biobb-flexserv

Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.

https://github.com/bioexcel/biobb_flexserv

Science Score: 67.0%

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CITATION.cff file
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codemeta.json file
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DOI references
Found 5 DOI reference(s) in README
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Links to: nature.com, zenodo.org
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Low similarity (6.3%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.

Basic Info

Host: GitHub
Owner: bioexcel
License: apache-2.0
Language: Python
Default Branch: master
Homepage:
Size: 6.01 MB

Statistics

Stars: 1
Watchers: 7
Forks: 0
Open Issues: 0
Releases: 0

Created almost 4 years ago · Last pushed 11 months ago

Metadata Files

Readme License Citation

biobb_flexserv

Introduction

biobbflexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures. biobbflexserv allows the generation of protein conformational ensembles from 3D structures and the analysis of its molecular flexibility. It is based on the work included in the FlexServ server (https://mmb.irbbarcelona.org/FlexServ/, Camps et. al., FlexServ: an integrated tool for the analysis of protein flexibility, Bioinformatics, Volume 25, Issue 13, 1 July 2009, Pages 1709–1710, https://doi.org/10.1093/bioinformatics/btp304). 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.

Installation:
```
pip install "biobb_flexserv>=5.1.0"
```
Usage: Python API documentation

Using ANACONDA:

Installation:

conda install -c bioconda "biobb_flexserv>=5.1.0"

Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation

Using DOCKER:

Installation:

docker pull quay.io/biocontainers/biobb_flexserv:5.1.0--pypl5321hdfd78af_0

Usage:

docker run quay.io/biocontainers/biobb_flexserv:5.1.0--pypl5321hdfd78af_0

Using SINGULARITY:

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

Installation:

singularity pull --name biobb_flexserv.sif https://depot.galaxyproject.org/singularity/biobb_flexserv:5.1.0--pypl5321hdfd78af_0

Usage:

singularity exec biobb_flexserv.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, EU HORIZON-EUROHPC-JU 101093290).

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

Owner

Name: BioExcel
Login: bioexcel
Kind: organization

Website: https://bioexcel.eu/
Repositories: 50
Profile: https://github.com/bioexcel

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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Total packages: 1
Total downloads:
- pypi 92 last-month
Total docker downloads: 17

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 10
Total maintainers: 3

pypi.org: biobb-flexserv

biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.

Homepage: https://github.com/bioexcel/biobb_flexserv
Documentation: http://biobb-flexserv.readthedocs.io/en/latest/
License: Apache Software License
Latest release: 5.1.0
published about 1 year ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 92 Last month
Docker Downloads: 17

Rankings

Dependent packages count: 7.0%

Average: 18.7%

Dependent repos count: 30.5%

Maintainers (3)

andriopau gbayarri adam.hospital

Last synced: 10 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

setup.py pypi

biobb_common ==3.8.1

.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/setup-micromamba v1 composite

biobb_flexserv/docs/requirements.txt pypi

recommonmark *
sphinx_rtd_theme *

ecosyste.ms

Data

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Open Source Science

biobb-flexserv

Science Score: 67.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

biobb_flexserv

Introduction

Version

Installation

Copyright & Licensing

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

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Issue Labels

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pypi.org: biobb-flexserv

Rankings

Maintainers (3)

Dependencies