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biobb-ml

Biobb_ml is the Biobb module collection to perform machine learning predictions.

https://github.com/bioexcel/biobb_ml

Science Score: 49.0%

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

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    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
  • ○
    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.1%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Biobb_ml is the Biobb module collection to perform machine learning predictions.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 8
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created almost 6 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

fair-software.eu

biobb_ml

Introduction

Biobb_ml is the Biobb module collection to perform machine learning predictions. 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.

Important: This package has been discontinued, superseeded by biobb_pytorch.

Version

v4.2.0 2024.1

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_ml:4.2.0--pyhdfd78af_0

  • Usage:

    docker run quay.io/biocontainers/biobb_ml:4.2.0--pyhdfd78af_0 <command>

Using SINGULARITY:

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

  • Installation:

    singularity pull --name biobb_ml.sif https://depot.galaxyproject.org/singularity/biobb_ml:4.2.0--pyhdfd78af_0

  • Usage:

    singularity exec biobb_ml.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 Horizon Europe 101093290, 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
  • Push event: 5
Last Year
  • Push event: 5

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 171
  • Total Committers: 2
  • Avg Commits per committer: 85.5
  • Development Distribution Score (DDS): 0.012
Top Committers
Name Email Commits
gbayarri g****i@i****g 169
Pau Andrio a****u@g****m 2
Committer Domains (Top 20 + Academic)
irbbarcelona.org: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 3
  • Total pull requests: 4
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: 32 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gbayarri (3)
Pull Request Authors
  • dependabot[bot] (4)
Top Labels
Issue Labels
stale (3)
Pull Request Labels
dependencies (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 59 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 2
pypi.org: biobb-ml

Biobb_ml is the Biobb module collection to perform machine learning predictions.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 59 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Forks count: 22.6%
Average: 23.2%
Downloads: 29.8%
Stargazers count: 31.9%
Maintainers (2)
andriopau gbayarri
Last synced: 7 months ago

Dependencies

biobb_ml/docs/requirements.txt pypi
  • biobb_ml ==3.7.0
  • docutils ==0.17.1
setup.py pypi
  • biobb_common ==3.8.1
  • h5py *
  • imbalanced-learn *
  • pandas *
  • scikit-learn *
  • seaborn *
  • tensorflow >=2.4.2