BioExcel Building Blocks release notes
Release changes
2024.1
2024.1 (27/05/2024)
- New biobb_haddock package, a module collection to compute information-driven flexible protein-protein docking.
- New biobb_pytorch package, a module collection to create and train ML & DL models using the popular PyTorch Python library.
- New Docker images and Dockerfiles for all BioBB workflows.
- Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows paper released.
- Now all BioBB workflows are available in Google Colab.
- All BioBB's updated to 4.2.0+ version.
2023.4
2023.4 (04/12/2023)
- New biobb_pdb_tools package, a swiss army knife for manipulating and editing PDB files.
- All BioBB workflows updated to latest version.
2023.3
2023.3 (08/09/2023)
- All BioBB's updated to 4.1.0+ version.
- Update to Python 3.8 or greater.
- Biopython is no longer linked to a fixed version.
- Major fixes in biobb_common.
2023.2
2023.2 (27/06/2023)
- New demonstration workflow: FAIR workflows to chart and characterize the conformational landscape of native proteins (10.7490/f1000research.1119506.1).
- BioBB-Wfs and BioBB-API webinar.
- biobb_pmx updated to the last PMX version, that accepts alchemical ligand modifications.
2023.1
2023.1 (13/04/2023)
- All BioBB's updated to 4.0.0+ version.
- Major fixes in biobb_common.
- New biobb_flexdyn package, a module collection for studies on the conformational landscape of native proteins.
- New biobb_flexserv package, a category for biomolecular flexibility studies on protein 3D structures.
- New biobb_godmd package, a module collection to compute protein conformational transitions with the GOdMD method.
2022.4
2022.4 (28/12/2022)
- All BioBB's updated to 3.9.0+ version.
- Major fixes in biobb_common.
- biobb_md has been discontinued, superseeded by biobb_gromacs.
2022.2
2022.2 (25/06/2022)
- New biobb_cp2k package, a module collection to allow setup and simulation of QM simulations using CP2K QM package.
- New tools for biobb_io and biobb_structure_utils.
2022.1
2022.1 (17/03/2022)
- Extended information in Python Docstrings improving workflow language interoperability.
- Released new BioBB Workflows website.
2021.4
2021.3
2021.3 (20/10/2021)
- All BioBB's updated to 3.7.0+ version.
- New biobb_dna, a package composed of different analyses for nucleic acid trajectories.
- New ABC MD Setup workflow.
- New Structural DNA helical parameters workflow.
2021.2
2021.2 (30/06/2021)
- All BioBB's updated to 3.6.0+ version.
- Update to Biopython 1.79.
- New biobb_cmip package, a module collection to compute classical molecular interaction potentials.
- New set of Protein-Ligand Docking workflows.
- New set of AMBER workflows.
2021.1
2021.1 (10/03/2021)
- New biobb_vs package, a module collection to perform virtual screening studies.
- New biobb_amber package, a category for AMBER MD package.
2020.4
2020.4 (25/12/2020)
- All BioBB's updated to 3.5.0+ version.
- Update to Biopython 1.78.
- New extended and improved JSON schemas (Galaxy and CWL-compliant).
- New MemProtMD DB REST API tools in biobb_io.
- New Resampling module in biobb_ml.
- New biobb_md grompp_mdrun block combination.
- New "shell" option in biobb_md Solvate.
- New biobb_model tools.
- Biobb_model now is using Modeller.
2020.3
2020.3 (15/10/2020)
- Dependency biobb_common has been updated to 3.0.1 version.
- PMX software has been updated to python 3 and thus, biobb_pmx breaks its dependence from docker.
2020.2
2020.2 (16/06/2020)
- All BioBB's updated to 3.0.0+ version.
- Update to Python 3.7.
- Update to Biopython 1.76.
- New biobb_ml package, a module collection to perform machine learning predictions.
- New workflow to perform free energy calculations over mutated structures (PMX).
2020.1
2020.1 (05/03/2020)
- All BioBB's updated to 2.0.0+ version.
- Compatibility with software containers (Docker, Singularity).
- New documentation, tutorials and website.
2019.4
2019.4 (20/11/2019)
- All BioBB's updated to 1.0.2+ version.
- New adapters for PyCompSs, CWL and Galaxy.
- New workflows for MD and protein mutations.