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biobb-morph

https://github.com/bioexcel/biobb_morph

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com, zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioexcel
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Size: 63.7 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

fair-software.eu

biobb_morph

Introduction

Biobb_morph is a Python library that provides tools for performing 3D morphological transformations of intervertebral disc (IVD) meshes. It enables the creation of patient-personalized 3D models by morphing a morph IVD mesh into a target shape. The library is part of the BioExcel Building Blocks (Biobb) framework. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v5.0.1 2024.2

Installation

Using PIP:

Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.

Using ANACONDA:

Using DOCKER:

  • Installation:

    docker pull quay.io/biocontainers/biobb_morph:5.0.1--pyhd7d9b99_0

  • Usage:

    docker run quay.io/biocontainers/biobb_morph:5.0.1--pyhd7d9b99_0 <command>

Using SINGULARITY:

MacOS users: it's strongly recommended to avoid Singularity and use Docker as containerization system.

  • Installation:

    singularity pull --name biobb_morph.sif https://depot.galaxyproject.org/singularity/biobb_morph:5.0.1--pyhd7d9b99_0

  • Usage:

    singularity exec biobb_morph.sif <command>

The command list and specification can be found at the Command Line documentation.

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: BioExcel
  • Login: bioexcel
  • Kind: organization

Center of Excellence for Computational Biomolecular Research

GitHub Events

Total
  • Public event: 1
  • Push event: 6
  • Fork event: 1
  • Create event: 2
Last Year
  • Public event: 1
  • Push event: 6
  • Fork event: 1
  • Create event: 2

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 15 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 2
pypi.org: biobb-morph

biobb_morph is the Biobb module collection to create patien-specific 3D meshes from IVD template examples.

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 15 Last month
Rankings
Dependent packages count: 9.7%
Average: 32.3%
Dependent repos count: 54.9%
Maintainers (2)
andriopau gbayarri
Last synced: 7 months ago

Dependencies

.github/workflows/citation.yaml actions
  • actions/checkout v2 composite
.github/workflows/fair-software.yml actions
  • fair-software/howfairis-github-action 0.2.1 composite
.github/workflows/github-to-gitlab-push-sync.yml actions
  • actions/checkout v4 composite
  • cniethammer/git-repo-sync main composite
.github/workflows/inactive_issues.yml actions
  • actions/stale v5 composite
.github/workflows/linting_and_testing.yml actions
  • JamesIves/github-pages-deploy-action v4 composite
  • actions/checkout v4 composite
  • mamba-org/setup-micromamba v2.0.0 composite
biobb_morph/docs/requirements.txt pypi
  • recommonmark *
  • sphinx_rtd_theme *
setup.py pypi
  • Rtree *
  • biobb_common ==5.0.0
  • matplotlib *
  • meshio *
  • numpy *
  • numpy-stl *
  • scikit-learn *
  • scipy *
  • torch *
  • trimesh *