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  • BioExcel 1st Annual Meeting: “Advanced Simulations for Biomolecular Research” SIG @ ECCB 2016

    4 September 2016

    The Hague, Netherlands

    BioExcel 1st Annual Meeting: “Advanced Simulations for Biomolecular Research” SIG @ ECCB 2016 https://tess.elixir-europe.org/events/bioexcel-1st-annual-meeting-advanced-simulations-for-biomolecular-research-sig-eccb-2016 The BioExcel Annual Meeting will take place as a satellite event during ECCB 2016 on 4th September in the Hague. SIG BioExcel is a major venue for knowledge exchange and networking for the computational biomolecular research community. It brings together stakeholders of 1) core applications that are supported by the center – HADDOCK (integrative modelling), GROMACS (molecular dynamics simulations) and CPMD (hybrid QM/MM methods) and 2) worklow environments and platforms for data integration and analysis such as Galaxy, Taverna, Open PHACTS, COMPSs and Copernicus. 2016-09-04 09:00:00 UTC 2016-09-04 17:00:00 UTC BioExcel World Forum, The Hague, Netherlands World Forum The Hague Netherlands 2517 JW [] [] [] [] [] []
  • GROMACS hackathon 2016

    17 - 19 October 2016

    Barcelona, Spain

    GROMACS hackathon 2016 https://tess.elixir-europe.org/events/gromacs-hackathon-2016 Get together with core GROMACS developers from around the world to hack together on code! Bring your own laptop and coding problem – new integrator, fancy free-energy method, cool analysis tool, automated parameterizer, workflow implementation, meta-dynamics driver, tricky bug to fix, API design question, etc. Be ready to ask and answer questions with the gurus, and come away with new code running, progressed or well planned! 2016-10-17 09:00:00 UTC 2016-10-19 17:00:00 UTC BioExcel Barcelona Supercomputing Center, Barcelona, Spain Barcelona Supercomputing Center Barcelona Spain [] [] [] [] [] []
  • BioExcel: workflow training for computational biomolecular research

    20 - 21 October 2016

    Barcelona, Spain

    BioExcel: workflow training for computational biomolecular research https://tess.elixir-europe.org/events/bioexcel-workflow-training-for-computational-biomolecular-research The purpose of this workshop is to (1) provide an overview of the most commonly used workflow managers in the computational biomolecular field, both in a theoretical and practical way, with hands-on practice sessions. (2) Find out about how BioExcel – Europe’s new Centre of Excellence for Computational BioMolecular Research – will help you to develop and run your own pipelines using these tools and introduce you to the BioExcel Workflows Interest Group. (3) Together with experts on the different workflow managers, identify the best approach for your particular workflow problem in a “Bring Your Own Workflow” session 2016-10-20 09:00:00 UTC 2016-10-21 17:00:00 UTC BioExcel Barcelona Supercomputing Center, Barcelona, Spain Barcelona Supercomputing Center Barcelona Spain [] [] [] [] [] []
  • Large-scale analytical workflows on the cloud using Galaxy and Globus

    16 November 2016

    Large-scale analytical workflows on the cloud using Galaxy and Globus https://tess.elixir-europe.org/events/large-scale-analytical-workflows-on-the-cloud-using-galaxy-and-globus We would like to invite you to attend the 8th webinar in BioExcel’s webinar series on computational methods and applications for biomolecular research, which will take place on 16th November 2016: Presenter: Ravi Madduri (introduction by Stian Soiland-Reyes) When: Wed 16th November 2016 16:00 CET (2016-11-16 15:00 UTC) Registration: Free In this BioExcel webinar we are delighted to have Ravi Madduri from Argonne National Laboratory and University of Chicago present Globus Genomics, a system developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data, combining Galaxy workflows with cloud technologies like Amazon EC2 and Globus File Transfer. This system achieves a high degree of end-to-end automation that encompasses every stage of data analysis including initial data retrieval from remote sequencing centers or storage (via the Globus file transfer system); specification, configuration, and reuse of multi-step processing pipelines (via the Galaxy workflow system); creation of custom Amazon Machine Images and on-demand resource acquisition via a specialized elastic provisioner (on Amazon EC2); and efficient scheduling of these pipelines over many processors (via the HTCondor scheduler). The system allows biomedical researchers to perform rapid analysis of large NGS datasets in a fully automated manner, without software installation or a need for any local computing infrastructure. Ravi’s work is part of the BD2K center Big Data for Discovery Science, building infrastructure for reproducible workflows using minids (minimal viable identifiers), analyzing data at scale using identified Docker containers, publish results in to Globus Publication services thus providing an end-to-end framework for reproducible research. In this BioExcel webinar, Ravi will present Globus Genomics and the technologies used to achieve large-scale analytical Galaxy workflows on the cloud. We think this will be of interest not just for the genomics community, but for any scientific workflow users who need to consider distributed deployments, data management and scalability. 2016-11-16 15:00:00 UTC 2016-11-16 16:00:00 UTC BioExcel Whole genome sequencing High-throughput sequencing Genomics Workflows University of ManchesterUniversity of ChicagoArgonne National Laboratory Please register at https://attendee.gotowebinar.com/register/5808939110698431491. You will then receive an email with details of how you can connect to the webinar. [] bioinformaticianssoftware engineersGalaxy usersCloud users workshops_and_courses first_come_first_served CloudGalaxyGlobusNGSNext generation sequencing data analysis
  • 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 [] [] [] [] []
  • BioExcel/PRACE Spring School 2017 – HPC for Life Sciences

    10 - 13 April 2017

    Stockholm, Sweden

    BioExcel/PRACE Spring School 2017 – HPC for Life Sciences https://tess.elixir-europe.org/events/bioexcel-prace-spring-school-2017-hpc-for-life-sciences BioExcel Center of Excellence is bringing together for the first time the main developers of four of the major and most popular codes for molecular modelling and simulations – GROMACS, AMBER, NAMD and VMD. This is a great opportunity for novice and experienced users to learn from the very authors of the software. The 2017 Spring School is organized jointly with PRACE, the main HPC resource provider in Europe. 2017-04-10 08:30:00 UTC 2017-04-13 17:00:00 UTC BioExcel KTH Main Campus, Stockholm, Sweden KTH Main Campus Stockholm Stockholm Sweden SE-100 44 Molecular modelling Data visualisation Simulation experiment [] Vera Matser - matser@ebi.ac.uk PRACE [] 60 workshops_and_courses first_come_first_served []
  • Foundation skills for HPC in computational biomolecular research

    3 - 7 July 2017

    Hinxton, United Kingdom

    Foundation skills for HPC in computational biomolecular research https://tess.elixir-europe.org/events/foundation-skills-for-hpc-in-computational-biomolecular-research This 5-day BioExcel Summer School will use project-based learning to empower life scientists to get the most out of using computers. Using example problems and challenges that life-scientists will come across in their day-to-day work, e.g. obtaining data, installing software, cleaning data, analysing data, this course will help participants gain the foundational computational skills needed to move into the domain of high-end computing. 2017-07-03 16:33:00 UTC 2017-07-07 14:00:00 UTC BioExcel EMBL-EBI South Building and ELIXIR Hub, Hinxton, United Kingdom EMBL-EBI South Building and ELIXIR Hub Hinxton Cambridgeshire United Kingdom Computational biology EMBL-EBI Vera Matser - matser@ebi.ac.uk [] [] workshops_and_courses [] []
  • Building pharmacological workflow blocks for virtual screening (BioExcel and OpenPHACTS)

    17 July 2017

    Building pharmacological workflow blocks for virtual screening (BioExcel and OpenPHACTS) https://tess.elixir-europe.org/events/building-pharmacological-workflow-blocks-for-virtual-screening BioExcel’s webinar series continues with Nick Lynch, who will introduce Open PHACTS, an integrated pharmacological data platform and [BioExcel strategic partner](http://bioexcel.eu/partnership-between-bioexcel-and-open-phacts-foundation/). Nick is joined by Stian Soiland-Reyes and Adam Hospital who will explain in details how BioExcel is building a Virtual Screening workflow combining Open PHACTS with the BioExcel-supported tools for biomolecular simulation and modelling. The [Open PHACTS Discovery Platform](http://www.openphacts.org/) brings together vast amounts of linked data in a single integrated, open infrastructure providing a platform for researchers to access and query publicly-available pharmacological data. The platform integrates major open data sources (e.g. ChEMBL, UniProt, WikiPathways, SureChEMBL, DrugBank, Disgenet and their associated Chemistry) on compounds, patents, diseases, targets and pathways; linked by identifiers, semantic and structural chemistry information, re-exposed as a collection of unified web APIs, workflow components plus tool integrations. The platform is maintained by the [Open PHACTS Foundation](), which is supported by members from biopharmaceutical industry and Research Organisations with an active developer and user community. [BioExcel](http://bioexcel.eu/) is an European Centre of Excellence that support academia and industry in the use of high-end computing in biomolecular research. Part of BioExcel’s roadmap for workflows is to develop Workflow Blocks for biomolecular simulation and modelling, which includes Open PHACTS as a data service. Such blocks, including the Open PHACTS platform, can be deployed in private or public cloud environments, and used to build portable pipelines. BioExcel is currently developing a series of [pilot use cases](http://bioexcel.eu/research/pilot-use-cases/), including a Virtual Screening workflow using Open PHACTS. In this webinar, **Nick Lynch** (Open PHACTS Foundation), **Stian Soiland-Reyes** (The University of Manchester) and **Adam Hospital** (IRB Barcelona) will present the Open PHACTS platform and how it will be used with BioExcel workflow blocks to build a virtual screening pipeline. [BioExcel webinars](http://bioexcel.eu/category/webinar/) include an audience Q&A session during which attendees can ask questions and make suggestions. Please [**register** at https://attendee.gotowebinar.com/register/295609582301212161](https://attendee.gotowebinar.com/register/295609582301212161) - you will then receive an email with details of how you can connect to the webinar. 2017-07-17 15:00:00 UTC 2017-07-17 16:00:00 UTC BioExcel Molecular modelling Workflows Pharmacology University of Manchester Stian Soiland-Reyes, The University of Manchester [] [] workshops_and_courses registration_of_interest []
  • 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 [] [] [] [] [] []
  • CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF

    28 February 2018

    CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF https://tess.elixir-europe.org/events/cwlexec-a-new-open-source-tool-to-run-cwl-workflows-on-lsf The [Common Workflow Language (CWL)](http://www.commonwl.org/) is a community-led specification for describing analysis _workflows_ and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and _high performance computing_ (HPC) environments. [IBM Spectrum LSF](https://www.ibm.com/us-en/marketplace/hpc-workload-management) (formerly IBM Platform LSF) is a complete workload management solution for demanding HPC environments. Featuring intelligent, policy-driven scheduling, it helps organizations accelerate research and design while controlling costs through superior resource utilization. Recognizing the popularity of CWL among LSF users, we introduce a new open source project **CWLEXEC** to support running CWL workflows on LSF. The project will feature smooth integration with LSF with high efficiency and scalability, self-healing of workflows, support user-specified submission options while keeping CWL definitions portable, and other benefits. * **Title**: CWLEXEC: A new open source tool to run CWL workflows on LSF * **Presenter:** Qingda Wang, Principal Architect, IBM Spectrum LSF Family Products and OEM * **Time**: 2018-02-28 14:00 GMT / 15:00 CET 2018-02-28 14:00:00 UTC 2018-02-28 15:00:00 UTC BioExcel Bioinformatics Genomics Workflows University of ManchesterBioExcel CoE Stian Soiland-Reyes http://ask.bioexcel.eu/ [] bioinformaticiansHPC users workshops_and_courses registration_of_interest WorkflowsCWLHPCLSF
  • 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 [] [] [] [] []
  • BioSimSpace – filling the gaps between molecular simulation codes

    27 June 2018

    BioSimSpace – filling the gaps between molecular simulation codes https://tess.elixir-europe.org/events/biosimspace-filling-the-gaps-between-molecular-simulation-codes [BioSimSpace](https://biosimspace.org) is a flagship software project from the [CCP-BioSim](https://ccpbiosim.ac.uk) and [HEC-BioSim](https://hecbiosim.ac.uk) biomolecular modelling communities. The project aims to make it easier for researchers to develop, share and re-use biomolecular simulation workflow nodes. The software problem in our community is that we have lots of different pieces of software that are all incompatible and are not interoperable. This forces the community to hand-write small scripts for converting between different file formats, or to generate different software input files. The resulting scripts are specific for the software and task performed, leading to the community generating lots of bespoke and brittle workflows. BioSimSpace solves this problem by providing an **interoperability layer** between the major molecular simulation packages. In effect, BioSimSpace provides the shims that fill in the gaps between codes. BioSimSpace Python scripts can be run from the command line, used as workflow nodes in packages such as Knime, or run on the cloud as Jupyter notebooks. In this talk, we will show how BioSimSpace has been implemented, will talk about its capabilities and our future plans, and will demonstrate some BioSimSpace workflow nodes running on the cloud. 2018-06-27 15:00:00 UTC 2018-06-27 16:00:00 UTC BioExcel Molecular modelling Molecular dynamics Workflows University of Manchester [] IntermediateBeginners [] [] GROMACSPythonKNIMEJupyter notebook
  • 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 [] [] [] [] []
  • 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 [] [] [] [] []
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