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biobb-flexdyn

biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

https://github.com/bioexcel/biobb_flexdyn

Science Score: 67.0%

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    CITATION.cff file
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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: nature.com, zenodo.org
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    Scientific vocabulary similarity
    Low similarity (6.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

Basic Info
  • Host: GitHub
  • Owner: bioexcel
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Size: 3.58 MB
Statistics
  • Stars: 1
  • Watchers: 7
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 3 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

fair-software.eu

biobb_flexdyn

Introduction

biobbflexdyn is a BioBB category for studies on the conformational landscape of native proteins. biobbflexdyn allows the generation of protein conformational ensembles from 3D structures and the analysis of its molecular flexibility. It is based on the work done in the flexdyn implementation study from the 3D-Bioinfo ELIXIR structural community (https://elixir-europe.org/communities/3d-bioinfo). 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

v5.1.0 2025.1

Installation

Using PIP:

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

Using ANACONDA:

Using DOCKER:

  • Installation:

    docker pull quay.io/biocontainers/biobb_flexdyn:5.1.0--pyhdfd78af_0

  • Usage:

    docker run quay.io/biocontainers/biobb_flexdyn:5.1.0--pyhdfd78af_0

Using SINGULARITY:

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

  • Installation:

    singularity pull --name biobb_flexdyn.sif https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.1.0--pyhdfd78af_0

  • Usage:

    singularity exec biobb_flexdyn.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

Citation (CITATION.cff) 

abstract: "BioExcel Building Blocks (BioBB) library. BioBB's are built as Python wrappers to provide an interoperable architecture. BioBB's have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments."
authors:
  - affiliation: "Barcelona Supercomputing Center (BSC)"
    family-names: "Andrio"
    given-names: "Pau"
    orcid: "https://orcid.org/0000-0003-2116-3880"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Hospital"
    given-names: "Adam"
    orcid: "https://orcid.org/0000-0002-8291-8071"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Bayarri"
    given-names: "Genís"
    orcid: "https://orcid.org/0000-0003-0513-0288"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "García"
    given-names: "Agustín"
    orcid: "https://orcid.org/0009-0002-2159-965X"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
    family-names: "Chaves"
    given-names: "Rubén"
  - affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)"
    family-names: "Orozco"
    given-names: "Modesto"
    orcid: "https://orcid.org/0000-0002-8608-3278"
  - affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
    family-names: "Gelpí"
    given-names: "Josep Ll."
    orcid: "https://orcid.org/0000-0002-0566-7723"
    email: "gelpi@ub.edu"
cff-version: 1.2.0
date-released: "2019-09-10"
keywords:
  - "BioExcel"
  - "BioBB"
  - "Bioinformatics"
  - "Computational Biology"
  - "Biomolecular Workflows"
license: "Apache-2.0"
message: "If you use this dataset, please cite it using the metadata from this file."
repository-code: "https://github.com/bioexcel/biobb"
title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
doi: "10.1038/s41597-019-0177-4"
url: "https://mmb.irbbarcelona.org/biobb/"
version: 5.0.0
preferred-citation:
  type: "article"
  authors:
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Andrio"
      given-names: "Pau"
      orcid: "https://orcid.org/0000-0003-2116-3880"
    - affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
      family-names: "Hospital"
      given-names: "Adam"
      orcid: "https://orcid.org/0000-0002-8291-8071"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Conejero"
      given-names: "Javier"
      orcid: "https://orcid.org/0000-0001-6401-6229"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Jordà"
      given-names: "Luis"
      orcid: "https://orcid.org/0000-0002-9407-9703"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Del Pino"
      given-names: "Marc"
      orcid: "https://orcid.org/0000-0001-5565-7577"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Laia"
      given-names: "Codó"
      orcid: "https://orcid.org/0000-0002-6797-8746"
    - affiliation: "University of Manchester (UOM)"
      family-names: "Soiland-Reyes"
      given-names: "Stian"
      orcid: "https://orcid.org/0000-0001-9842-9718"
    - affiliation: "University of Manchester (UOM)"
      family-names: "Goble"
      given-names: "Carole"
      orcid: "https://orcid.org/0000-0003-1219-2137"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Lezzi"
      given-names: "Daniele"
      orcid: "https://orcid.org/0000-0001-5081-7244"
    - affiliation: "Barcelona Supercomputing Center (BSC)"
      family-names: "Badia"
      given-names: "Rosa M"
      orcid: "https://orcid.org/0000-0003-2941-5499"
    - affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University  of Barcelona (UB)"
      family-names: "Orozco"
      given-names: "Modesto"
      orcid: "https://orcid.org/0000-0002-8608-3278"
    - affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
      family-names: "Gelpí"
      given-names: "Josep Ll."
      orcid: "https://orcid.org/0000-0002-0566-7723"
      email: "gelpi@ub.edu"
  doi: "10.1038/s41597-019-0177-4"
  journal: "Nature Scientific Data"
  month: 9
  start: 169
  title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
  issue: 1
  volume: 6
  year: 2019

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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 96 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 3
pypi.org: biobb-flexdyn

biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 96 Last month
Rankings
Dependent packages count: 7.0%
Average: 18.7%
Dependent repos count: 30.5%
Maintainers (3)
andriopau gbayarri adam.hospital
Last synced: 6 months ago

Dependencies

.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 v3 composite
  • mamba-org/provision-with-micromamba main composite
setup.py pypi
  • biobb_common ==4.0.0
biobb_flexdyn/docs/requirements.txt pypi
  • recommonmark *
  • sphinx_rtd_theme *