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@bioexcel

BioExcel

Center of Excellence for Computational Biomolecular Research

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  1. biobb biobb Public

    Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

    Python 65 10

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 52 25

  3. gromacs-2022-cp2k-tutorial gromacs-2022-cp2k-tutorial Public

    Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface

    Makefile 42 9

  4. cp2K_qmmm_tutorials_for_biological_simulations cp2K_qmmm_tutorials_for_biological_simulations Public

    Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.

    Jupyter Notebook 24 8

  5. biobb_amber biobb_amber Public

    Biobb_amber is a BioBB category for AMBER MD package.

    Python 14 3

  6. biobb_structure_checking biobb_structure_checking Public

    Python 13 2

Repositories

Showing 10 of 124 repositories
  • biobb_pytorch Public

    Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.

    bioexcel/biobb_pytorch’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Apr 17, 2026
  • biobb_dyna Public

    Biobb_dyna (Dynamical Network Analysis) is the BioBB module collection for building and analyzing dynamical correlation networks from molecular dynamics simulations to study allosteric communication and signal propagation.

    bioexcel/biobb_dyna’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Apr 13, 2026
  • biobb_workflows Public

    Global repository for all the BioExcel Building Blocks Workflows

    bioexcel/biobb_workflows’s past year of commit activity
    Common Workflow Language 8 4 0 0 Updated Apr 1, 2026
  • biobb-airflow Public

    This repo hosts a Docker Compose implementation for Apache Airflow.

    bioexcel/biobb-airflow’s past year of commit activity
    Shell 0 Apache-2.0 0 0 0 Updated Mar 23, 2026
  • biobb_mem Public
    bioexcel/biobb_mem’s past year of commit activity
    Python 0 Apache-2.0 0 3 0 Updated Mar 23, 2026
  • biobb_adapters Public

    Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.

    bioexcel/biobb_adapters’s past year of commit activity
    Common Workflow Language 0 Apache-2.0 5 6 0 Updated Mar 23, 2026
  • biobb_analysis Public

    Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.

    bioexcel/biobb_analysis’s past year of commit activity
    Python 4 Apache-2.0 3 1 1 Updated Mar 19, 2026
  • biobb_haddock Public

    biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking.

    bioexcel/biobb_haddock’s past year of commit activity
    Python 2 Apache-2.0 0 1 0 Updated Mar 17, 2026
  • biobb_flexserv Public

    Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.

    bioexcel/biobb_flexserv’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Mar 17, 2026
  • biobb_flexdyn Public

    biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

    bioexcel/biobb_flexdyn’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Mar 17, 2026
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