Robin Long
SEEK ID: https://workflowhub.eu/people/34
Location:
United Kingdom
ORCID:
https://orcid.org/0000-0003-2249-645X
Joined: 16th Jun 2020
Expertise: Not specified
Tools: Not specified
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BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
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The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
This BioExcel best practice guide outlines the development process for writing a workflow using the Common Workflow Language (CWL), from creating and selecting tools like BioBB, through early experimentation, reuse and testing, to optimization and ensuring reproducibility before publication in workflow repositories.
Creators: Stian Soiland-Reyes, Douglas Lowe, Robin Long
Submitter: Stian Soiland-Reyes
External Link
Abstract (Expand)
Authors: Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital
Date Published: 7th Mar 2021
Publication Type: Journal
This BioExcel best practice guide discusses the workflow engines available for the Common Workflow Language (CWL).
Creators: Robin Long, Douglas Lowe, Stian Soiland-Reyes
Submitter: Stian Soiland-Reyes
Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.
OpenBabel and ACPype packages are used to **add hydrogens, energetically ...
Type: Jupyter
Creators: Genís Bayarri, Adam Hospital, Douglas Lowe
Submitters: Robin Long, Genís Bayarri
Common Workflow Language example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI). This workflow returns a resulting protein structure and simulated 3D trajectories.
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