Tutorials for BioExcel Building Blocks (BioBB)
Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.
SEEK ID: https://workflowhub.eu/collections/1
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Computational biomolecular simulation workflows with BioExcel Building Blocks - Part 1
Overview of BioBB - Added over 3 years ago -
Computational biomolecular simulation workflows with BioExcel Building Blocks - Part 2
BioBB from Jupyter Notebook - Added over 3 years ago -
Jupyter Notebook Amber Protein MD Setup tutorial
First tutorial for BioBB in Jupyter - AmberTools package version - Added over 3 years ago -
Jupyter Notebook Protein MD Setup tutorial
First tutorial for BioBB in Jupyter - Added over 3 years ago -
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in CWL
CWL version of above - Added over 3 years ago -
Jupyter Notebook Protein Ligand Complex MD Setup tutorial
Jupyter tutorial - Added over 3 years ago -
Jupyter Notebook Mutation Free Energy Calculations
Jupyter tutorial - Added over 3 years ago -
Jupyter Notebook Amber Protein Ligand Complex MD Setup tutorial
Jupyter tutorial. AmberTools package version - Added over 3 years ago -
Jupyter Notebook Protein-ligand Docking tutorial (PDBe REST API)
Jupyter tutorial. PDBe REST-API version - Added over 3 years ago -
Jupyter Notebook Protein-ligand Docking tutorial (Fpocket)
Jupyter tutorial. Fpocket version - Added over 3 years ago -
Jupyter Notebook Protein-ligand Docking tutorial (Cluster90)
Jupyter tutorial. PDB Cluster90 Binding Site version - Added over 3 years ago -
Jupyter Notebook GMX Notebook Automatic Ligand Parameterization tutorial
Jupyter tutorial. - Added over 3 years ago -
Jupyter Notebook Amber Constant pH MD Setup tutorial
Jupyter tutorial. - Added over 3 years ago -
Documentation for BioExcel Building Blocks (BioBB)
- Added over 3 years ago
Maintainers
Views: 1612
Created: 5th Jul 2021 at 11:35
Last updated: 29th Sep 2021 at 15:26
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Teams: IBISBA Workflows, GalaxyProject SARS-CoV-2, BioBB Building Blocks, Common Workflow Language (CWL) community, BioExcel Best Practice Guides, Specimen Data Refinery, FAIR Computational Workflows, Vertebrate Genomes Pipelines in Galaxy, TRE-FX, EuroScienceGateway, Biodiversity Genomics Europe (general), BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection, BY-COVID (general), BioDT additional pipelines, BioDT Use Case 4.1.1.1 Biodiversity dynamics, BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats, BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security, BioDT Use Case 4.1.3.1 Invasive species, BioDT Use Case 4.1.3.2 Endangered species, BioDT Use Case 4.1.4.1 Disease outbreaks, BioDT Use Case 4.1.4.2 Pollinators, BioDT Use Case 4.1.1.2 Ecosystem services, ELIXIR Training, ELIXIR Tools platform
Organizations: The University of Manchester, ELIXIR-UK
https://orcid.org/0000-0001-9842-9718
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/
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/
