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6 events found

Scientific topics: Workflows 


Event types: Workshops and courses 


Keywords: lifescience  or Workflows 

  • 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 The [Common Workflow Language (CWL)]( 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]( (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 [] bioinformaticiansHPC users workshops_and_courses registration_of_interest WorkflowsCWLHPCLSF
  • Introduction to Linux and Workflows for Biologists

    14 - 18 May 2018

    Edinburgh, United Kingdom

    Elixir node event
    Introduction to Linux and Workflows for Biologists 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 - [] [] workshops_and_courses [] BioinformaticsLinuxWorkflows
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1

    20 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1 #### Computational requirements for running the H3ABioNet GWAS workflows The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics: Installing and using Nextflow Installing and using Github Use of containers for packaging and running tools Pulling the GWAS pipeline from Github and running it As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements: Either a Linux machine or an Apple running macOS Ideally you should have machine with at least 2-4 cores and 8GB of RAM. Java 8 Nextflow installed (see installation instructions at Python 3 Please also install either Docker OR the following dependencies using pip3: Pandas, Matplotlib, Openpyxl, SciPy, NumPy PLINK 1.9 [Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]: 2018-08-20 15:00:00 UTC 2018-08-20 16:30:00 UTC H3ABioNet Population genomics Genotyping experiment Computational biology Workflows GWAS study Bioinformatics H3ABioNet H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chipAnyone who wants to learn more about GWAS workshops_and_courses [] NextflowDockerH3ABioNetGWASWorkflowsGenotyping array analysis bioinformaticsAfricaPopulation GenomicsReproducible ScienceH3Africa genotyping arrayHigh performance computingCloud computingGWAS workflowH3ABioNet GWAS 2018 Lecture Series
  • Workshop on Research Objects (RO2018)

    29 October 2018

    Amsterdam, Netherlands

    Workshop on Research Objects (RO2018) In this workshop we will explore recent advancements in Research Objects and publishing of research data. **Deadlines**: * 2018-07-01 Abstracts due * 2018-07-15 Research articles and software/data articles due A travel bursary is available for accepted speakers, sponsored by [BioExcel]( (H2020-675728) ## Research Objects Scholarly Communication has evolved significantly in recent years, with an increasing focus on **Open Research**, [FAIR]( sharing and community-developed open source methods. A question remains on how to publish, archive and explore digital research outputs. A number of initiatives have begun to explore how to package and describe research outputs, data, methods, workflows, provenance and structured metadata, reusing existing Web standards and formats. Such efforts aim to address the challenges of structuring multi-part research outcomes with their context, handling distributed and living content and porting and safely exchange what we collectively can call **Research Objects** between platforms and between researchers. In the workshop **RO2018**, part of [IEEE eScience 2018]( in Amsterdam, we will explore recent advancements in Research Objects and publishing of research data with peer-reviewed presentations, invited talks, short demos, lightning talks and break-out sessions to further build relationships across scientific domains and RO practitioners. ## Call for Papers RO2018 welcomes submissions of academic abstracts (1-2 pages), data/software articles (3-6 pages) and short research articles (4-8 pages) on cross-cutting case studies or specific research on topics including, but not limited to: FAIR metrics; platforms, infrastructure and tools; lifecycles; access control and secure exchange; examples of exploitation and application; executable containers; metadata, packaging and formats; credit, attribution and peer review; dealing with scale and distribution; driving adoption within current scholarly communications and alignments with community efforts; and domain-specific and cross-domain Research Objects. Further details on submitting: []( ## Timeline 2018-07-01 Abstracts due 2018-07-15 Research articles and software/data articles due 2018-08-31 Notification of acceptance 2018-08-31 IEEE eScience 2018 early-bird registration deadline 2018-10-29 RO2018 workshop at IEEE eScience 2018 2018-10-29 09:00:00 UTC 2018-10-29 17:00:00 UTC The University of Manchester,, IEEE Mövenpick Hotel Amsterdam City Centre, 11, Piet Heinkade, Amsterdam, Netherlands Mövenpick Hotel Amsterdam City Centre, 11, Piet Heinkade Amsterdam Amsterdam Netherlands Workflows Software engineering Ontology and terminology Informatics Data submission, annotation and curation Data identity and mapping Data integration and warehousing Data architecture, analysis and design Data management Computer science [] For any questions, email the Workshop Organizers at BioExcel [] workshops_and_courses [] digital archivesdata repositorylinked dataWorkflows
  • WEBINAR: Launch, monitor and manage data pipelines on any infrastructure with Nextflow Tower

    5 August 2021


    WEBINAR: Launch, monitor and manage data pipelines on any infrastructure with Nextflow Tower Do you collaborate on distributed data analysis? Needing to launch, monitor, and manage data pipelines on different infrastructures? Maybe [Nextflow Tower]( could help you to code, deploy and enjoy! Nextflow Tower is a centralised command-post for the management of Nextflow data pipelines. It brings monitoring, logging & observability to distributed workflows and simplifies the deployment of pipelines on any cloud, cluster or laptop. **In this demonstration you’ll get an overview of Nextflow Tower’s capabilities, hear how it’s being used and learn some technical details about its deployment.** Users can launch pre-configured pipelines with ease while the flexible API provides programmatic integration to meet the needs of organisations building on top of Nextflow Tower. Workflow developers can publish pipelines to shared workspaces and administrators can set up and manage the infrastructure required to run data analysis at scale. Given its design for highly distributed, infrastructure agnostic computation, Australian BioCommons and our partners are interested in what benefits Nextflow Tower might provide for institutional, national and commercial compute and cloud services. We thought you might like to hear about it too, so this is an open invitation to listen in and bring your questions. **Who the webinar is for:** Anyone interested in hearing about Nextflow Tower **Presenter:** Dr Evan Floden, CEO & Co-founder, Seqera Labs **Date/time:** 5 August 2021 - 10:00-11:00 AEST / 9:30 - 10:30 ACST / 08:00-10:00 AWST / 02:00 - 03:00 CEST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here](** 2021-08-05 10:00:00 UTC 2021-08-05 11:00:00 UTC Australian BioCommons Online, Australia Online Australia Workflows Data management Australian Biocommons Christina Hall [] [] 500 workshops_and_courses first_come_first_served WorkflowsDistributed data analysis
  • WEBINAR: Where to go when your bioinformatics outgrows your compute

    19 August 2021


    WEBINAR: Where to go when your bioinformatics outgrows your compute Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey. We also describe bioinformatics and computing support services available to Australian researchers. **Who the webinar is for** This webinar is intended for biological researchers who wish to understand what computational infrastructure is available outside their institution’s compute facilities. Some familiarity with the concepts of high performance computing is recommended. We think you will enjoy this webinar if you have experienced one of the following: • Your high performance computing jobs fail because of walltime limits • Not having enough disk to process your data • Feeling intimidated by the compute resources and time required to process large datasets If you’re considering applying for access to compute through the NCMAS allocation scheme you can find out more about tailoring your application to bioinformatics projects in our next webinar [High performance bioinformatics: submitting your best NCMAS application]( **Presenters:** Georgina Samaha and Dr Tracy Chew, Sydney Informatics Hub, University of Sydney **Date/time:** 19 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](** 2021-08-19 12:00:00 UTC 2021-08-19 13:00:00 UTC Australian BioCommons Australia Australia Workflows Bioinformatics Australian Biocommons Melissa Burke [] Biologistsbioinformaticians 500 workshops_and_courses first_come_first_served HPCHigh performance computingComputeBioinformaticsWorkflowsNCMAS

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