BioExcel Building Blocks (BioBB)

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Summary

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

Documentation

The latest documentation of our BioBB collections can be found in our readthedocs sites: - biobb_amber [GitHub]: Biobbamber is a BioBB category for AMBER MD package, allowing setup and simulation of atomistic MD simulations using AMBER MD package and its associated AMBER tools. - biobb_analysis [[GitHub]](https://github.com/bioexcel/biobbanalysis): Biobbanalysis is the Biobb module collection to perform analysis of molecular dynamics simulations. - biobb_chemistry [[GitHub]](https://github.com/bioexcel/biobbchemistry): Biobbchemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations. - biobb_cmip [[GitHub]](https://github.com/bioexcel/biobbcmip): Biobbcmip is the Biobb module collection to compute classical molecular interaction potentials. - biobb_common [[GitHub]](https://github.com/bioexcel/biobbcommon): Biobbcommon is the base package required to use the biobb packages. - biobb_cp2k [[GitHub]](https://github.com/bioexcel/biobbcp2k): Biobbcp2k is the Biobb module collection to compute classical molecular interaction potentials. - biobb_dna [[GitHub]](https://github.com/bioexcel/biobbdna): Biobbdna is the Biobb module collection to perform analyses and transformations on nucleic acid trajectories and helical parameter data. - biobb_flexdyn [[GitHub]](https://github.com/bioexcel/biobbflexdyn): Biobbflexdyn is the Biobb module collection for studies on the conformational landscape of native proteins. - biobb_flexserv [[GitHub]](https://github.com/bioexcel/biobbflexserv): Biobbflexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures. - biobb_godmd [[GitHub]](https://github.com/bioexcel/biobbgodmd): Biobbgodmd is the Biobb module collection to compute protein conformational transitions with the GOdMD method. - biobb_gromacs [[GitHub]](https://github.com/bioexcel/biobbgromacs): Biobbgromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite. - biobb_haddock [[GitHub]](https://github.com/bioexcel/biobbhaddock): Biobbhaddock is the Biobb module collection to compute information-driven flexible protein-protein docking. - biobb_io [[GitHub]](https://github.com/bioexcel/biobbio): Biobbio is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. - biobb_md [[GitHub]](https://github.com/bioexcel/biobbmd): Biobbmd is the Biobb module collection to perform molecular dynamics simulations. IMPORTANT: This package has been discontinued, superseeded by biobb_gromacs. - biobb_mem [[GitHub]](https://github.com/bioexcel/biobbmem): Biobbmem is a BioBB category for membrane analysis and manipulation. It allows analysis of membrane properties and manipulation of membrane systems using tools like MDAnalysis and LiPyphilic. - biobb_ml [[GitHub]](https://github.com/bioexcel/biobbml): Biobbml is the Biobb module collection to perform machine learning predictions. IMPORTANT: This package has been discontinued, superseeded by biobb_pytorch. - biobb_model [[GitHub]](https://github.com/bioexcel/biobbmodel): Biobbmodel is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms. - biobbpdbtools [[GitHub]](https://github.com/bioexcel/biobbpdbtools): Biobb PDB Tools is a swiss army knife for manipulating and editing PDB files. - biobb_pmx [[GitHub]](https://github.com/bioexcel/biobbpmx): Biobbpmx is the Biobb module collection to perform PMX executions. - biobb_pytorch [[GitHub]](https://github.com/bioexcel/biobbpytorch): Biobbpytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library. - biobbstructureutils [[GitHub]](https://github.com/bioexcel/biobbstructureutils): Biobbstructureutils is the Biobb module collection to modify or extract information from a PDB structure file. - biobb_vs [[GitHub]](https://github.com/bioexcel/biobbvs): Biobbvs is the Biobb module collection to perform virtual screening studies. - biobbadapters [GitHub]: Biobbadapters is the Biobb module collection to use the building blocks with several workflow managers. - biobb_template [[GitHub]](https://github.com/bioexcel/biobbtemplate): Boilerplate code and template examples to create your own Biobbs.

More information of the BioBB collections available at the official website: https://mmb.irbbarcelona.org/biobb/documentation/source

Videos

• BioExcel Building Blocks in BioExcel YouTube channel: https://www.youtube.com/@BioExcelCoE/search?query=biobb

Workflows

• All the workflows are available at the official website: https://mmb.irbbarcelona.org/biobb/workflows or in the BioExcel GitHub repository.

Version

v5.1.0 2025.1

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

• (c) 2015-2025 Barcelona Supercomputing Center
• (c) 2015-2025 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.