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Scientific topics: Workflows 

  • Building Workflows in Digital Health

    29 June 2022

    Manchester, United Kingdom

    Building Workflows in Digital Health http://tess.elixir-uk.org/events/building-workflows-in-digital-health Orchestration Workflows are widely used in computational data analysis, enabling innovation and decision-making. Often the analysis components are numerous, and written by third parties, without an eye on interoperability. In addition, many competing workflow systems exist, potentially limiting portability of workflows written for any one specific workflow system. This hinders the transfer of workflows between different systems and projects, limiting their re-usability. The Common Workflow Language (CWL) project (https://www.commonwl.org/) was established in order to produce free and open standards for describing command-line tool-based workflows. The CWL language is declarative and provides a focused set of common abstractions enabling the expression of computational workflows constructed from diverse software tools. Explicit declaration of requirements for runtime environments and software containers enables portability and reuse. Workflows written according to the CWL standards are a reusable description of that analysis, runnable on a diverse set of computing environments. 2022-06-29 10:00:00 UTC 2022-06-29 17:00:00 UTC N8CIR University Place, University of Manchester, Manchester, United Kingdom University Place, University of Manchester Manchester United Kingdom M13 9PL Bioinformatics Workflows Data architecture, analysis and design University of Manchester [] [] workshops_and_courses registration_of_interest workflowsdata-analysiscomputational methods
  • Modular, reproducible bioinformatics workflows with the targets R package

    30 June 2022

    Modular, reproducible bioinformatics workflows with the targets R package http://tess.elixir-uk.org/events/modular-reproducible-bioinformatics-workflows-with-the-targets-r-package Modern bioinformatics pipelines can be incredibly complex, but all tend to follow a common pattern: they start with raw data, then pass the data through various programs until arriving at a final result. If this is done in an ad-hoc, unorganized fashion, the results may never be reproducible or even worse, unreliable and/or wrong. Pipeline management software is therefore essential to obtain results that are robust and reproducible. The targets R package is a recently developed workflow manager that comes with many excellent features for bioinformatics, including data caching, pipeline-level parallelization, and HPC support. **In this hands-on workshop, I will demonstrate how targets can be used in concert with other tools like docker and conda to orchestrate modular, reproducible bioinformatics pipelines. The workshop will feature variant-calling as an example, but the concepts and tools can be applied to nearly any analysis.** **Pre-requisites:** Basic familiarity with R. Installations of recent versions of R, conda, and docker. **Duration:** 2 hours 2022-06-30 07:30:00 UTC 2022-06-30 09:30:00 UTC International Society for Computational Biology Workflows [] Batool Almarzouq (batool@liverpool.ac.uk) [] This workshop is aimed at researchers who are either generating or integrating molecular interaction data in their research. This could be protein-protein interaction as well as protein-RNA 30 workshops_and_courses [] Variant-callingworkflowsR/BioconductorbioinformaticsReproducibilityReproducibleResearch
  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line http://tess.elixir-uk.org/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here] (https://unimelb.zoom.us/webinar/register/WN_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Whole genome sequencing Sequencing Genomics Bioinformatics Workflows Australian Biocommons training@biocommons.org.au [] [] 500 workshops_and_courses first_come_first_served []

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