BioExcel Building Blocks release notes

Release changes
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)

2023.1

2023.1 (13/04/2023)

  • All BioBB's updated to 4.0.0+ version
  • Major fixes in biobb_common
  • New biobb_flexdyn, a module collection for studies on the conformational landscape of native proteins.
  • New biobb_flexserv, a category for biomolecular flexibility studies on protein 3D structures.
  • New biobb_godmd, 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.
2022.3

2022.3 (19/09/2022)

  • All BioBB's updated to 3.8.0+ version
  • Major fixes in biobb_common
  • The package biobb_md has been discontinued, superseeded by the new biobb_gromacs.
2022.2

2022.2 (25/06/2022)

  • New biobb_cp2k, 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
  • New biobb_haddock, a module collection to compute information-driven flexible protein-protein docking
  • Released new BioBB Workflows website
2021.4

2021.4 (24/12/2021)

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