BioBB Building Blocks
OverviewThe 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 use will be equivalent across the workflow systems.
All the building blocks share a unique syntax, requiring input files, output files and input parameters (properties), irrespective of the biomolecular simulation program wrapped. The available building blocks are divided in categories (biobb modules) depending on their functionalities and tools wrapped.
Here we share workflows that demonstrate usage of the BioBB building blocks for use cases with biomolecular simulation. For further details, see:
Space: BioExcel
SEEK ID: https://workflowhub.eu/projects/11
Funding codes:- H2020-INFRAEDI-02-2018-823830
- H2020-EINFRA-2015-1-675728
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, 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 ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
Abstract (Expand)
Authors: Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital
Date Published: 1st Mar 2021
Publication Type: Misc
Abstract (Expand)
Authors: Pau Andrio, Adam Hospital, Javier Conejero, Luis Jordá, Marc Del Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble, Daniele Lezzi, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpi
Date Published: 1st Dec 2019
Publication Type: Journal
Presented at the BioExcel Summer School 2021 this lecture introduces the BioExcel Building Blocks (BioBB).
See also part 2.
Creators: Adam Hospital, Pau Andrio, Genís Bayarri
Submitter: Stian Soiland-Reyes
External LinkPresented at the BioExcel Summer School 2021 this lecture shows how to use BioExcel Building Blocks (BioBB).
See also part 1.
Creator: Adam Hospital
Submitter: Stian Soiland-Reyes
In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields ...
Creators: Pau Andrio, Genís Bayarri, Adam Hospital
Submitter: Stian Soiland-Reyes
This workflow provides a pipeline to setup DNA structures for the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium.
DownloadThis 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).
This workflow performs the process of setting up a simulation system containing a protein, step by step, using the AMBER tools of the BioExcel Building Blocks library (biobb).
This workflow performs the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).
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).
Selection of BioExcel Building Blocks (BioBB) Workflows, across three workflow languages (jupyter notebooks, CWL, and Galaxy), demonstrating the use of BioBB tool descriptors for each of these systems.
Maintainers: Douglas Lowe, Stian Soiland-Reyes, Adam Hospital, Genís Bayarri, Pau Andrio
# items: 5
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Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.
