Common Workflow Language with BioExcel Building Blocks (biobb)

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This tutorial aims to illustrate the process of building up a CWL workflow using the BioExcel Building Blocks library (biobb). The tutorial is based on the Protein Gromacs MD Setup Jupyter Notebook tutorial.

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Settings

Biobb modules used

• biobb_io: Tools to fetch data to be consumed by the rest of the Biobb building blocks.
• biobb_model: Tools to model macromolecular structures.
• biobb_md: Tools to setup and run Molecular Dynamics simulations.
• biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Software requirements

• cwltool: Common Workflow Language tool description reference implementation.
• docker: Docker container platform.

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Tutorial

Click here to view tutorial in Read the Docs

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Version

June 2020 Release

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

• (c) 2015-2020 Barcelona Supercomputing Center
• (c) 2015-2020 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.