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  • RNA-seq, 1 hp

    13 - 16 March 2017

    Elixir node event
    RNA-seq, 1 hp https://tess.elixir-europe.org/events/rna-seq-1-hp-bb9f6240-741a-4ea8-aa48-deda7e1198b4 Course content This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: Gene and isoform detection using short RNA-seq reads Gene and isoform detection using long RNA-seq reads Gene and isoform detection combining RNA-seq data with other data sources Quality assessment of RNA-seq data Differential expression analysis using RNA-seq data on multiple cells Downstream analysis after identifying differentially expressed genes. 2017-03-13 09:00:00 UTC 2017-03-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • R Programming Foundations for Life Scientists, 2 hp

    27 March - 1 April 2017

    Elixir node event
    R Programming Foundations for Life Scientists, 2 hp https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists-2-hp-56fa30d4-110b-45eb-a88c-682e65f58c51 Course content The course is addressed to life scientists with little or moderate experience in programming but enthusiastic about learning how to use R to make their work smoother and easier. The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting with some more attention paid to 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. We start by learning how to use R as a simple calculator, what are variable types, how to use data structures, how to implement repeating actions with and without loops, how to take actions based on certain condition. We gradually proceed to loading data, importing data from common file formats, we do some basic matrix algebra; learn how to perform basic statistical tests and how to visualize results. We will also put stress on giving you tools to access help and information on R-related challenges and issues, we will spend some time on learning how to install external packages, how to find bugs and address common installation issues. We also mention some more advanced topics and tell you more about BioConductor that is an invaluable tool for a computational biologist. You will also learn how to document your work and how to generate automatic reports. We try to illustrate all these concepts with some real-life examples and interesting lab tasks. The course will be given by experienced computational biologists from SciLifeLab and Uppsala University. Dr. Marcin Kierczak responsible for the content of the course is an experienced R user/coder, who has previously developed R packages and has experience in teaching programming and R to different audiences. 2017-03-27 09:00:00 UTC 2017-04-01 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Quality Assurance and Quality Control in Metabolomics

    12 - 13 October 2017

    Birmingham, United Kingdom

    Elixir node event
    Quality Assurance and Quality Control in Metabolomics https://tess.elixir-europe.org/events/quality-assurance-and-quality-control-in-metabolomics-ea29a17f-d41e-4488-808b-b137b7c82b93 This 2-day course will provide a comprehensive theoretical overview and hands-on experience of the application of quality assurance (QA) and quality control (QC) in metabolomics. It will include both theoretical and practical components to provide hands-on experience of using the mass spectrometer (a maximum of 4 people working on the instrument in a session) and the analysis of data. Experts who have developed the application of QA and QC procedures within the field will lead the course. 2017-10-12 09:00:00 UTC 2017-10-13 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • NERC-MDIBL Environmental Genomics and Metabolomics 2018

    4 - 9 March 2018

    Birmingham, United Kingdom

    Elixir node event
    NERC-MDIBL Environmental Genomics and Metabolomics 2018 https://tess.elixir-europe.org/events/nerc-mdibl-environmental-genomics-and-metabolomics-2018 This NERC funded short course will provide a hands-on approach to guide genomics and metabolomics research applied to the environmental scientists. Participation in the course is open to everyone but priority is given to NERC-funded PhD students and early-career scientists. The course will include ~1.5 days generic environmental omics training and ~3.5 days specialized genomics or metabolomics training. Case studies using multi-omics data will be provided so that you gain practical experience of analyzing and interpreting multi-omics data. Distinguished visiting academics will provide keynote lectures on each day of the course to highlight environmental omics applictions that draw on the expertise of the guest faculty. 2018-03-04 09:00:00 UTC 2018-03-09 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT Genomics Metabolomics [] [] [] [] [] []
  • Tools for Reproducible Research

    22 - 24 March 2018

    Elixir node event
    Tools for Reproducible Research https://tess.elixir-europe.org/events/tools-for-reproducible-research #url https://www.scilifelab.se/events/reproducible-research-vt18/ #training Course leaders: Leif Wigge (leif.wigge@scilifelab.se) and Rasmus Ågren (rasmus.agren@scilifelab.se) Location: Air/Fire, Stockholm SciLifeLab National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities with interest in making their computational analysis more reproducible.  Responsible teachers: Leif Wigge, Rasmus Ågren Contact information: leif.wigge@scilifelab.se and rasmus.agren@scilifelab.se Apply here: https://www.scilifelab.se/events/reproducible-research-vt18/   2018-03-22 09:00:00 UTC 2018-03-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RNA-seq

    14 - 17 May 2018

    Elixir node event
    RNA-seq https://tess.elixir-europe.org/events/rna-seq Course information: https://www.scilifelab.se/events/rnaseqvt18/ Course leader Johan Reimegård (johan.reimegard@scilifelab.se) #training Course content This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: Gene and isoform detection using short RNA-seq reads Gene and isoform detection using long RNA-seq reads Gene and isoform detection combining RNA-seq data with other data sources Quality assessment of RNA-seq data Differential expression analysis using RNA-seq data on multiple cells Downstream analysis after identifying differentially expressed genes. Entry requirements Basic knowledge in linux is a requirement! We will not teach Linux at the course and you will have considerable trouble to follow the practical sessions if you are not reasonably used to work in a linux environment. Be able to bring your own laptop for the practical computational exercises. If you don’t have a laptop to bring please contact education@scilifelab.uu.se before you register. Some programming/scripting experience is desirable, but not required. Experience working on the SNIC center Uppmax is desirable, but not required. Participants of the SciLifeLab Course “Introduction to Bioinformatics using NGS data” (or alike) are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the workshops will be considerably more detailed on the covered topics. Due to space constraints for the computer exercises, there are a maximum number of allowed 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. Date and time 2017-11-07 - 2017-11-09 Location Husargatan 3, Uppsala Important dates Application open: June 19 Application deadline: September 28 Confirmation to accepted students: October 9 Responsible teachers: Johan Reimegård If you don’t receive information according to the dates above, contact education@scilifelab.uu.se Course fee A course fee of 1300 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.     2018-05-14 09:00:00 UTC 2018-05-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Genome Annotation

    15 - 18 May 2018

    Elixir node event
    Introduction to Genome Annotation https://tess.elixir-europe.org/events/introduction-to-genome-annotation Course Information: https://www.scilifelab.se/events/geneeann-vt18/ Course leader Henrik Lantz (henrik.lantz@nbis.se) #training Apply here: https://docs.google.com/forms/d/e/1FAIpQLSeOLov4kGj8t50KZSS7Tsc2TSuuj91ZY-E33Mw263pfBaXMsQ/viewform  Course content Genome annotation is the process in which loci of interest in a genome are identified, both in structure and function. The structural part includes identifying the number and size of exons and introns, size of UTRs, and number of isoforms. The functional annotation, in turn, focuses on inferring the biological role of different transcripts. The course is aimed at researchers that are involved in on-going or upcoming genome projects and wish to deepen their understanding of the various forms of data and computational steps required to achieve a comprehensive annotation. The focus of the course will be on non-model eukaryote organisms, and in particular the structural annotation of protein coding genes. We will use de novo gene finders, protein alignments and RNA-seq data to infer the structure of genes, and show how to combine these different lines of evidence to get the most stable and informative annotation. We will also infer the function of these genes using similarity to known proteins as well as the presence of functional domains. Topics covered will include: ·       Project planning ·       Gene finders ·       Protein alignment ·       RNA-seq assembly ·       Combined structural annotation using Maker2 ·       Functional annotation ·       Procaryote annotation ·       The NBIS annotation service Entry requirements Participants must be comfortable navigating a linux shell and execute programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data (genome assembly, transcriptome assembly, SNP calling) is a plus. Applicants are also encouraged to bring their own laptops, but there will be computers to use for participants unable to do so. Due to space constraints for the computer exercises, there are a maximum number of allowed 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. 2018-05-15 09:00:00 UTC 2018-05-18 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Single cell RNA sequencing data analysis

    21 - 24 May 2018

    Elixir node event
    Single cell RNA sequencing data analysis https://tess.elixir-europe.org/events/single-cell-rna-sequencing-data-analysis-2986aebb-b31b-499d-9bd0-e7cc04658a51 #url https://www.scilifelab.se/events/scRNAseq-VT18/ National course open for PhD students, postdocs, researchers and other employees in need of single cell RNA-seq data analysis skills within all Swedish universities Course name: Single cell RNA sequencing data analysis Course dates: 2018-05-21 to 2018-05-23 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna Important dates Application opens: February 1 Application closes: April 23 Confirmation to accepted students: April 27 Responsible teachers: Åsa Björklund If you do not receive information according to the above dates please contact: asa.bjorklund@scilifelab.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.. *Please note that NBIS cannot invoice individuals Course content This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: An overview of the current scRNAseq techniques Basic overview of pipelines for processing raw reads into expression values Quality control of scRNAseq data Dimensionality reduction and clustering techniques Data normalization Differential gene expression for scRNAseq data Examples on how to use these tools in a research project. Entry requirements Required for being able to follow the course and complete the computer exercises Basic knowledge in Linux is a requirement. We will not teach Linux at the course and you may have considerable trouble to follow the practical sessions if you are not reasonably used to work in a Linux environment. Be able to bring your own laptop with R installed for the practical computational exercises. Instructions on installation will be sent by email to accepted participants. Some programming/scripting experience is required (preferably in R). Desirable: Experience working on the SNIC center Uppmax is desirable, but not required. We encourage accepted participants to do an Uppmax tutorial before the course. Previous experience with RNA-seq analysis and/or participation in NGS/RNA-seq course is an advantage. Due 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. Link to application: https://goo.gl/forms/89JPQcm0j7zKtjLN2 2018-05-21 09:00:00 UTC 2018-05-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    21 - 26 May 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-8ba319ee-3569-4b1f-839d-1f2cbc483a10 Course Information: https://www.scilifelab.se/events/ngsdatavt18lkp/ #training Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se and Malin Larsson, malin.larsson@scilifelab.se Course content The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Topics covered will include: Basic Linux usage NGS read-to-reference alignment (genomic and RNA-Seq) Variant calling in populations De novo assembly of RNA-sequence data Reference-guided RNA-Seq expression analysis Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. Entry requirements A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable To get the maximum benefit from the course we would like you to Have relevant previous experience in sequencing or analysis Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing Be able to bring your own laptop for the practical computational exercises It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Important dates Application open: August 1 Application deadline: October 7 Confirmation to accepted students: October 23 Responsible teachers: Manfred Grabherr If you don’t receive information according to the dates above, contact education@scilifelab.uu.se Course fee A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.   2018-05-21 09:00:00 UTC 2018-05-26 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RaukR, Advanced R for Bioinformatics, Summer course

    10 - 22 June 2018

    Elixir node event
    RaukR, Advanced R for Bioinformatics, Summer course https://tess.elixir-europe.org/events/advanced-r-for-bioinformatics-summer-school #training #url: https://www.scilifelab.se/events/raukr-advanced-r-for-bioinformatics-summer-school/ #url: https://nbisweden.github.io/workshop-RaukR-1806/  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. Course leaders: Marcin Kierczak (marcin.kierczak@scilifelab.se), Sebastian Dilorenzo (sebastian.dilorenzo@nbis.se) Course description Join us in medieval Visby this June to improve your R skills and have a nice time! In Life Science and Bioinformatics, R is increasingly being used to transform and analyse data, perform statistical analysis and produce publication-ready visualizations. This Summer course will focus on advanced R functionality, to increase the participants skillset and understanding of what is possible to do today. You are very welcome to apply or see the homepage for more information. Please, help us spread the word to interested participants! Guest speakers Martin Morgan (Director at Bioconductor) Paula Moraga (Lancaster Univ., RLadies) Yhui Xie (RStudio) Course content Reproducibility with R Writing R packages R scripts S3, S4 and Reference Classes Code debugging and optimization R markdown tidyverse Bioconductor ggplot2 Interactive plots Statistics in R Machine Learning Shiny web applications Working with maps Area specific workshops (RNAseq, spatial stats etc) Working with your own dataset Course fee Academic: 8500 SEK (Includes participation in all official activities and events, course materials, breakfast, lunch and accommodations). Participants from outside of academia should contact us for a fee quote. The fee does not include travel costs. Important dates  Application open: March 17 Application deadline: April 15 Notification of acceptance/decline: April 25 2018-06-10 09:00:00 UTC 2018-06-22 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Advanced Python programming

    11 - 16 June 2018

    Elixir node event
    Advanced Python programming https://tess.elixir-europe.org/events/advanced-python-programming #training More information will follow Course leader: Sergiu Netotea (sergiu.netotea@scilifelab.se) 2018-06-11 09:00:00 UTC 2018-06-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Metabolomics: Understanding Metabolism in the 21st Century

    23 July - 17 August 2018

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics: Understanding Metabolism in the 21st Century https://tess.elixir-europe.org/events/metabolomics-understanding-metabolism-in-the-21st-century Metabolomics is an emerging field that aims to measure the complement of metabolites (the metabolome) in living organisms. The metabolome represents the downstream effect of an organism’s genome and its interaction with the environment. Metabolomics has a wide application area across the medical and biological sciences. The course provides an introduction to metabolomics, describes the tools and techniques we use to study the metabolome and explains why we want to study it. By the end of the course you will understand how metabolomics can revolutionise our understanding of metabolism. 2018-07-23 09:00:00 UTC 2018-08-17 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    10 - 15 September 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-5ae594b9-4fa3-4e1e-addd-ec9cc2b6a98b #training More information will follow Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se  Course content The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Topics covered will include: Basic Linux usage NGS read-to-reference alignment (genomic and RNA-Seq) Variant calling in populations De novo assembly of RNA-sequence data Reference-guided RNA-Seq expression analysis Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. Entry requirements A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable To get the maximum benefit from the course we would like you to Have relevant previous experience in sequencing or analysis Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing Be able to bring your own laptop for the practical computational exercises It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. 2018-09-10 09:00:00 UTC 2018-09-15 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Elixir-EXCELERATE Train-the-Trainer course

    9 - 12 October 2018

    Elixir node event
    Elixir-EXCELERATE Train-the-Trainer course https://tess.elixir-europe.org/events/elixir-excelerate-train-the-trainer-course #training ELIXIR-EXCELERATE, in collaboration with ELIXIR Sweden and ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event. Course information/Course webpage: https://elixir-iib-training.github.io/website/2018/10/09/train-the-trainer-stockholm.html  Application form: https://docs.google.com/forms/d/e/1FAIpQLSc0KwSjcBJ6wemxCBhgDrfg4OxccFbbDM_ZA-0Ui4jEe_eV1Q/viewform  Important dates Course date: 9-11 October, 2018 We will accept a maximum of 20 participants. Priority will be given to candidates from ELIXIR Sweden and other ELIXIR nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 20 participants. Venue Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden Room: Air Fee There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR-EXCELERATE TtT Exchange Programme Travel Grant when they fill their application form. Instructors Allegra Via (Training Coordinator ELIXIR-IIB, IBPM-CNR) Jessica Lindvall (Training Coordinator ELIXIR-SE, NBIS) Local organisers Jessica Lindvall, NBIS (National Bioinformatics Infrastructure Sweden), Elixir-SE Description The course is made up of four sessions, covering: Learning principles and how they apply to training and teaching Teaching techniques that can be used to enhance learner engagement and participation Assessment and feedback in training and teaching Lesson, course, and materials design Application form Target Audience Whoever is interested in becoming a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. How learning works? How can I use learning principles and theories to improve my teaching? How can I make my teaching more engaging and effective? How should I adjust my teaching to different types of learners? How can I help slow learners? How can I assess whether my students are actually understanding my lessons? Are they actually learning? What is the best balance between theory and practice? How can I best assess whether learning is occurring and/or has occurred? What works in a classroom and what doesn’t? How can I become a better teacher? Etc. Learning Objectives: To get acquainted with Learning principles and how they apply to training To be able to select and utilise training techniques that can be used to enhance learner engagement and participation To learn how to use assessment and feedback in training To learn about session, course, and materials design Learning Outcomes: Learners can name learning principles that a good teacher/instructor should have in mind Learners can describe at least three training techniques, drawing on learning principles Learners can design a training session and a course Learners can develop assessment questionnaires Learners can enumerate types of materials needed for each part of a training session or course Preliminary Programme TimeActivity DAY 1 10.00 - 10.30Introductions, who is who and what we need to achieve 10.30 - 12.30Session 1: Review of learning principles and how they apply to training and teaching 12.30 - 13.30Lunch time 13.30 - 14.30Cont. Session 1 14.30 - 17.00Session 2: Training techniques that can be used to enhance learner engagement and participation DAY 2 09.00 - 11.30Cont. Session 2 11.30 - 12.30Lunch time 12.30 - 15.30Session 3: Session, course, and materials design 15.30 - 17.00Session 4: Assessment and feedback in training DAY 3 09.00 - 11.30Cont. Session 4 11.30 - 12.00Wrap-up 2018-10-09 09:00:00 UTC 2018-10-12 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Genome sequencing technologies, assembly, variant calling and statistical genomics

    22 October - 2 November 2018

    Oslo, Norway

    Elixir node event
    Genome sequencing technologies, assembly, variant calling and statistical genomics https://tess.elixir-europe.org/events/genome-sequencing-technologies-assembly-variant-calling-and-statistical-genomics-3d1544a3-a560-4b49-9e8c-af9167caea91 2018-10-22 09:00:00 UTC 2018-11-02 17:00:00 UTC NORBIS, the Norwegian national research school in bioinformatics, biostatistics and systems biology Gaustadalléen 23, 23, Gaustadalléen, Oslo, Norway Gaustadalléen 23, 23, Gaustadalléen Oslo Oslo kommune Norway Sequencing Statistics and probability Bioinformatics Genomics university of Oslo contact-norbis@uib.no NORBIS PhD studentsPost DocsResearchers [] registration_of_interest genomicsbioinformaticsGenome sequence analysis
  • ChIP-seq data analysis

    7 - 10 November 2018

    Elixir node event
    ChIP-seq data analysis https://tess.elixir-europe.org/events/chip-seq-data-analysis-adf544b3-77df-4f8d-9bf8-b0446bbff0fa Course name: ChIP-seq data analysis Course dates: 2018-11-07 and 2018-11-09 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna, Room Fire ------------------------------------------------ National course open for PhD students, postdocs, researchers and other employees in need of ChIP-seq data analyses skills within all Swedish universities Important dates Application opens: now https://docs.google.com/forms/d/e/1FAIpQLSfJR1YbBeKqDUFbDDxAEVZh-h-je_4Ve4I9iVRRs7dsANCPGg/viewform Application closes: 2018-09-28 Confirmation to accepted students: 2018-10-06 Responsible teachers: Agata Smialowska, Olga Dethlefsen If you do not receive information according to the above dates please contact agata.smialowska@nbis.se, olga.dethlefsen@nbis.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks. *Please note that NBIS cannot invoice individuals Course content This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data via a series of lectures, group work and computer practicals. Topics covered will include: ●Quality controls of raw sequencing reads ●Reads trimming and filtering ●Alignment to the reference genome ●Peak-independent quality metrics ●Peak calling ●Peak-dependent quality metrics and visualization ●Differential binding analysis ●Functional analysis, incl. finding nearest genes, exons and custom features, obtaining enriched Gene Ontology terms and pathways Entry requirements Required for being able to follow the course and complete the computer exercises ●Basic knowledge in Linux ●Ability to bring your own laptop with R installed for the practical exercises ●Programming/scripting experience, preferably in R Desirable ●Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run Uppmax tutorial before the course ●Previous experience with NGS data analyses ●Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” Due 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. 2018-11-07 09:00:00 UTC 2018-11-10 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • R Programming Foundations for Life Scientists

    12 - 17 November 2018

    Elixir node event
    R Programming Foundations for Life Scientists https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists #training More information will follow Course leader: Marcin Kierczak (marcin.kierczak@scilifelab.se) and Sebastian DiLorenzo (sebastian.dilorenzo@nbis.se) Course description The course is addressed to life scientists with little or moderate experience in programming but enthusiastic about learning how to use R to make their work smoother and easier. The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting with some more attention paid to 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. We start by learning how to use R as a simple calculator, what are variable types, how to use data structures, how to implement repeating actions with and without loops, how to take actions based on certain condition. We gradually proceed to loading data, importing data from common file formats, we do some basic matrix algebra; learn how to perform basic statistical tests and how to visualize results. We will also put stress on giving you tools to access help and information on R-related challenges and issues, we will spend some time on learning how to install external packages, how to find bugs and address common installation issues. We also mention some more advanced topics and tell you more about BioConductor that is an invaluable tool for a computational biologist. You will also learn how to document your work and how to generate automatic reports. We try to illustrate all these concepts with some real-life examples and interesting lab tasks. The course will be given by experienced computational biologists from SciLifeLab and Uppsala University. Dr. Marcin Kierczak responsible for the content of the course is an experienced R user/coder, who has previously developed R packages and has experience in teaching programming and R to different audiences. Course literature We recommend the following books for the course: N. Matloff, “The Art of R Programming”   Book   Free PDF R.I. Kabacoff, “R in Action”   Book/Ebook and preview   38% discount code: ria38 Entry requirements Good general computer literacy is expected, but no previous experience in programming or R is required. You are expected to know basic concepts in mathematics and statistics, but the emphasis on the course is to learn how to use R. Participants are expected to use their own computers with pre-installed R and R Studio (detailed instructions will be given upon acceptance). Due to space constraints for the computer exercises, there are a maximum number of allowed 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. 2018-11-12 09:00:00 UTC 2018-11-17 00:00:00 UTC Software engineering [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    12 - 17 November 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-d4329625-5393-441f-a409-91037a6d81de Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se and Jeanette Tångrot (jeanette.tangrot@nbis.se) and Nina Norgren (nina.norgren@scilifelab.se) Location: room NA340, Naturvetarhuset, Umeå universitet Course content The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Apply here: https://fm.webforum.com/scilifelab/form.asp?sid=583883780 Topics covered will include: Basic Linux usage NGS read-to-reference alignment (genomic and RNA-Seq) Variant calling in populations De novo assembly of RNA-sequence data Reference-guided RNA-Seq expression analysis Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. Entry requirements A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable To get the maximum benefit from the course we would like you to Have relevant previous experience in sequencing or analysis Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing Be able to bring your own laptop for the practical computational exercises It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. For more information and application form, please visit https://www.scilifelab.se/events/introduction-to-bioinformatics-using-ngs-data-umea/ 2018-11-12 09:00:00 UTC 2018-11-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Biostatistics

    13 - 15 November 2018

    Elixir node event
    Biostatistics https://tess.elixir-europe.org/events/biostatistics More information will follow 2018-11-13 09:00:00 UTC 2018-11-15 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RNA-seq

    14 - 17 November 2018

    Elixir node event
    RNA-seq https://tess.elixir-europe.org/events/rna-seq-715ffd57-3ca8-4948-a1e7-10e47853d649 Course information: https://www.scilifelab.se/events/rna-seq-data-analysis/ Course leader: Johan Reimegård (johan.reimegard@scilifelab.se) Local Course leaders: Jeanette Tångrot (jeanette.tangrot@nbis.se) and Nina Norgren (nina.norgren@scilifelab.se) #training Course content: This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. A selection of tutorials will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: RNA seq introduction RNA seq transcript assembly and annotation RNA seq read mapping programs RNA seq QC analysis Differential expression analysis Gene set enrichment analysis Entry requirements: Basic knowledge in linux is a requirement! We will not teach Linux at the course and you will have considerable trouble to follow the practical sessions if you are not reasonably used to work in a linux environment. Be able to bring your own laptop for the practical computational exercises. Experience working in R and some programming/scripting experience is desirable, but not required. Experience working on the SNIC center Uppmax is desirable, but not required. Experience working with NGS data analysis is desirable. Participants of the SciLifeLab Course “Introduction to Bioinformatics using NGS data” (or alike) are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the workshops will be considerably more detailed on the covered topics. There are a maximum number of allowed 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. 2018-11-14 09:00:00 UTC 2018-11-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Python Programming with Application to Bioinformatics

    19 - 24 November 2018

    Elixir node event
    Python Programming with Application to Bioinformatics https://tess.elixir-europe.org/events/python-programming-with-application-to-bioinformatics Course name: Python programming with applications to bioinformatics Course dates: 2018-11-19 to 2018-11-23 Course location: SciLifeLab Uppsala, Entrance C11, BMC,, Husargatan 3, 752 37 Uppsala, Sverige National course open for PhD students, postdocs, researchers and other employees in need of fundamental Python skills within all Swedish universities Important dates Application opens: August 21 Application closes: October 11 Confirmation to accepted students: October 16 Responsible teacher: Nina Norgren If you do not receive information according to the above dates please contact: Nina Norgren (nina.norgren@scilifelab.se) Link to application https://goo.gl/forms/yf4fL6xgZynCgiAU2 Course fee A course fee* of 2000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner *Please note that NBIS cannot invoice individuals Course content This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead 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. Course content ●Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments ●Different ways to control program flow using loops and conditional tests ●Regular expressions and pattern matching ●Writing functions and best-practice ways of making them usable ●Reading from and writing to files ●Code packaging and Python libraries ●How to work with biological data using external libraries. Learning objectives ●Edit and run Python code ●Write file-processing python programs that produce output to the terminal and/or external files. ●Create stand-alone python programs to process biological data ●Know how to develop your skills in Python after the course (including debugging) Format Presentations and demonstrations. 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. Entry requirements 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 course are available at SciLifeLab for it. Bring your own laptop with python installed for the practical exercises. Due to limited space the course can accommodate 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. 2018-11-19 09:00:00 UTC 2018-11-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • De Novo Genome Assembly

    20 - 23 November 2018

    Elixir node event
    De Novo Genome Assembly https://tess.elixir-europe.org/events/de-novo-genome-assembly Course name: De Novo Genome assembly Course dates: 2018-11-20 to 2018-11-22 Course location: Husargatan 3, Uppsala National course open for PhD students, postdocs, researchers and other employees in need of genome assembly skills within all Swedish universities. The course is run by the SciLifeLab bioinformatics platform NBIS (https://www.nbis.se). Important dates Application closes: October 15 Confirmation to accepted students: October 22 Link to application https://goo.gl/forms/Oins4D9QZVoncbGy1 Responsible teachers: Henrik Lantz If you do not receive information according to the above dates please contact: henrik.lantz@nbis.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks. *Please note that NBIS cannot invoice individuals Course content The course is mostly aimed at researchers getting into their first de novo genome assembly project, but will also include information of use for the more experienced researcher. We will cover assembly of both prokaryotes and eukaryotes and spend a lot of time on learning how to run the analyses in hands-on computer exercises. Applicants will be taken through all steps of a genome assembly project, from the quality assessment of data, through assembly, to validation of assemblies. After this course, the students will be well aware of common practices in genome assembly projects and will know how to avoid common pitfalls. Topics covered will include: ●Different sequencing technologies and their use in genome assembly, including Illumina, PacBio, Oxford Nanopore, 10X Genomics, and Hi-C data ●Quality assessment of data ●Data filtering including Quality based cleaning and adapter trimming ●Assembly of genomes including overview of commonly used programs ●Assembly validation and polishing ●Contamination analyses Entry requirements This is an advanced course. Participants must be comfortable navigating a linux shell and executing programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data is beneficial. Applicants are encouraged to bring their own laptops, but there will be computers to use for participants unable to do so. Due to limited space the course can accommodate a maximum of 14 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. 2018-11-20 09:00:00 UTC 2018-11-23 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • ChIP-seq data analysis

    22 - 24 November 2018

    Elixir node event
    ChIP-seq data analysis https://tess.elixir-europe.org/events/chip-seq-data-analysis-97a03dfd-91d5-4607-8d84-816d76e86682 #training More information will follow Course leaders: Agata Smialowska (agata.smialowska@nbis.se) and Olga Dethlefsen (olga.dethlefsen@nbis.se) Course description: This course provides a practical introduction to analyzing ChIP-seq data. It is aimed for those already working with NGS data analyses but in need of learning best practice bioinformatics methods for processing and analyses of ChIP-seq data. Upon completion of the course, attentive participants will be able to plan and run most common ChIP-seq data analyses. Course content This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data including: Quality controls of raw sequencing reads Reads trimming and filtering Alignment to the reference genome Peak-independent quality metrics Peak calling Peak-dependent quality metrics and visualization Differential binding analysis Functional analysis, incl. finding nearest genes, exons and custom features, obtaining enriched Gene Ontology terms and pathways Entry requirements Required for being able to follow the course and to complete computer exercises: At least basic knowledge in Linux Ability to bring your own laptop with R installed for the computer exercises Programming / scripting experience, preferably in R Desired: Experience working on Uppmax or another HPC Previous experience with NGS data analyses Completing SciLifeLab / NBIS courses “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” Selection criteria The course can accommodate 15 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. 2018-11-22 09:00:00 UTC 2018-11-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Tools for Reproducible Research

    28 - 30 November 2018

    Elixir node event
    Tools for Reproducible Research https://tess.elixir-europe.org/events/tools-for-reproducible-research-685e62e3-a7e4-466e-90de-6c4220fcde6d Course name: Tools for Reproducible Research Course dates: 2018-11-28 - 2018-11-29 Course location: Kemivägen 8A, 412 58 Göteborg National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities with interest in making their computational analysis more reproducible. Important dates Application opens: 2018-09-01 Application closes: 2018-10-26 Confirmation to accepted students: 2018-11-09 Responsible teachers: Rasmus Ågren (rasmus.agren@scilifelab.se) and Leif Wigge (leif.wigge@scilifelab.se) If you do not receive information according to the above dates please contact: Rasmus Ågren Course fee A course fee* of 1300 SEK will be invoiced to accepted participants. This includes lunches, dinner, coffee and snacks. *Please note that NBIS cannot invoice individuals Course content In this course you will learn how to make your data analyses reproducible. In particular, you will learn: · good practices for data analysis · how to use the version control system git to track edits and collaborate on coding · how to use the package and environment manager Conda · how to use the workflow manager Snakemake · how to use R Markdown to generate automated reports · how to use Jupyter notebooks to document your ongoing analysis · how to use Docker to distribute containerized computational environments Entry requirements Required for being able to follow the course and to complete computer exercises: · familiarity with using the terminal (e.g. be familiar with commands such as ls, cd, touch, mkdir, pwd, etc.) · bring your own laptop running Linux or Mac OS (if you run Windows and are interested in participating, please contact the course leaders by email, see above, before applying) · some knowledge in R and/or Python is beneficial but not strictly required Link to application https://docs.google.com/forms/d/e/1FAIpQLSdcZtJvg20p2WdS7zG8lqVtb5x1_JZYwiDJ8yI2VD0x4WEeCg/viewform 2018-11-28 09:00:00 UTC 2018-11-30 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Metabolomics for the Microbiologist

    30 January - 1 February 2019

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Microbiologist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-microbiologist This three-day course will introduce the attendees in how untargeted metabolomics can be applied to study microbial systems in academic and industrial research. The course will provide an overview of the metabolomics pipeline from experimental design to sample preparation and data acquisition to data analysis/interpretation. The course will be led by experts in the field of metabolomics and will include lectures, hands-on laboratory sessions in sample preparation and data acquisition and computer workshops focused on data processing and data analysis. 2019-01-30 09:00:00 UTC 2019-02-01 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Course: single-cell RNA sequencing data analysis

    4 - 7 February 2019

    Elixir node event
    Course: single-cell RNA sequencing data analysis https://tess.elixir-europe.org/events/course-single-cell-rna-sequencing-data-analysis Course name: Single cell RNA sequencing data analysis Course dates: 2019-02-04 to 2019-02-06 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna National course open for PhD students, postdocs, researchers and other employees in need of single cell RNA-seq data analysis skills within all Swedish universities Important dates Application opens: December 10 2018 Application closes: January 20 Confirmation to accepted students: January 22 Responsible teachers: Åsa Björklund If you do not receive information according to the above dates please contact: asa.bjorklund@scilifelab.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.. *Please note that NBIS cannot invoice individuals Course content This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: ●An overview of the current scRNAseq techniques ●Basic overview of pipelines for processing raw reads into expression values ●Quality control of scRNAseq data ●Dimensionality reduction and clustering techniques ●Data normalization ●Differential gene expression for scRNAseq data ●Examples on how to use these tools in a research project. Entry requirements Required for being able to follow the course and complete the computer exercises ●Basic knowledge in Linux is a requirement. We will not teach Linux at the course and you may have considerable trouble to follow the practical sessions if you are not reasonably used to work in a Linux environment. ●Be able to bring your own laptop with R installed for the practical computational exercises. Instructions on installation will be sent by email to accepted participants. ●Some programming/scripting experience is required (preferably in R). Desirable: ●Experience working on the SNIC center Uppmax is desirable, but not required. We encourage accepted participants to do an Uppmax tutorial before the course. ●Previous experience with RNA-seq analysis and/or participation in NGS/RNA-seq course is an advantage. Due 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. Link to application: https://goo.gl/forms/0x9ssllId5Jxn9dB3 2019-02-04 09:00:00 UTC 2019-02-07 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Course: Introduction to Bioinformatics using NGS data

    4 - 9 February 2019

    Elixir node event
    Course: Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/course-introduction-to-bioinformatics-using-ngs-data https://www.scilifelab.se/events/introduction-to-bioinformatics-using-ngs-data-uppsala/ 2019-02-04 09:00:00 UTC 2019-02-09 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Metabolomics for the Environmental Scientist

    28 February - 1 March 2019

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Environmental Scientist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-environmental-scientist This 2-day NERC-funded Advanced Training Short Course will provide environmental scientists with an overview of the metabolomics pipeline. The course is intended for environmental scientist with little or no previous experience of metabolomics and who are interested to discover how this relatively new and powerful approach could be integrated into their research. Experts working in the NERC Metabolomics facility-NBAF-Birmingham will teach the course. 2019-02-28 09:00:00 UTC 2019-03-01 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Metabolomics for the Clinical Scientist

    11 March 2019

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Clinical Scientist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-clinical-scientist The 1-day course in partnership with the Phenome Centre Birmingham will provide clinicians with an overview of the metabolomics pipeline highlighting the benefits of this technique to the medical field and an introduction to the Phenome Centre Birmingham and the MRC-NIHR National Phenome Centre. The course will provide a suitable introduction to metabolomics prior to taking additional training courses at either the Birmingham Metabolomics Training Centre or the Imperial International Phenome Training Centre. 2019-03-11 09:00:00 UTC 2019-03-11 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Metabolomics Data Processing and Data Analysis

    18 March - 12 April 2019

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics Data Processing and Data Analysis https://tess.elixir-europe.org/events/metabolomics-data-processing-and-data-analysis This online course will explore the tools and approaches that are used to process and analyse metabolomics data, we will investigate the challenges that are typically encountered in the analysis of metabolomics data and provide solutions to overcome these problems. The course will be delivered using a combination of short videos, articles, discussions, and online workshops with step-by-step instructions and test data sets. 2019-03-18 09:00:00 UTC 2019-04-12 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
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