BioBB Building Blocks
OverviewThe BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools.
The 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.
All the building blocks share a unique syntax, requiring input files, output files and input parameters (properties), irrespective of the program wrapped.
The available building blocks are divided in categories (biobb modules) depending on their functionalities and tools wrapped.
Space: BioExcel
SEEK ID: https://workflowhub.eu/projects/11
Public web page: https://mmb.irbbarcelona.org/biobb/
Organisms: Sars-cov-2
WorkflowHub PALs: No PALs for this Team
Team created: 16th Jun 2020
Related items
Teams: BioBB Building Blocks
Organizations: Barcelona Supercomputing Center (BSC-CNS)
Teams: BioBB Building Blocks
Organizations: Institute for Research in Biomedicine (IRB)
Teams: BioBB Building Blocks, UX trial team
Organizations: The University of Manchester
https://orcid.org/0000-0003-2249-645X
Teams: BioBB Building Blocks
Organizations: The University of Manchester
https://orcid.org/0000-0002-1248-3594
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
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Teams: BioBB Building Blocks
Web page: https://bioexcel.eu/
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).
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Summary
This tutorial aims to 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).
Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml
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Summary
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.
Workflow engine is a jupyter notebook. Auxiliary libraries used are nb_conda_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code
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Summary
This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).
Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels,
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CWL version of the md_list.cwl workflow for HPC.
