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DTSTART;TZID=Europe/Stockholm:20210830T080000
DTEND;TZID=Europe/Stockholm:20210903T170000
DTSTAMP:20260415T140149
CREATED:20210607T141128Z
LAST-MODIFIED:20210608T125759Z
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SUMMARY:Summer School Advanced topics in single cell Transcriptomics - Online
DESCRIPTION:Overview\n\n\n\nNBIS (SciLifeLab Bioinformatics Platform) and SIB (Swiss Institute of Bioinformatics) are pleased to co-organize this online course in Advanced topics in single cell Transcriptomics. \n\n\n\nThis jointly collaborative effort between the SIB and NBIS (SciLifeLab Bioinformatics Platform) was launched in 2019 as an every-second-year seasonal school where the thematic topic mirrors the life science demand of knowledge up-skilling. In 2019 we did a seasonal school on the topic of single-cell omics analysis and this year we are repeating this theme as the demand is still extremely high. \n\n\n\nIn recent years\, single-cell transcriptomics has become a widely used technology to study heterogeneous and dynamic biological systems. A large number of new tools and approaches have been developed for analyzing this new type of data. The goal of this joint School is to provide PhD students and postdocs with theoretical and mostly hands-on knowledge on selected advanced topics in Single Cell analysis. In particular\, the participants will be split into small groups to develop mini projects (more details provided later to accepted students. \n\n\n\nFor this one week course in single-cell transcriptomic we are delighted to have several excellent researchers and experts from both the Swedish and the Swiss Life Science community such as teachers such as Alma Andersson\, Åsa Björklund\, Volker Bergen\, Paulo Czarnewski\, Emma Dann\, Charlotte Soneson\, Panagiotis Papasaikas\, Geert van Geest and others. \n\n\n\nTarget audience\n\n\n\nThis course is designed for intermediate users and we consider the knowledge of basic steps in single-cell analysis as a prerequisite. \n\n\n\nCourse and Application details\n\n\n\nApplication is now open at SIB announcement Summer School Advanced topics in single cell Transcriptomics. The SIB page will be regularly updated with more detailed information. \n\n\n\nAny questions please contact Jessica Lindvall (Training coordination\, NBIS)\, jessica.lindvall@nbis.se and Grégoire Rossier (Training coordination\, SIB)\, Gregoire.Rossier@sib.swiss        \n\n\n\nImportant dates\n\n\n\nDeadline for free-of-charge cancellation is set to 28/07/2021. Cancellation after this date will not be reimbursed. \n\n\n\nCourse fee\n\n\n\nThe registration fees for academics are 300 CHF (appriximately 270 Euro) and 1500 CHF (approximately 1370 Euro) for for-profit companies.
URL:https://www.scilifelab.se/event/summer-school-advanced-topics-in-single-cell-transcriptomics-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210906T080000
DTEND;TZID=Europe/Stockholm:20210910T170000
DTSTAMP:20260415T140149
CREATED:20210603T124622Z
LAST-MODIFIED:20210615T135807Z
UID:10000396-1630915200-1631293200@www.scilifelab.se
SUMMARY:ELIXIR Omics Integration and Systems Biology - Online
DESCRIPTION:The National Bioinformatics Infrastructure Sweden (NBIS) / ELIXIR Sweden is pleased to announce the workshop in Omics Integration and Systems Biology. This workshop is open for PhD students\, postdocs\, group leaders and core unit staff from European institutions looking for an introduction to multi-omics integration and systems biology approaches. \n\n\n\nThis workshop will include lectures and hands-on exercises from NBIS / Scilifelab experts from Stockholm\, Lund and Gothenburg\, as well as guest sessions from: \n\n\n\nRicard Argelaguet\, PhD\, Babraham Institute\, United KingdomKim-Anh Lê Cao\, PhD\, Melbourne University\, AustraliaPedro Beltrao\, PhD\, EMBL-EBI\, United KingdomNikolaus Sonnenschein\, PhD\, DTU Technical University of Denmark\, Denmark\n\n\n\n More information to come on the course website. \n\n\n\nImportant Dates \n\n\n\n\nApplication opens: 3 JuneApplication closes: 9 AugustConfirmation to accepted students: 16 August\n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\nFee \n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. \n\n\n\n* Please note that NBIS cannot invoice individuals. \n\n\n\nContent \n\n\n\nThe aim of this workshop is to provide an integrated view of data-driven hypothesis generation through biological network analysis\, constraint-based modelling\, and supervised and unsupervised integration methods. A general description of different methods for analysing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods and pitfalls in their integration. The techniques will be discussed in terms of their rationale and applicability. The course will also include hands-on sessions and several seminars by invited speakers. \n\n\n\nSome of the covered topics include: \n\n\n\nData pre-processing and cleaning prior to integration\n\n\n\nApplication of key machine learning methods for multi-omics analysis including deep learning\n\n\n\nMulti-omics integration\, clustering and dimensionality reduction\n\n\n\nBiological network inference\, community and topology analysis and visualization\n\n\n\nCondition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic\, proteomic\, metabolomic and fluxomig data\n\n\n\nIdentification of key biological functions and pathways\n\n\n\nIdentification of potential biomarkers and targetable genes through modeling and biological network analysis\n\n\n\nApplication of network approaches in meta-analyses\n\n\n\nSimilarity network fusion and matrix factorization techniques\n\n\n\nIntegrated data visualization techniques\n\n\n\nFurther details about the course content may be found on the course website. \n\n\n\nEntry requirements \n\n\n\nThis is a course is open for PhD students\, postdocs\, group leaders and core unit staff from European institutions. Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. \n\n\n\nPractical exercises can be performed using R or Python\, so we only accept students with previous experience in one of those programming languages. We will not discuss how to process specific omics\, and the students are referred to other NBIS courses for this matter. \n\n\n\nRequired: \n\n\n\nBasic knowledge in R or Python;Basic understanding of frequentist statistics;A computer with web camera\, Zoom\, and permissions for installing software.\n\n\n\nDesirable: \n\n\n\nExperience with analysis of NGS and other omic data;Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “Introduction to biostatistics and machine learning”Basic conda and git knowledge\n\n\n\nThis workshop can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria including entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nContact information  \n\n\n\nFor questions about this workshop please contact: edu.omics-integration@nbis.se
URL:https://www.scilifelab.se/event/elixir-omics-integration-and-systems-biology-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210908T080000
DTEND;TZID=Europe/Stockholm:20210910T170000
DTSTAMP:20260415T140149
CREATED:20210527T110708Z
LAST-MODIFIED:20210906T135301Z
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SUMMARY:Workshop on Plotting in R - ONLINE
DESCRIPTION:National course open for PhD students (prioritized)\, postdocs\, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R.The course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus RingnerContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\n\nApplication\n\n\n\nCourse website\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: June 01Application deadline: July 30Confirmation to accepted participants: August 06 \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 1700 SEK.*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nThis course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. \n\n\n\nCourse content\n\n\n\nIn this course you will learn how to visualize your data in R.In particular\, you will learn: \n\n\n\n·          how to format the data necessary for ggplot·          how to make bar-charts\, box-plots and others using ggplot·          how to make PCA plots in ggplot·          how to use R packages for heatmaps·          how to plot data on maps using R (optional)·          how to plot and handle phylogenetic trees in R (optional)·          how to make interactive plots in R using Rshiny·          how to host a Rshiny app in one of the available servers \n\n\n\nLearning outcomes \n\n\n\nBy the end of the course the participant will be able to: \n\n\n\n·          handle data in R for visualizations·          apply the grammar efficiently in ggplot to get the desired plot·          combine different data and/or different plots that are of publication-grade·          write your own simple Rshiny app·          deploy Rshiny apps in public servers.  \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\nfamiliarity with using R and Rstudioa computer with a webcam running R and Rstudio You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseyou will be asked to install different R packages necessary for the course prior to the course. \n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 25 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/workshop-on-plotting-in-r-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
LOCATION:
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210929T090000
DTEND;TZID=Europe/Stockholm:20211001T130000
DTSTAMP:20260415T140149
CREATED:20210615T081112Z
LAST-MODIFIED:20210615T090743Z
UID:10000401-1632906000-1633093200@www.scilifelab.se
SUMMARY:Snakemake BYOC (bring-your-own-code) workshop (ONLINE)
DESCRIPTION:National workshop open for PhD students (prioritized)\, postdocs\, researchers and others from all Swedish universities who have previously participated in the NBIS Tools for reproducible research course or with demonstrated experience in writing Snakemake workflows. \n\n\n\n\n\n\n\n\nCourse website\n\n\n\nCourse application\n\n\n\n\n\n\n\n\nImportant dates \n\n\n\nApplication opens:  June 15 \n\n\n\nApplication closes: August 31 \n\n\n\nConfirmation to accepted students:  September 3 \n\n\n\nResponsible teachers:  Verena Kutschera\, John Sundh\, Per Unneberg \n\n\n\nContact information: edu.byoc-snakemake@nbis.se \n\n\n\nWorkshop fee \n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 1\,700 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nWorkshop content \n\n\n\nAs data analysis projects grow and change over time\, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up\, perform and monitor defined sequences of computational tasks (“workflows”)\, thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. \n\n\n\nThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. \n\n\n\nThis Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \n\n\n\nLearning outcomes \n\n\n\nAfter participation in the BYOC workshop\, participants will: \n\n\n\nBe able to create Snakemake workflows for bioinformatics data analysisDemonstrate knowledge of the structure and syntax of different types of Snakemake workflowsDemonstrate knowledge of advanced features of the Snakemake workflow language\n\n\n\n\n\n\n\nEntry requirements \n\n\n\nPrevious participation in the NBIS Tools for reproducible research workshop. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflowsYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improveA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required). You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the workshop.\n\n\n\nThe workshop can accommodate a maximum of 16 participants. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.
URL:https://www.scilifelab.se/event/snakemake-byoc-bring-your-own-code-workshop-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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