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Computational biomolecular simulation workflows with

BioExcel building blocks

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BioExcel Virtual Training

22,23,24 / 11 / 2021

Adam Hospital, IRB Barcelona, Spain

Genís Bayarri , IRB Barcelona, Spain

Lucía Fabio, IRB Barcelona, Spain

Pau Andrio, BSC Barcelona, Spain

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bioexcel.eu

Partners

Funding

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  • Session 1 (Nov 22nd, 15h-17h CET)
    • Introduction to the BioExcel Building Blocks (BioBB) library
    • Introduction to the BioExcel Cloud Portal

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  • Session 2 (Nov 23rd, 15h-17h CET)
    • BioBB workflows with Jupyter Notebooks
    • GROMACS Protein MD setup workflow as example

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  • Session 3 (Nov 24th, 15h-17h CET)
    • BioBB workflows with Command Line Interface
    • GROMACS Protein MD setup workflow as example

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Agenda

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Session 1: ��Introduction to the BioExcel Building Blocks library and workflows� + �Introduction to the BioExcel Cloud Portal�+ �Introduction to the hands-on sessions

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  • Were you able to follow the instructions�(Biobb training - Online interacting environment) ? (Y/N)

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  • Were you able to launch a Jupyter Notebook? (Y/N)

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  • Extend & Discuss

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Questions (2)

Example: Y N

Please answer in the Zoom chat panel

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https://bioexcel.ebi.ac.uk/

BioExcel Cloud Portal

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BioExcel Cloud Portal – ELIXIR SSO

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BioExcel Cloud Portal – Tools

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BioExcel Cloud Portal – Tools

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BioExcel Cloud Portal – Binder

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BioExcel Cloud Portal – Binder

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BioExcel Cloud Portal – Jupyter Notebook

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BioExcel Cloud Portal – File Explorer

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BioExcel Cloud Portal – Editor

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BioExcel Cloud Portal – Terminal

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BioExcel Cloud Portal – BioBB CLI workflows

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BioExcel Cloud Portal – Alternatives - MyBinder

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BioExcel Cloud Portal – Alternatives – Local installation

1) CONDA software installation

2) Workflow CONDA environment installation

http://mmb.irbbarcelona.org/biobb/availability/tutorials

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Questions

https://bioexcel.ebi.ac.uk/

http://mmb.irbbarcelona.org/biobb/

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