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  • 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
  • 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
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 3

    27 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 3 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-lecture-3 ### Genotype calling from Illumina files The third of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce genotyping SNP array chips with particular emphasis on the H3Africa genotype chip. The lecture will cover common file formats when obtaining genotyping chip data from a service provider such as Illumina and software used for genotype calling. This lecture will also cover genotype calling, sample and probe quality control, probe viewing and exporting of data using GenomeStudio. Converting the data to PLINK format and some tips on troubleshooting and common pitfalls will be discussed. 2018-08-27 15:00:00 UTC 2018-08-27 16:00:00 UTC H3ABioNet Population genomics Bioinformatics Genotyping experiment Genomics Computational biology H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses [] Genotype callingH3ABioNetGenotype callingGenome StudioH3Africa genotyping arrayAfrican populationsArray processingIllumina arraysFile formatsAnnotationsNon-polymorphicTop/Bottom annotationGenotype array probesIntensitiesConvert to PLINK format BioinformaticsGenome Wide Association Studies
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