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

Abstract

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.

Fig. 1

BioExcel building block architecture. BioBB’s structure split in three main layers: The inner layer corresponds to the original tool unaltered, the second one, the Python compatibility layer provides a standardized interface, the third one, the outer workflow manager adaptation layer translates the Python standard interface to each specific WF manager.

Fig. 2

Recommended distribution and deployment flow of the BioBBs. Distribution and packaging tools used to facilitate BioBB’s installation and execution in a wide range of platforms: HPC, Cloud computing, user workstations and even browser interfaces.