The new release of the BioExcel building blocks library (v2.0.0) is now available.

The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools such as GROMACS, ACpype, Ambertools, pmx or OpenBabel. The 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.

Workflows built up from the biobb library are reusable & reproducible thanks to the possibility to package them in a single Python script with a defined Conda environment, or in a CWL specification file, to be shared and reproduced anywhere else. Besides, they are prepared for the exascale computing, thanks to their compatibility with HPC-ready workflow managers such as PyCOMPSs or Toil.

BioExcel Building Blocks are divided in categories (biobb modules) depending on their functionalities and tools wrapped. Every module is available from an independent GitHub repository and from associated BioConda packages and Docker/Singularity containers. Documentation for all modules is generated using readthedocs.

Information about the library including how to download, install, and use it, as well as a collection of jupyter notebook demonstration tutorials showing biomolecular workflows built using it can be found in the biobb landing web site:

BioExcel Virtual Training events are periodically organized including hands-on sessions on building biomolecular workflows using the BioExcel Building Blocks library.


BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.
Pau Andrio, Adam Hospital, Javier Conejero, Luis Jord√°, 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). DOI: