About
The BioExcel Building Blocks (BioBB) is a new software library devised to help in the generation of interoperable and reproducible biomolecular simulation workflows. Designed and developed entirely by the BioExcel CoE, the library follows the recommendations of the ELIXIR European Life Science infrastructure and the FAIR principles for software development. The result is a set of interoperable units based on a collection of Python wrappers encapsulating biomolecular simulation and structural bioinformatics software components, including MD simulations, docking, molecular interactions, structural ensemble generation, molecular flexibility analyses, and conformational transitions. The source code is freely accessible from GitHub, installable via Conda, Docker and Singularity containers, and compatible with different workflow languages.
The library increases the usability of biomolecular simulation workflows. A uniform syntax and the interoperability layer added to the biomolecular simulation tools eases the building and use of BioBB workflows. The packaging systems used make the workflows highly reproducible. All these assets are exemplified by a collection of demonstration workflows tackling transversal biomolecular simulation processes. These workflows are available in different “flavours”: Jupyter Notebooks, Common Workflow Language (CWL), Galaxy and pure Python.
The library is also enabling scalability in biomolecular simulation workflows. The compatibility with HPC-focused workflow managers allow an efficient usage of supercomputers. Workflow managers can direct the distribution of the work along the available resources. Work parallelization can be transparently applied both to the tool level (e.g. GROMACS) and also to independent calculations included in the pipeline (e.g. programmatic loops), considerably reducing the time to results.
BioExcel Building Blocks (BioBB), a software library for interoperable biomolecular simulation workflows
Whether you are new to BioBB or you already have some experience, we have collated a number of relevant learning and support resources to help you out. Access the BioBB documentation, dedicated support forum, lectures, tutorials and more!
Find out more about our user-driven development plans for BioBB which feature three main categories: application building blocks, demonstration workflows and pre-exascale workflows. A roadmap until the end of 2024 is presented.
References
Wieczór et al. (2023) WIREs Comput Mol Sci. 13(1):e1622 (DOI: 10.1002/wcms.1622)
Bayarri et al. (2022) Nucleic Acids Research 50; W99–W107 (DOI: 10.1093/nar/gkac380)
Bayarri et al. (2022) Bioinformatics 38: 3302–3303 (DOI: 10.1093/bioinformatics/btac316)
Ejarque et al. (2022) 2022 IEEE 18th International Conference on e-Science pp.357-366. (DOI: 10.1109/eScience55777.2022.00049)
Soiland-Reyes et al. (2022) Data Intelligence 2022; 4: 342–357. (DOI: 10.1162/dint_a_00135)
Andrio et al. (2019) Sci Data 6, 169 (DOI: 10.1038/s41597-019-0177-4)
