The BioExcel Building Blocks (BioBB) library is a collection of portable wrappers on top of common biomolecular simulation tools Andrio, P., et al. BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. Sci Data 6, 169 (2019). Created and implemented within the BioExcel CoE, the library is designed to i) increase the interoperability between the tools wrapped; ii) ease the implementation of biomolecular simulation workflows; and iii) increase the reusability and reproducibility of the generated workflows. The library is being developed following the FAIR principles for research software development best practices. The result is a collection of building block modules, classified according to the tool being wrapped (e.g. biobb_amber for AMBER MD package) or the functionalities offered by the tools being wrapped (e.g. biobb_vs for Virtual Screening, biobb_chemistry for chemoinformatics). Each of the module is built from a combination of software packaging (Pip, BioConda, BioContainers), documentation (ReadTheDocs, OpenAPI, Swagger), registry and findability (bio.tools, BioSchemas, OpenEBench, WorkflowHub), source code (GitHub) and WfMS integration -adapters- (CWL, Galaxy, PyCOMPSs, Jupyter Notebook).
A collection of demonstration workflows have been developed to showcase the library possibilities. Built using the Jupyter Noteboook GUI, the demonstration workflows offer a graphical and interactive interface, including documentation (integrated markdown) related to the workflow and the building blocks used, and also information about the pipeline and the biomolecular simulation methods used. The set of demonstration workflows are available separately on the BioExcel GitHub repository, with step-by-step instructions on how to reproduce them in a local machine using the Conda packaging software. There is also a global repository for all the BioExcel Building Blocks Workflows. In this repository, there are all the versions for each workflow manager: Common Workflow Language (CWL), Galaxy, Jupyter Notebooks and Pure Python.
All the information regarding the BioExcel Building Blocks library can be found in the central BioBB web page. Links to source code, documentation, packages, containers, tutorials, and information from training events (e.g. BioExcel Summer/Winter School) can be found in the different web sections.
Feedback and contact: http://mmb.irbbarcelona.org/biobb/contact
The latest documentation of our biobb collections can be found in our readthedocs sites:
Copyright & Licensing
Licensed under the Apache License 2.0, see the file LICENSE for details.