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kubeflow-test

Testing kubeflow for training and serving.

https://github.com/njskywalker/kubeflow-test

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (10.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Testing kubeflow for training and serving.

Basic Info
  • Host: GitHub
  • Owner: njskywalker
  • License: apache-2.0
  • Language: HTML
  • Default Branch: kubeflow-test
  • Size: 47 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorials aim to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.

Settings

Biobb modules used

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobb_amber: Tools to setup and run Molecular Dynamics simulations using the Ambertools MD package.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
  • biobbstructureutils: Tools to modify or extract information from a PDB structure file.
  • biobb_chemistry: Tools to to perform chemical conversions.

Auxiliary libraries used

  • jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
  • plotly: Python interactive graphing library integrated in Jupyter notebooks.
  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
  • simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.
  • gfortran: Fortran 95/2003/2008/2018 compiler for GCC, the GNU Compiler Collection.
  • libgfortran5: Fortran compiler and libraries from the GNU Compiler Collection.

Conda Installation

console git clone https://github.com/bioexcel/biobb_wf_amber.git cd biobb_wf_amber conda env create -f conda_env/environment.yml conda activate biobb_wf_amber

Launch

Protein MD Setup tutorial

console jupyter-notebook biobb_wf_amber/notebooks/md_setup/biobb_wf_amber_md_setup.ipynb

Protein-Ligand Complex MD Setup tutorial

console jupyter-notebook biobb_wf_amber/notebooks/md_setup_lig/biobb_wf_amber_md_setup_lig.ipynb

Constant pH MD Setup tutorial

console jupyter-notebook biobb_wf_amber/notebooks/md_setup_ph/biobb_wf_amber_md_setup_ph.ipynb

ABC MD Setup tutorial

console jupyter-notebook biobb_wf_amber/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb

Tutorials

Click here to view tutorials in Read the Docs

Version

2024.1 Release

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 H2020 823830, EU H2020 675728).

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

Owner

  • Name: Neb Jovanovic
  • Login: njskywalker
  • Kind: user

GitHub Events

Total
  • Public event: 1
  • Push event: 19
Last Year
  • Public event: 1
  • Push event: 19

Dependencies

.github/workflows/citation.yaml actions
  • actions/checkout v3 composite
  • peter-murray/workflow-application-token-action v3 composite
.github/workflows/inactive_issues.yml actions
  • actions/stale v5 composite
biobb_wf_amber/docs/requirements.txt pypi
  • recommonmark *
  • sphinx_rtd_theme *
binder/environment.yml conda
  • biobb_amber 4.2.0
  • biobb_analysis 4.2.0
  • biobb_chemistry 4.2.0
  • biobb_io 4.2.0
  • biobb_structure_utils 4.2.0
  • gfortran 11.3.0
  • libgfortran5 11.3.0
  • nglview
  • plotly
  • simpletraj
conda_env/environment.yml conda
  • biobb_amber 4.2.0
  • biobb_analysis 4.2.0
  • biobb_chemistry 4.2.0
  • biobb_io 4.2.0
  • biobb_structure_utils 4.2.0
  • gfortran 11.3.0
  • jupyter
  • libgfortran5 11.3.0
  • nglview
  • plotly
  • simpletraj
biobb_wf_amber/kubeflow-pipeline/pyproject.toml pypi
  • biobb-amber >=5.0.4
  • kfp >=2.11.0
  • kfp-kubernetes >=1.4.0
biobb_wf_amber/kubeflow-pipeline/uv.lock pypi
  • attrs 25.1.0
  • biobb-amber 5.0.4
  • biobb-common 5.0.0
  • biopython 1.85
  • cachetools 5.5.1
  • certifi 2025.1.31
  • charset-normalizer 3.4.1
  • click 8.1.8
  • colorama 0.4.6
  • docstring-parser 0.16
  • google-api-core 2.24.1
  • google-auth 2.38.0
  • google-cloud-core 2.4.1
  • google-cloud-storage 2.19.0
  • google-crc32c 1.6.0
  • google-resumable-media 2.7.2
  • googleapis-common-protos 1.67.0
  • idna 3.10
  • jsonschema 4.23.0
  • jsonschema-specifications 2024.10.1
  • kfp 2.11.0
  • kfp-kubernetes 1.4.0
  • kfp-pipeline-spec 0.6.0
  • kfp-server-api 2.3.0
  • kubernetes 30.1.0
  • numpy 2.2.3
  • oauthlib 3.2.2
  • pipelinelib 1.0.0
  • proto-plus 1.26.0
  • protobuf 4.25.6
  • pyasn1 0.6.1
  • pyasn1-modules 0.4.1
  • python-dateutil 2.9.0.post0
  • pyyaml 6.0.2
  • referencing 0.36.2
  • requests 2.32.3
  • requests-oauthlib 2.0.0
  • requests-toolbelt 0.10.1
  • rpds-py 0.23.1
  • rsa 4.9
  • six 1.17.0
  • tabulate 0.9.0
  • typing-extensions 4.12.2
  • urllib3 1.26.20
  • websocket-client 1.8.0