Large-scale analytical workflows on the cloud using Galaxy and Globus
16 November 2016Large-scale analytical workflows on the cloud using Galaxy and Globus http://bioexcel.eu/webinar-8-2016-11-16-workflows-galaxy-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
CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF
28 February 2018CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF https://bioexcel.eu/webinar-cwlexec-a-new-open-source-tool-to-run-cwl-workflows-on-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
Introduction to Linux and Workflows for Biologists
14 - 18 May 2018
Edinburgh, United KingdomIntroduction to Linux and Workflows for Biologists https://genomics.ed.ac.uk/services/introduction-linux-and-workflows-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 - email@example.com   workshops_and_courses  BioinformaticsLinuxWorkflows
H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1
20 August 2018H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1 https://www.youtube.com/watch?v=4_-pxWFUpfU&list=PLcQ0XMykNhCQJPz0amnbz9BPM4Bu0Nkgf https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series #### 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 https://www.nextflow.io/) 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]: https://github.com/h3abionet/h3agwas/blob/master/README.md 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 firstname.lastname@example.org 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, NetherlandsWorkshop on Research Objects (RO2018) http://www.researchobject.org/ro2018/ https://tess.elixir-europe.org/events/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](http://bioexcel.eu) (H2020-675728) ## Research Objects Scholarly Communication has evolved significantly in recent years, with an increasing focus on **Open Research**, [FAIR](https://doi.org/10.1038/sdata.2016.18)data 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](https://www.escience2018.com) 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: [http://www.researchobject.org/ro2018/submitting-to-ro2018/](http://www.researchobject.org/ro2018/submitting-to-ro2018/) ## 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, researchobject.org, 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 email@example.com BioExcel  workshops_and_courses  digital archivesdata repositorylinked dataWorkflows
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