio trainingFunctional annotationSubmission to DBBacterial annotation\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\nMandatory to complete a short command line course prior to the event. This will be made available to enrolled participants\n\n\n\nThe course is limited to 25 people\, and maximum 2 participants per national ELIXIR node (except Norway). The course is an advanced course. Based on the information collected upon registration\, the course organizers will enroll participants.
URL:https://www.scilifelab.se/event/genome-assembly-and-annotation-2021-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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