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DTSTART;TZID=Europe/Stockholm:20240311T080000
DTEND;TZID=Europe/Stockholm:20240315T170000
DTSTAMP:20260624T063849
CREATED:20231220T151424Z
LAST-MODIFIED:20240213T125934Z
UID:10001073-1710144000-1710522000@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\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\nMore details about the course can be found at the previous year webpage: RNAseq course 2023 \n\n\n\nThe course will follow similar structure and topics. \n\n\n\nNOTE: in March 2024\, the course will be a 5-day-course on-site in Uppsala. \n\n\n\nRegister here\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:At least 6 GB of RAM.Operating system Win10\, OS X or Linux\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\nCourse fee\n\n\n\nA course fee* of 3000 SEK for non-profit organisations will be invoiced to accepted participants. This includes lunches\, coffee\, snacks\, and one course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nImportant dates:\n\n\n\n\nApplication open: December 19\, 2023\n\n\n\nApplication deadline: February 19\, 2024\n\n\n\n\nResponsible teacher/s:Johan Reimegård\, Julie Lorent\, Nima Rafati \n\n\n\nContact information for questions regarding the courseedu.rnaseq@nbis.se
URL:https://www.scilifelab.se/event/rna-seq-data-analysis-2/
LOCATION:Uppsala University\, Uppsala\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240212T090000
DTEND;TZID=Europe/Stockholm:20240216T170000
DTSTAMP:20260624T063849
CREATED:20231113T100039Z
LAST-MODIFIED:20231113T125832Z
UID:10001025-1707728400-1708102800@www.scilifelab.se
SUMMARY:Single Cell RNA-Seq Data Analyses Workshop
DESCRIPTION:This workshop will introduce the best practice bioinformatics methods for analysing single cell RNA-seq data via a series of lectures and computer practicals. The total course duration is 5 days which includes 4 days of lectures and exercises followed by a “Bring Your Own Data” day where you get to practice your skills on a dataset of your choosing. \n\n\n\n\n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) \n\n\n\nResponsible teachers: Åsa Björklund\, Susanne Reinsbach\, Roy Francis \n\n\n\nContact information: edu.sc@nbis.se    \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: 13 Nov 2023 \n\n\n\nApplication closes: 17 Jan 2024 \n\n\n\nConfirmation to accepted participants: Weeks 3-4\, 2024 \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 3000 SEK for academic participants\, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee.  \n\n\n\n\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\nComparison of analysis toolkits: Seurat\, Scran and Scanpy\n\n\n\n\n\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\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space\, the course accommodates a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria such as correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/single-cell-rna-seq-data-analyses-workshop/
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:20231207T131500
DTEND;TZID=Europe/Stockholm:20231207T140000
DTSTAMP:20260624T063849
CREATED:20231204T135638Z
LAST-MODIFIED:20231204T135723Z
UID:10001058-1701954900-1701957600@www.scilifelab.se
SUMMARY:Multi Omics Data Integration - A translational perspective
DESCRIPTION:The forefront of deriving valuable insights into cellular functions involves the analysis of multi-omics data along with clinical  information. The integration of multi-omics data\, which encompasses information from diverse biomolecular layers\, holds promise for systematically and comprehensively understanding complex biology. Integrated approaches involve combining individual omics data either sequentially or simultaneously\, offering a means to explore the intricate interplay of molecules. This method proves valuable in assessing the flow of information across omics levels\, thereby bridging the gap from genotype to phenotype. Integrative approaches\, through their holistic examination of biological phenomena\, have the potential to enhance prognostic and predictive accuracy for disease phenotypes. Consequently\, they stand to contribute significantly to improved treatment and prevention strategies. In this talk I will show multiple approaches to integrate diverse data types and how we can use them in a translational medicine. \n\n\n\njoin zoom meeting\n\n\n\nAnimesh Acharjee\, PhDAssistant Professor\, Institute of Cancer and Genomic Sciences\, University of Birmingham\, United Kingdom \n\n\n\nBiography \n\n\n\n\n\n\n\nDr. Acharjee’s research interests encompass integrative data analytics\, predictive biomarker discovery\, bioinformatics methods for diagnostics\, and network biology. His multidisciplinary approach reflects his commitment to bridging the gap between computational methodologies and biological insights. Throughout his illustrious career\, Dr. Acharjee has been recognized with numerous fellowships\, including those from the British Council\, the  Dutch Government\, and Newton fellowships. These accolades underscore his dedication to advancing scientific knowledge and his contributions to the fields of bioinformatics\, data analytics\, and biostatistics. Dr. Acharjee’s journey continues to be marked by a relentless pursuit of excellence in research and a commitment to unraveling the intricacies of metabolicdiseases through innovative methodologies.
URL:https://www.scilifelab.se/event/multi-omics-data-integration-a-translational-perspective/
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:20231206T080000
DTEND;TZID=Europe/Stockholm:20231208T170000
DTSTAMP:20260624T063849
CREATED:20231002T115541Z
LAST-MODIFIED:20231002T115646Z
UID:10000980-1701849600-1702054800@www.scilifelab.se
SUMMARY:DDLS Biomarker Discovery: from theory to real world examples
DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of understanding biomarker research and methods. \n\n\n\nWorkshop location:  SciLifeLab\, Tomtebodavägen 23A\, Solna \n\n\n\nVenue:  Air&Fire (G2690) and Milky Way (A2631) \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-10-01 \n\n\n\nApplication closes: 2023-10-30 \n\n\n\nConfirmation to accepted students: 2023-11-15 \n\n\n\n \n\n\n\nCourse Leaders and teachers: Animesh Acharjee\, Clemens Wittenbecher\, Markus Mayrhofer\, Mun-Gwan Hong\, Paul Pyl\, Prasoon Agarwal \n\n\n\nplease contact edu.biomarkers@nbis.se for course-specific questions \n\n\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\nWorkshop fee\n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunch and coffee. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nWorkshop content\n\n\n\nThe main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research\, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery. \n\n\n\nTopics covered will include: \n\n\n\n\nBiomarker study design for “context of use”\n\n\n\nTypes of biomarkers\, diagnostic\, prognostic\, and wellness\n\n\n\nBiomarkers are in use for various diseases such as cancer\, cardiovascular diseases\n\n\n\nBiomarker discovery from various omics data including proteome\, microbiome\n\n\n\nBiomarker and multi-omics data integration\n\n\n\nMachine learning methods\, lasso logistic regression and random forest\, to identify biomarkers\n\n\n\nPerformance indicators\, e.g. sensitivity and specificity\n\n\n\nInternal/external validation\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required to be able to follow the workshop and complete the exercises: \n\n\n\n\nAbility to bring your own laptop with R installed for the practical exercises\n\n\n\nBasic Programming/scripting experience in R\n\n\n\nor took an R course NBIS prepared.\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nSome basic knowledge of biostatistics\n\n\n\nPrevious experience in biomarker-related studies\n\n\n\n\nDue to limited space\, the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/ddls-biomarker-discovery-from-theory-to-real-world-examples/
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:20231204T090000
DTEND;TZID=Europe/Stockholm:20231206T170000
DTSTAMP:20260624T063849
CREATED:20230906T082705Z
LAST-MODIFIED:20231106T132742Z
UID:10000967-1701680400-1701882000@www.scilifelab.se
SUMMARY:Snakemake “bring-your-own-code” (BYOC) workshop - Cancelled
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. CANCELLED! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-09-11 \n\n\n\nApplication closes: 2023-10-29 \n\n\n\nConfirmation to accepted students: 2023-11-06 \n\n\n\nCourse Leader and teachers: Verena Kutschera (CL)\, Marcel Martin\, John Sundh. In case you have any workshop-specific questions\, please contact: edu.byoc-snakemake@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you confirm your participation but do not do so (no-show) you will be invoiced 2\,000 SEK*.*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse 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\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nBe able to create Snakemake workflows for bioinformatics data analysis\n\n\n\nDemonstrate knowledge of the structure and syntax of different types of Snakemake workflows\n\n\n\nDemonstrate knowledge of advanced features of the Snakemake workflow language\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required for being able to follow the course: \n\n\n\n\nPrevious participation in the NBIS Tools for reproducible research course. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.).\n\n\n\nYour 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 improve. \n\n\n\nA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required).\n\n\n\n\nDue to limited space the course can accommodate a maximum of 12 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/snakemake-bring-your-own-code-byoc-workshop-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:20231124T100000
DTEND;TZID=Europe/Stockholm:20231124T160000
DTSTAMP:20260624T063849
CREATED:20231019T124448Z
LAST-MODIFIED:20231122T105255Z
UID:10001004-1700820000-1700841600@www.scilifelab.se
SUMMARY:SciLifeLab Bioinformatics Platform NBIS celebrates 15 years
DESCRIPTION:NBIS celebrates 15 years and organises an Anniversary Symposium on Friday 24 November at 10:00 – 16:00 with mingle afterwards in Uppsala\, SciLifeLab Trippelrummet.On the agenda so far:KeynotesPresentation of Human Protein Atlas (HPA) by Mathias UhlénPresentation of Bigpicture by Jeroen van der LaakUser presentations2–3 user presentations (users of the national bioinformatics infrastructure NBIS)NBIS presentationsPresentation of NBIS 15 years and ELIXIR 10 years by Bengt PerssonPresentation of WABI 10 years by Björn NystedtHuman data — 1+MG och GDI (Anna Hagwall/Johan Viklund)Presentation of our Training activities by Jessica LindvallPresentation of computational support by Jonas SöderbergData management – enable FAIR data for Swedish research (Niclas Jareborg)Mingle afterwards with drinks and finger food.Preliminary programme and link to registration available \n\n\n\nRead more
URL:https://www.scilifelab.se/event/scilifelab-bioinformatics-platform-nbis-celebrates-15-years/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/10/nbis-eventlogo-nb.png
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231120T090000
DTEND;TZID=Europe/Stockholm:20231124T160000
DTSTAMP:20260624T063849
CREATED:20230911T091422Z
LAST-MODIFIED:20230911T091932Z
UID:10000970-1700470800-1700841600@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research
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: Erik Fasterius\, John SundhContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Sep 11\, 2023 \n\n\n\nApplication deadline: Oct 20\, 2023 \n\n\n\nConfirmation to accepted participants: Oct 27\, 2023 \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches\, coffee and snacks\, and course dinner. 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\nLearning outcomes \n\n\n\nBy 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\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/
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:20231113T090000
DTEND;TZID=Europe/Stockholm:20231117T170000
DTSTAMP:20260624T063849
CREATED:20230607T141335Z
LAST-MODIFIED:20230607T141419Z
UID:10000906-1699866000-1700240400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within Swedish academia\, introducing the analysis of next generation sequencing data. \n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI) \n\n\n\nResponsible teachers: Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nContact information: edu.intro-ngs@nbis.se  \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jun 7\, 2023 \n\n\n\nApplication deadline: October 4\, 2023 \n\n\n\nConfirmation to accepted participants: Week 41 (October 9-12) \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 3000 SEK for academic participants\, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee.  \n\n\n\n\n\n\n\nCourse description\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\n\n\n\n\nCourse content\n\n\n\nBriefly\, the workshop covers the followings major topics: \n\n\n\n\nWorking on the UNIX/LINUX command line\n\n\n\nBioinformatic/NGS data formats and QC\n\n\n\nDNA variant calling workflow essentials\n\n\n\nRNA sequence analysis workflow essentials\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nAfter this workshop you should be able to: \n\n\n\n\nDescribe the basic principles of next generation sequencing.\n\n\n\nUse the Linux command line interface to manage simple file processing operations\, and organise directory structures.\n\n\n\nConnect to and work on a remote high performance compute cluster.\n\n\n\nApply programs in Linux for analysis of NGS data.\n\n\n\nSummarise 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\nExplain common NGS file formats.\n\n\n\nInterpret quality control of NGS reads.\n\n\n\nExplain the steps involved in variant calling using whole genome sequencing data.\n\n\n\nIndependently perform a basic variant calling workflow on example data.\n\n\n\nDemonstrate hands-on experience with handling raw RNA sequencing data\, QC and quantification of gene expression.\n\n\n\nExplain the steps involved in differential gene expression using RNA seq data.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nTo be able to follow the workshop you need to: \n\n\n\n\nBYOL\, bring your own laptop configured according to precourse instructions.\n\n\n\nHave a background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable.\n\n\n\nTo get the maximum benefit from the workshop you should:\n\n\n\nHave a research project where you are currently using or are planning to use next generation sequencing.\n\n\n\n\n\n\n\n\n\n\nSelection criteria\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 workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers\, and we will prioritise applications  from Swedish academia.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-3/
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:20231106T090000
DTEND;TZID=Europe/Stockholm:20231110T170000
DTSTAMP:20260624T063849
CREATED:20230818T135627Z
LAST-MODIFIED:20230915T130032Z
UID:10000955-1699261200-1699635600@www.scilifelab.se
SUMMARY:DDLS Population genomics in practice
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of hands-on and practical skills for the analyses of population genomics data. \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-08-17 \n\n\n\nApplication closes: 2023-09-30 \n\n\n\nConfirmation to accepted students: 2023-10-10 \n\n\n\nCourse Leader and teachers: Per Unneberg (CL)\, Nikolay Oskolkov\, Jason Hill\, André Soares \n\n\n\nIn case you miss information on any of the above dates\, please contact: edu.population-genomics-in-practice@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 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\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an introduction to commonly used methods in population genomics. As the focus of the course is on hands-on work\, the topics have been designed to cover the fundamental analyses that are common in many population genomics studies. The course consists of lectures and exercises\, with a focus on the practical aspects of analyses. Whereas lectures introduce some background theory\, their primary aim is to set the stage for accompanying exercises. \n\n\n\nTopics covered will include: \n\n\n\n\nFoundations of population genetics\n\n\n\nIntroduction to simulation and the coalescent\n\n\n\nBasics of variant calling\n\n\n\nVariant filtering and sequence masks\n\n\n\nCharacterization and interpretation of DNA sequence variation\n\n\n\nCalculation and interpretation of summary statistics from variation data\n\n\n\nInvestigating population structure with admixture modelling and principal component analyses\n\n\n\nDemographic modelling using sequentially Markovian coalescent models and linkage disequilibrium\n\n\n\nSelection scans\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ndescribe the different forces of evolution and how they influence genetic variation\n\n\n\nunderstand and interpret genealogical trees and how they relate to genetic variation data\n\n\n\ndescribe the basics of the coalescent\n\n\n\nperform simple coalescent simulations with msprime\n\n\n\nrun simple SLiM forward simulation models\n\n\n\ndescribe and run the steps of a variant calling pipeline\, including quality control of raw reads\, read mapping\, and variant calling\n\n\n\nknow how and when to filter raw variant calls using manual coverage filters\n\n\n\ndescribe and calculate nucleotide diversity from variation data\n\n\n\nanalyse population structure with admixture modelling and dimensionality reduction methods\n\n\n\nperform demographic modelling with sequential Markovian coalescent models\n\n\n\ndescribe methods that identify regions undergoing adaptation and selection\n\n\n\nrun selection scans\, score identified regions and interpret findings in the context of genome annotations\n\n\n\n\n\n\n\n\n\n\nEntry Requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge in R or Python\n\n\n\nBasic knowledge of variant calling\, or the equivalent of NBIS course “Introduction to Bioinformatics using NGS data”\n\n\n\nBasic knowledge of population genetics\n\n\n\nBasic understanding of frequentist statistics\n\n\n\nA computer\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with analysis of NGS and other omic data\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/population-genomics-in-practice/
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:20231023T090000
DTEND;TZID=Europe/Stockholm:20231027T170000
DTSTAMP:20260624T063849
CREATED:20230811T112638Z
LAST-MODIFIED:20230811T120144Z
UID:10000948-1698051600-1698426000@www.scilifelab.se
SUMMARY:R Foundations for Life Scientists
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of  programming in R. \n\n\n\n\n\n\n\nImportant dates & Information\n\n\n\nApplication opens: 2023-08-20 \n\n\n\nApplication closes: 2023-09-20 \n\n\n\nConfirmation to accepted students: 2023-09-27 \n\n\n\nCourse Leader and teachers: Nima Rafati (CL)\, Prasoon Argawal (CL)\, Marcin Kierczak (CT)\, Sebastian DiLorenzo (CT) \n\n\n\nIn case you miss information on any of the above dates\, please contact us via edu.r@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\nThe course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting emphasizing the parts useful for life scientists. After introductory lectures on good programming practices\, basic software design theory and a brief overview of R\, we will delve into programming. \n\n\n\nTopics covered will include: \n\n\n\n\nVariables and Operators\n\n\n\nMatrices\, lists\, and dataframes\n\n\n\nData manipulation\n\n\n\nVisualization\n\n\n\nR packages\n\n\n\nBioconductor\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nDescribe different data structures commonly used in R.\n\n\n\nWork with different data types.\n\n\n\nImport and export data from and to R environment. \n\n\n\nManipulate data.\n\n\n\nWork with dataframes and lists.\n\n\n\nVisualize the data.\n\n\n\nExplain about R packages and steps to create them.\n\n\n\nInstall R packages from Bioconductor. \n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nGood general computer literacy\n\n\n\nBasic knowledge in mathematics and statistics\n\n\n\n\nDue to limited space the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/r-foundations-for-life-scientists/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231017T080000
DTEND;TZID=Europe/Stockholm:20231019T170000
DTSTAMP:20260624T063849
CREATED:20230810T125629Z
LAST-MODIFIED:20231013T081404Z
UID:10000946-1697529600-1697734800@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices - Cancelled
DESCRIPTION:This national workshop in Data Management is a co-arranged event between Uppsala University and Chalmers University\, and provides an introduction for PhD students\, postdocs\, researchers\, and other employees within all Swedish universities. The workshop will introduce important aspects of research data management through a series of lectures\, demonstrations\, and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. CANCELLED – next time (preliminary) in Stockholm\, April 2024 \n\n\n\nTopics covered will include: \n\n\n\n\nOpen Science and FAIR in practice\n\n\n\nOrganising data\, files and folders in research projects\n\n\n\nDescribing data with metadata\n\n\n\nPublishing data to public data repositories\n\n\n\nCleaning tabular data and metadata with OpenRefine\n\n\n\nWriting basic recipes for data analysis and visualisation with R\n\n\n\nVersioning data\, documents and scripts\n\n\n\nWriting Data Management Plans\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: now \n\n\n\nApplication closes: 2023-09-27 \n\n\n\nInformation to accepted students will be sent:  2023-09-29 \n\n\n\n\n\n\n\nContact\n\n\n\nedu.intro-dm@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\nFormat\n\n\n\nThis workshop runs in parallel on-site in Uppsala\, and Göteborg. Lectures will be streamed online from our Uppsala site (mainly) to the Gothenburg classrooms\, and vice versa. Teachers and teaching assistants will be present at both locations all week to help with exercises and questions. When registering you will be asked to select a preferred site. \n\n\n\n\n\n\n\nVenues\n\n\n\nUppsala \n\n\n\nTrippelrummet (E10:1307-1309)\, SciLifeLab Navet\, Entrance C11\, Biomedical Centre (BMC) \n\n\n\nHusargatan 3\, 752 37 Uppsala \n\n\n\nGothenburg \n\n\n\nCLS Room Scrum 1\, University library\, 2nd floor  \n\n\n\nHörsalsvägen 2 (entrance)\, 412 96 Gothenburg \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals. \n\n\n\n\n\n\n\nEntry requirements\n\n\n\nNo previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. Installation instructions will be provided before the course starts\, and the course organisers arrange a pre-course event approximately one week prior to first course day. \n\n\n\n\n\n\n\nCredits & Certificate\n\n\n\nPlease note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop. \n\n\n\nDue to limitations in space and capacity the course can accommodate a maximum of 25 participants per site.  If we receive more applications\, participants will be selected based on several criteria\, including correct entry information\, motivation to attend the course\, as well as gender and geographical balance. \n\n\n\nFor more detailed information about the workshop\, please visit the workshop website.
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-5/
LOCATION:Uppsala University\, Uppsala and Chalmers University\, Gothenburg
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20231009T090000
DTEND;TZID=Europe/Stockholm:20231013T170000
DTSTAMP:20260624T063849
CREATED:20230614T070145Z
LAST-MODIFIED:20230615T091559Z
UID:10000913-1696842000-1697216400@www.scilifelab.se
SUMMARY:Python programming with applications to bioinformatics
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of fundamental Python skills within all Swedish universities \n\n\n\nResponsible teachers: Nina Norgren\, Dimitris Bampalikis\, Jeanette Tångrot \n\n\n\nContact information: edu.intro-python@nbis.se \n\n\n\nVenues: SciLifeLab Uppsala\, Trippelrummet\, BMC & Umeå University\, Naturvetarhuset\, room NAT.D.370 \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: June 15 \n\n\n\nApplication deadline: September 8 \n\n\n\nConfirmation to accepted participants: September 15 \n\n\n\n\n\n\n\nCourse fee\n\n\n\n A course fee* of 3000 SEK will be invoiced to accepted participants. This includes lunches\, coffee and snacks\, and course dinner \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse description\n\n\n\nThis course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course\, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. \n\n\n\nFormat \n\n\n\nThis course runs in parallel both on-site in Uppsala and in Umeå. Lectures will be streamed online from our Uppsala site to the Umeå site. Several teaching assistants will be present both in the Umeå and Uppsala classroom all week to help with exercises and questions. When registering you will be asked to which site you apply. \n\n\n\nThe course consists of a mix of presentations\, demonstrations\, and practical exercises (either in the lab with assistants or on your own). Prior to the course\, you can read a companion book “Programming Python”\, or “Learning Python”. Such a book will also prove useful for your programming tasks\, after the course is over. It is however not required\, and material will be presented in class. \n\n\n\n\n\n\n\nCourse content\n\n\n\n\nCore concepts about Python syntax: Data types\, blocks and indentation\, variable scoping\, iteration\, functions\, methods and arguments\n\n\n\nDifferent ways to control program flow using loops and conditional tests\n\n\n\nRegular expressions and pattern matching\n\n\n\nWriting functions and best-practice ways of making them usable\n\n\n\nReading from and writing to files\n\n\n\nCode packaging and Python libraries\n\n\n\nHow to work with biological data using external libraries.\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\n\nDescribe and apply basic concepts in Python\, such as:LoopsIf/else statementsFunctions\n\nReading/writing to files\n\n\n\n\n\nBeing able to edit and run Python code\n\n\n\nWrite file-processing Python programs that produce output to the terminal and/or external files\n\n\n\nCreate stand-alone python programs to process biological data\n\n\n\nKnow how to develop your skills in Python after the course (including debugging)\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage\, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises. \n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants in Uppsala and 15 in Umeå. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to 1.5 hp credits\, however the estimated credits are just recommendations. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/python-programming-with-applications-to-bioinformatics-2/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230918T080000
DTEND;TZID=Europe/Stockholm:20230922T170000
DTSTAMP:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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:20260624T063849
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
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220912T080000
DTEND;TZID=Europe/Stockholm:20220916T170000
DTSTAMP:20260624T063849
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
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