BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
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- 22/11/2021
24/11/2021 BioExcel Virtual Training #3 - Virtual Trainings - 09/11/2020
13/11/2020 BioExcel Virtual Training #2 - Virtual Trainings - 23/10/2020 BioExcel Virtual Training AZ - Virtual Trainings
- 16/09/2020 BioExcel Webinar #48 - Webinars
- 23/05/2023 BioExcel Webinar #69 - Webinars
- 29/05/2024 BioExcel Webinar #78 - Webinars
- 04/09/2020 Pre Exascale Tutorial - Tutorials
- 23/06/2020 Summer School 2020.1 - Workshops
- 23/06/2020 Summer School 2020.2 - Workshops
- 08/06/2021 Summer School 2021.1 - Workshops
- 08/06/2021 Summer School 2021.2 - Workshops
- 13/06/2022 Summer School 2022 - Workshops
- 11/09/2023 Summer School 2023 - Workshops
- 08/02/2022 CSC 2022 - Workshops
- 09/12/2019
12/12/2019 BioExcel Virtual Training #1 - Virtual Trainings - 02/02/2021 CSC / BioExcel workshop - Workshops
- 27/05/2024
2024.1
version
- New biobb_haddock package, a module collection to compute information-driven flexible protein-protein docking.
- New biobb_pytorch package, a module collection to create and train ML & DL models using the popular PyTorch Python library.
- New Docker images and Dockerfiles for all BioBB workflows.
- Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows paper released.
- Now all BioBB workflows are available in Google Colab.
- All BioBB's updated to 4.2.0+ version.
- 04/12/2023
2023.4
version
- New biobb_pdb_tools package, a swiss army knife for manipulating and editing PDB files.
- All BioBB workflows updated to latest version.
- 08/09/2023
2023.3
version
- All BioBB's updated to 4.1.0+ version.
- Update to Python 3.8 or greater.
- Biopython is no longer linked to a fixed version.
- Major fixes in biobb_common.
- 27/06/2023
2023.2
version
- New demonstration workflow: FAIR workflows to chart and characterize the conformational landscape of native proteins (10.7490/f1000research.1119506.1).
- BioBB-Wfs and BioBB-API webinar.
- biobb_pmx updated to the last PMX version, that accepts alchemical ligand modifications.
- 13/04/2023
2023.1
version
- All BioBB's updated to 4.0.0+ version.
- Major fixes in biobb_common.
- New biobb_flexdyn package, a module collection for studies on the conformational landscape of native proteins.
- New biobb_flexserv package, a category for biomolecular flexibility studies on protein 3D structures.
- New biobb_godmd package, a module collection to compute protein conformational transitions with the GOdMD method.
- 28/12/2022
2022.4
version
- All BioBB's updated to 3.9.0+ version.
- Major fixes in biobb_common.
- biobb_md has been discontinued, superseeded by biobb_gromacs.
- 25/06/2022
2022.2
version
- New biobb_cp2k package, a module collection to allow setup and simulation of QM simulations using CP2K QM package.
- New tools for biobb_io and biobb_structure_utils.
- 17/03/2022
2022.1
version
- Extended information in Python Docstrings improving workflow language interoperability.
- Released new BioBB Workflows website.
- 24/12/2021
2021.4
version
- Major fixes in biobb_common.
- Released new BioBB REST API.
- 20/10/2021
2021.3
version
- All BioBB's updated to 3.7.0+ version.
- New biobb_dna, a package composed of different analyses for nucleic acid trajectories.
- New ABC MD Setup workflow.
- New Structural DNA helical parameters workflow.
- 30/06/2021
2021.2
version
- All BioBB's updated to 3.6.0+ version.
- Update to Biopython 1.79.
- New biobb_cmip package, a module collection to compute classical molecular interaction potentials.
- New set of Protein-Ligand Docking workflows.
- New set of AMBER workflows.
- 10/03/2021
2021.1
version
- New biobb_vs package, a module collection to perform virtual screening studies.
- New biobb_amber package, a category for AMBER MD package.
- 25/12/2020
2020.4
version
- All BioBB's updated to 3.5.0+ version.
- Update to Biopython 1.78.
- New extended and improved JSON schemas (Galaxy and CWL-compliant).
- New MemProtMD DB REST API tools in biobb_io.
- New Resampling module in biobb_ml.
- New biobb_md grompp_mdrun block combination.
- New "shell" option in biobb_md Solvate.
- New biobb_model tools.
- Biobb_model now is using Modeller.
- 15/10/2020
2020.3
version
- Dependency biobb_common has been updated to 3.0.1 version.
- PMX software has been updated to python 3 and thus, biobb_pmx breaks its dependence from docker.
- 16/06/2020
2020.2
version
- All BioBB's updated to 3.0.0+ version.
- Update to Python 3.7.
- Update to Biopython 1.76.
- New biobb_ml package, a module collection to perform machine learning predictions.
- New workflow to perform free energy calculations over mutated structures (PMX).
- 05/03/2020
2020.1
version
- All BioBB's updated to 2.0.0+ version.
- Compatibility with software containers (Docker, Singularity).
- New documentation, tutorials and website.
- 20/11/2019
2019.4
version
- All BioBB's updated to 1.0.2+ version.
- New adapters for PyCompSs, CWL and Galaxy.
- New workflows for MD and protein mutations.
BioExcel
Building Blocks, a software library for interoperable
biomolecular simulation workflows.
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 Nature
Scientific Data, 09/2019, Volume 6, Issue 1, p.169,
(2019)
BioExcel is funded by the European Union Horizon 2020 program under grant agreements 823830, 675728.