BioExcel
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 great performance and scalability capabilities for extreme-scale utilization of the worlds largest high-performance computing (HPC) and high-throughput computing (HTC) compute resource. BioExcel has developed an extensive training program to address competence gaps in extreme-scale scientific computing for beginners, advanced users and HPC/HTC system maintainers.
The centre maintains an extensive and growing network of industrial researchers in the pharmaceutical, chemical and food industries, and offers tailored products and consultancy services, while code development is done in close collaborations with hardware and software vendors to ensure compatibility and support for cutting-edge features. BioExcel works closely with various governmental, non-profit, educational and policy projects and initiatives.
Web page: https://bioexcel.eu/
Funding codes:- H2020-INFRAEDI-02-2018-823830
- H2020-EINFRA-2015-1-675728
This work has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830, H2020-EINFRA-2015-1-675728.
Related items
Teams: BioBB Building Blocks, EuroScienceGateway
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: 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
Organizations: The University of Manchester
https://orcid.org/0000-0001-9842-9718
Team developing BioExcel best practice guides
Space: BioExcel
Public web page: https://docs.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/
Tutorial and specification for packaging IEEE 2791-2020 (BioCompute Objects/BCOs) as RO-Crate Research Objects.
BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.
RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.
BCO RO-Crate is the combination ...
Creators: Stian Soiland-Reyes, Jonathon Keeney, Hadley King, Janisha Patel, Alex Coleman
Submitter: Stian Soiland-Reyes
External LinkThis 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
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
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
BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.
RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.
BCO RO-Crate is the combination of these two approaches, packaging a BCO and the workflow it describes in a RO-Crate.
This webinar describes ...
Creator: Stian Soiland-Reyes
Submitter: Stian Soiland-Reyes
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
Presented 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
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
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
Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB ...
Protein Conformational ensembles generation
Workflow included in the ELIXIR 3D-Bioinfo Implementation Study:
Building on PDBe-KB to chart and characterize the conformation landscape of native proteins
This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
...
Protein Conformational ensembles generation
Workflow included in the ELIXIR 3D-Bioinfo Implementation Study:
Building on PDBe-KB to chart and characterize the conformation landscape of native proteins
This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
...
Protein Conformational ensembles generation
Workflow included in the ELIXIR 3D-Bioinfo Implementation Study:
Building on PDBe-KB to chart and characterize the conformation landscape of native proteins
This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
...
Protein Conformational ensembles generation
Workflow included in the ELIXIR 3D-Bioinfo Implementation Study:
Building on PDBe-KB to chart and characterize the conformation landscape of native proteins
This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
...
AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
Based on the official GROMACS tutorial.
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 ...
AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
Based on the official GROMACS tutorial.
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the **BioExcel Building ...
AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
Based on the official GROMACS tutorial.
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 ...
Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code ...
Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
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), ...
Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
This workflow must be run in biobb.usegalaxy.es. Please, click here to access.
Based on the official GROMACS tutorial.
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 ...
Protein MD Analysis tutorial using BioExcel Building Blocks (biobb)
This workflow computes a set of Quality Control (QC) analyses on top of an uploaded MD trajectory. QC analyses include positional divergence (RMSd), change of shape (Radius of Gyration), identification of flexible regions (atomic/residue fluctuations), and identification of different molecular conformations (trajectory clustering).
Copyright & Licensing
This software has been developed in the [MMB ...
Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
Based on the official GROMACS tutorial.
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).
Copyright & Licensing
This software has been developed in ...
