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  • 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
  • ELIXIR TtR course: Basic genomics using advanced analysis tools

    20 - 21 December 2018

    Ljubljana, Slovenia

    Elixir node event
    ELIXIR TtR course: Basic genomics using advanced analysis tools https://tess.elixir-europe.org/events/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools **NEW DATE FOR THE COURSE HAS BEEN SET: Dec. 20-21** **ELIXIR TtR course: Basic genomics using advanced analysis tools Genomic Data Science with Galaxy** **December 20-21, 2018**, Faculty of Medicine, Vrazov trg 2, Ljubljana (Slovenia) Galaxy is an open source, web-based platform for data intensive biomedical research. The Galaxy Platform provides user friendly software for producing reproducible genomic pipelines for data analysis. This workshop will provide a 2 day introductory session to Galaxy software system. The course will be in English. The course will take place in the computer classroom at the Institute of Biostatistics and Medical Informatics (IBMI), Faculty of Medicine, Vrazov trg 2, Ljubljana. **The limit of participants is 20**. This course will focus on introducing the Galaxy user interface and how it can be used for basic genomic analyses. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Community. We will cover the basic features of Galaxy, including where to find tools, how to import and use your data, and an introduction to workflows. This session is recommended for anyone who has not used, or only rarely uses Galaxy. **Program topics:** Quick introduction to Galaxy UI (20.12. morning) From peaks to genes (20.12. morning) Reference-based RNA-seq - Quality control (20.12. afternoon) Reference-based RNA-seq - Sequencing (21.12. morning) Lecturers will be **Christophe Antoniewski** and **Olivier Inizan** from ELIXIR France. Course is organised by **ELIXIR Slovenia** in collaboration with **ELIXIR France**. ELIXIR is an European ESFRI priority research infrastructure for bioinformatics that provides databases, (software) tools, services and training (including training materials) for information, cloud storage and supercomputers in the area of life sciences. It coordinates, develops, integrates and sustains life science (bioinformatics) resources across Europe. **Prerequisites:** Wi-Fi enabled laptop with a modern web browser. Latest versions of Google Chrome, Firefox, Safari and Opera will work best. **Location: Faculty of Medicine, University of Ljubljana** If you have any questions about this course, please contact ELIXIR-SI 2018-12-20 09:00:00 UTC 2018-12-21 12:00:00 UTC ELIXIR Slovenia and Faculty of Medicine, University of Ljubljana University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia University of Ljubljana, Faculty of Medicine Ljubljana Central Slovenia Slovenia SI-1000 Genomics University of Ljubljana, Faculty of Medicine elixir@mf.uni-lj.si [] life scientistsPostgraduate studentsbeginner bioinformaticians 20 workshops_and_courses registration_of_interest galaxygenomicstrainingeLearningEeLP
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