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DTSTART;TZID=Europe/Stockholm:20230130T080000
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DTSTAMP:20260408T144733
CREATED:20221130T151251Z
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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:20230206T090000
DTEND;TZID=Europe/Stockholm:20230210T170000
DTSTAMP:20260408T144733
CREATED:20221124T091335Z
LAST-MODIFIED:20221214T103757Z
UID:10000738-1675674000-1676048400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data - Lund\, Umeå and Uppsala
DESCRIPTION:This intense one-week workshop provides an introduction to the analysis of next generation sequencing data. The workshop is open to PhD students\, post-docs\, and other researchers affiliated to Swedish academia and healthcare. It is organised by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication opens: 21-Nov-2022Application closes: 31-Dec-2022Information to accepted students will be sent:  Week 2\, 2023 \n\n\n\n\n\n\n\nVenues\n\n\n\nThis workshop runs in parallel on-site in Uppsala\, Umeå and Lund. Lectures will be streamed online from our Uppsala site (mainly) to the other classrooms. Several teaching assistants will be present in the Umeå\, Lund and Uppsala classrooms all week to help with exercises and questions. When registering you will be asked to select a preferred site. \n\n\n\nUppsalaTrippelrummet (E10:1307-1309)Entrance C11Biomedical Centre (BMC) / SciLifeLab / Uppsala UniversityHusargatan 3752 37 Uppsala \n\n\n\nUmeåUB341Universitetsbibioteket plan 3Umeå University901 87 Umeå \n\n\n\nLundSölvegatan 35Lund University223 62 Lund \n\n\n\n\n\n\n\nFor more detailed information about workshop syllabus\, learning outcomes and entry requirements\, please visit the workshop website. \n\n\n\nwebsite & Application\n\n\n\n\n\n\n\nContact\n\n\n\nEmail: edu.intro-ngsMalin Larsson\, Martin Dahlö\, Roy Francis \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\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\nLectures 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\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. 
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-2/
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20230208T090000
DTEND;TZID=Europe/Stockholm:20230210T170000
DTSTAMP:20260408T144733
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:20230214T120000
DTEND;TZID=Europe/Stockholm:20230214T130000
DTSTAMP:20260408T144733
CREATED:20230120T101420Z
LAST-MODIFIED:20230207T103736Z
UID:10000793-1676376000-1676379600@www.scilifelab.se
SUMMARY:FunCoup network analysis workshop
DESCRIPTION:Network biology is a new paradigm to understand the complex interactions of the molecules in an organism using an integrative and systems approach. This workshop is intended for scientists interested in learning more about and applying network analysis in their research. We will describe and demonstrate the comprehensive network database FunCoup (https://funcoup.sbc.su.se/) and show how it can be used to answer various research questions at the systems biology level.  \n\n\n\n\n\n\n\n \n\n\n\nPROGRAM: \n\n\n\n1. Introduction to FunCoup and its unique features for analyzing functional coupling between genes/proteins\, as well as accompanying analysis tools such as PathBIX and MaxLink. \n\n\n\n2. Demonstration of FunCoup and accompanying tools\, as well as programmatic usage of FunCoup in an R notebook. \n\n\n\n\n\nRegistration\n\n\n\nLink to zoom
URL:https://www.scilifelab.se/event/funcoup-network-analysis-workshop/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
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