BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

BioExcel Building Blocks

Increasing usability

Making biomolecular simulation
tools interoperable

Making biomolecular simulation
workflows accessible,
easy to build and use

Enabling scalability

Making biomolecular
simulation workflows
exascale ready

Enabling real science

Building biomolecular simulation workflows
to solve scientific problems

Online Info
Release notes
  • 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
About us

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.