Register event
79 events found

Content provider: Birmingham Metabolomics Tra...  or NBIS  or Edinburgh Genomics  or ABACBS 

  • 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 [] [] [] [] []
  • RNA-Seq Data Analysis Workshop Using R

    18 - 21 April 2017

    RNA-Seq Data Analysis Workshop Using R https://tess.elixir-europe.org/events/rna-seq-data-analysis-workshop-using-r The RNA-Seq Data Analysis With R workshop will introduce attendees to the R software environment and the specific skills and applications used in R-based RNA-Seq data analysis. Register: http://www.bioplatforms.com/rna-data-analysis-with-r-2017/ 2017-04-18 23:00:00 UTC 2017-04-21 01:30:00 UTC RNA-Seq [] [] [] workshops_and_courses [] []
  • R Software Carpentry Workshop

    19 - 21 April 2017

    R Software Carpentry Workshop https://tess.elixir-europe.org/events/r-software-carpentry-workshop Introductory programming workshop covering the Unix shell, reproducible programming in R and version control with Git and Github. Registration: http://www.abacbs.org/combineworkshops/r-swc-melb-april-2017 2017-04-19 22:00:00 UTC 2017-04-21 06:00:00 UTC [] [] [] workshops_and_courses [] []
  • Intro to Python

    19 - 20 April 2017

    Intro to Python https://tess.elixir-europe.org/events/intro-to-python-01409037-ab76-4b9d-bf0d-be280f28dd86 Held at the Clayton campus at Monash University. For more information and to register: https://www.eventbrite.com/e/introduction-to-python-tickets-32835513906 2017-04-19 23:00:00 UTC 2017-04-20 06:00:00 UTC [] [] [] workshops_and_courses [] []
  • GeneMappers 2017

    26 - 28 April 2017

    GeneMappers 2017 https://tess.elixir-europe.org/events/genemappers-2017 http://www.genemappers.org/ Welcome to GeneMappers 2017 A warm welcome to the 12th GeneMappers Conference, to be held at the Novotel Hotel on the Waterfront in vibrant Geelong, Victoria, from Wednesday April 26th to Friday 28th 2017. In the past, The GeneMappers Conference has focused on approaches for the genetic dissection of common human diseases. The next GeneMappers will expand this theme to include genomic analyses of host-pathogen relationships, and other organisms as it relates to human disease and clinically relevant traits. We will look towards the future: with mechanism of gene action and translation of genetic research themes of particular interest. Geelong is ideally placed at the entrance to the Bellarine Peninsula, with its wineries, fine dining and historic towns such as Queenscliff, and is also at the gateway to the Surf Coast and Great Ocean Road. The conference venue is surrounded by cafes, restaurants and accommodation options in the midst of Geelong’s beautiful, revived waterfront. Our conference dinner on Friday evening will be a highlight and held on “The Pier”, within walking distance to the hotel and suspended over Port Philip Bay. Geelong is only a 1 hr drive from Melbourne’s Tullamarine Airport and Melbourne City, and only 20 kms from Avalon Airport. Both airports are connected to Geelong by road and regular public transport (bus) services. This GeneMappers will be an excellent venue for families: we will be hosting a family break out room, there is an in-house swimming pool for Novotel guests, and there are plenty of walking and playground options nearby, including a child-safe beach. The conference is also outside Easter school holidays for most Australian States, and yet finishes at the start of a weekend, providing the family an opportunity to explore this exciting region. We hope that this conference will inspire you and your work and we look forward to welcoming you to GeneMappers 2017, Geelong. 2017-04-26 02:00:00 UTC 2017-04-28 06:30:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to R

    8 - 9 May 2017

    Introduction to R https://tess.elixir-europe.org/events/introduction-to-r-f0d42cab-8f83-4e47-96df-22378b625f75 This hands-on workshop will introduce the fundamentals of the R software environment, a powerful, popular and free statistical and graphical programming language. Participants will learn about the structure of the R language, how to add functionality through packages, and how to process data and generate tables, figures and reports using R. Researchers looking for analysis capabilities beyond those provided by Excel. No prior knowledge of R is required, but a familiarity with the command-line will be useful. The workshop is relevant for all disciplines, although some examples and exercises will focus on biological datasets. Further details and registration: http://qfab.org/workshops/introduction-r-09-may-2017 2017-05-08 23:00:00 UTC 2017-05-09 07:00:00 UTC [] [] [] workshops_and_courses [] []
  • COMBINE R for Bioinformatics workshop

    18 - 19 May 2017

    Carlton, Australia

    COMBINE R for Bioinformatics workshop https://tess.elixir-europe.org/events/combine-r-for-bioinformatics-workshop Bioconductor is an Open-Source repository for bioinformatics software in R Statistical Programming Language. Bioconductor provides core technologies and infrastructures that facilitates day-to-day bioinformatics data analysis, including data retrieval, data processing and data analysis. This is a one-day intensive workshop on Bioconductor core packages such as GenomicFeatures, GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, GEOquery, AnnotationHub and other annotation packages. An intermediate knowledge of R is required. Instructors: Anna Quaglieri, Paul Harrison, Maria Doyle, Agnieszka Aleksandra Golicz and Soroor Hediyeh-Zadeh Details: What: COMBINE R for Bioinformatics workshop Date: 19th May 2017 Time: 9am – 5pm Location: Lab14, 700 Swanston St, Carlton VIC 3053 Registration: http://www.abacbs.org/combineworkshops/bioconductor-melb-may-2017 Price: Student $15, Non-student $30 This event is sponsored by Melbourne Bioinformatics. 2017-05-18 23:00:00 UTC 2017-05-19 07:00:00 UTC Soroor Hediyeh-Zadeh combine@combine.org.au LAB-14, 700, Swanston Street, Carlton, Australia LAB-14, 700, Swanston Street Carlton Melbourne City Australia Genomics Bioinformatics [] Melbourne Bioinformatics [] workshops_and_courses first_come_first_served R-programming
  • COMBINE Unix/R Workshop Brisbane

    27 - 29 June 2017

    COMBINE Unix/R Workshop Brisbane https://tess.elixir-europe.org/events/combine-unix-r-workshop-brisbane Unix/R workshop at the University of Queensland, Brisbane https://www.abacbs.org/combineworkshops/unix-r-brisbane-june-2017 2017-06-27 22:00:00 UTC 2017-06-29 06:00:00 UTC [] [] [] workshops_and_courses [] []
  • RNAseq workshop in R, Brisbane

    5 - 7 July 2017

    RNAseq workshop in R, Brisbane https://tess.elixir-europe.org/events/rnaseq-workshop-in-r-brisbane RNAseq workshop in R, University of Queensland, Brisbane https://www.abacbs.org/combineworkshops/rnaseq-bris-july-2017 2017-07-05 23:00:00 UTC 2017-07-07 07:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to R

    12 - 13 July 2017

    Clayton, Australia

    Introduction to R https://tess.elixir-europe.org/events/introduction-to-r-ab6dceb1-f7e0-4583-9b7e-4344a50535f3 This workshop will teach the fundamentals of R. You will learn to quickly visualize and summarize data from experiments involving multiple experimental factors and measurements. Register here: https://www.eventbrite.com/e/introduction-to-r-tickets-34994825465 2017-07-12 23:00:00 UTC 2017-07-13 06:00:00 UTC Monash Bioinformatics Platform Room E365 (Level 3, East wing, 20 Chancellors Walk- Menzies Building), Monash University Clayton Campus, Wellington Road, Clayton, Australia Room E365 (Level 3, East wing, 20 Chancellors Walk- Menzies Building), Monash University Clayton Campus, Wellington Road Clayton Australia Bioinformatics Monash University [] [] workshops_and_courses [] bioinformatics R-programming
  • GATK Best Practices for Variant Discovery

    17 - 19 July 2017

    Edinburgh, United Kingdom

    Elixir node event
    GATK Best Practices for Variant Discovery https://tess.elixir-europe.org/events/gatk-best-practices-for-variant-discovery This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the Best Practices developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq-specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. 2017-07-17 09:00:00 UTC 2017-07-19 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom Bioinformatics Genomics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] Variant discoveryGenomicsBioinformatics
  • 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 [] [] [] [] [] []
  • Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl

    23 - 24 November 2017

    Edinburgh, United Kingdom

    Elixir node event
    Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl https://tess.elixir-europe.org/events/introduction-to-chip-seq-data-analysis-and-visualisation-using-ensembl-d125d464-c708-4919-8322-19d50246c22d ChIP-seq (Chromatin ImmunoPrecipitation followed by Sequencing) is a popular high-throughput sequencing assay to identify binding sites of DNA-associated proteins and histone modifications. Determining how proteins interact with DNA and the epigenetic landscape is essential for elucidating the regulation of gene expression. The aim of this workshop is to familiarise the participants with the primary analysis of ChIP-seq data sets by providing a balanced set of lectures and practicals on analysis methodologies. Practicals include publicly available ChIP-seq datasets, processed using widely used and open-source software programs (e.g. FASTQC, BWA, samtools, bedtools, wiggletools, MACS2, MEME, TOMTOM, ngsplot) and visualised on the Ensembl genome browser. 2017-11-23 09:00:00 UTC 2017-11-24 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Genomics ChIP-seq Bioinformatics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsChIP-seqGenomics
  • Introduction to Python for Biologists

    19 - 23 February 2018

    Edinburgh, United Kingdom

    Elixir node event
    Introduction to Python for Biologists https://tess.elixir-europe.org/events/introduction-to-python-for-biologists-bcd1d1d1-24fc-47b6-b586-fc239d27888e Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way. 2018-02-19 09:00:00 UTC 2018-02-23 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Bioinformatics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsProgrammingPython
  • 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 [] [] [] [] []
  • Data Manipulation and Visualisation with Python

    9 - 13 April 2018

    Edinburgh, United Kingdom

    Elixir node event
    Data Manipulation and Visualisation with Python https://tess.elixir-europe.org/events/data-manipulation-and-visualisation-with-python One of the strengths of the Python language is the availability of mature, high-quality libraries for working with scientific data. Integration between the most popular libraries has lead to the concept of a "scientific Python stack": a collection of packages which are designed to work well together. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. 2018-04-09 09:00:00 UTC 2018-04-13 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Bioinformatics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsProgrammingPython
  • Introduction to Linux and Workflows for Biologists

    14 - 18 May 2018

    Edinburgh, United Kingdom

    Elixir node event
    Introduction to Linux and Workflows for Biologists https://tess.elixir-europe.org/events/introduction-to-linux-and-workflows-for-biologists-866df86c-a827-433d-9445-af7726bcf5a1 Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. 2018-05-14 09:00:00 UTC 2018-05-18 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Workflows Bioinformatics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsLinuxWorkflows
  • 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 [] [] [] [] []
  • Advanced Python for Biologists

    9 - 13 July 2018

    Edinburgh, United Kingdom

    Elixir node event
    Advanced Python for Biologists https://tess.elixir-europe.org/events/advanced-python-for-biologists-3fb71294-dcb9-4381-bdae-81701ef20595 Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at people who already have a basic knowledge of Python and are interested in using the language to tackle larger problems. In it, we will look in detail at the parts of the language which are particularly useful in scientific programming, and at the tools Python offers for making development faster and easier. The workshop will use examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to (1) take advantage of the advanced language features in their own programs and (2) use appropriate tools when developing software programs. 2018-07-09 09:00:00 UTC 2018-07-13 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Bioinformatics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsProgrammingPython
  • 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 [] [] [] [] []
  • Linux for Genomics

    1 October 2018

    Edinburgh, United Kingdom

    Elixir node event
    Linux for Genomics https://tess.elixir-europe.org/events/linux-for-genomics-4e98de3e-0102-46ab-9720-22f1122fd31d Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command-line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were especially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF). 2018-10-01 09:00:00 UTC 2018-10-01 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Genomics Bioinformatics Edinburgh Genomics Donald Dunbar - donald.dunbar@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsGenomicsLinux
  • Introduction to RNA-seq Data Analysis

    2 - 3 October 2018

    Edinburgh, United Kingdom

    Elixir node event
    Introduction to RNA-seq Data Analysis https://tess.elixir-europe.org/events/introduction-to-rna-seq-data-analysis-5989e86e-a408-481d-b3c7-5a1413b0e4a6 RNA sequencing (RNA-seq) is quickly becoming the method of choice for transcriptome profiling. Nevertheless, it is a non-trivial task to transform the vast amount of data obtained with high-throughput sequencers into useful information. Thus, RNA-seq data analysis is still a major bottleneck for most researchers in this field. The ability of correctly interpreting RNA-seq results, as well as knowledge on the intrinsic properties of these data, are essential to avoid incorrect experimental designs and the application of inappropriate analysis methodologies. The aim of this workshop is to familiarise researchers with RNA-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs will be used. 2018-10-02 09:00:00 UTC 2018-10-03 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN RNA-Seq Genomics Bioinformatics Edinburgh Genomics Donald Dunbar - donald.dunbar@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsGenomicsRNA-seq
Note, this map only displays events that have geolocation information in TeSS.
For the complete list of events in TeSS, click the grid tab.