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

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 like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments. We thank The Barcelona Supercomputing Center for providing all the HPC resources to launch the test executions presented in this manuscript. Te project was supported by the following grants: BioExcel Center of Excellence (Horizon 2020 Framework Programme. Grants 675728, and 823830). Elixir-Excelerate (Horizon 2020 Framework Programme. Grant 676559). Spanish National Institute for Bioinformatics (Institute of Health Carlos III. Grants PT13/0001/0019, PT13/0001/0028, PT17/0009/0001). Spanish Government, Severo Ochoa Grant SEV2015-0493, TIN2015-65316-P, Generalitat de Catalunya. 2014-SGR-1051, 2017-SGR-1110.