biobb-md

Biobb_md is the Biobb module collection to perform molecular dynamics simulations.

https://github.com/bioexcel/biobb_md

Science Score: 54.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
○
Academic publication links
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Committers with academic emails
1 of 6 committers (16.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary

Last synced: 7 months ago · JSON representation ·

Repository

Biobb_md is the Biobb module collection to perform molecular dynamics simulations.

Basic Info

Host: GitHub
Owner: bioexcel
License: apache-2.0
Language: Python
Default Branch: master
Homepage: https://mmb.irbbarcelona.org/biobb/
Size: 36 MB

Statistics

Stars: 7
Watchers: 6
Forks: 3
Open Issues: 0
Releases: 0

Created almost 8 years ago · Last pushed 10 months ago

Metadata Files

Readme License Citation

biobb_md

Introduction

Biobb_md is the Biobb module collection to perform molecular dynamics simulations. 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_gromacs.

Version

v3.7.2 2021.3

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.

Installation:
```
pip install "biobb_md>=3.7.2"
```
Usage: Python API documentation

Using ANACONDA:

Installation:

conda install -c bioconda "biobb_md>=3.7.2"

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_md:3.7.2--pyhdfd78af_0

Usage:

docker run quay.io/biocontainers/biobb_md:3.7.2--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_md.sif https://depot.galaxyproject.org/singularity/biobb_md:3.7.2--pyhdfd78af_0

Usage:

singularity exec biobb_md.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

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), 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: 4.2.0
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

GitHub Events

Total

Push event: 2

Last Year

Push event: 2

Committers

Last synced: about 3 years ago

All Time

Total Commits: 295
Total Committers: 6
Avg Commits per committer: 49.167
Development Distribution Score (DDS): 0.231

Top Committers

Name	Email	Commits
Pau Andrio	a**u@g**m	227
gbayarri	g**i@i**g	51
Adam Hospital Gasch	a**l@i**g	11
Josep Ll. Gelpi	g**i@u**u	4
Robin Long	r**1@h**k	1
domagoj	d**n@g**m	1

Committer Domains (Top 20 + Academic)

irbbarcelona.org: 2 hotmail.co.uk: 1 ub.edu: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 0
Total pull requests: 3
Average time to close issues: N/A
Average time to close pull requests: 30 days
Total issue authors: 0
Total pull request authors: 3
Average comments per issue: 0
Average comments per pull request: 0.33
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

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

Pull Request Authors

longr (1)
DomFijan (1)
jlgelpi (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 159 last-month
Total docker downloads: 46

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 2
(may contain duplicates)
Total versions: 25
Total maintainers: 2

pypi.org: biobb-md

Deprecated Package: biobb_md is no longer maintained and has been superseded by the biobb_gromacs package. Biobb_md is the Biobb module collection to perform molecular dynamics simulations.

Homepage: https://github.com/bioexcel/biobb_md
Documentation: http://biobb_md.readthedocs.io/en/latest/
License: Apache Software License
Latest release: 3.7.2
published over 3 years ago

Versions: 19
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 117 Last month
Docker Downloads: 46

Rankings

Docker downloads count: 3.2%

Dependent packages count: 4.8%

Average: 15.2%

Forks count: 16.8%

Stargazers count: 20.3%

Dependent repos count: 21.6%

Downloads: 24.7%

Maintainers (2)

andriopau gbayarri

Last synced: 8 months ago

pypi.org: biobb-wf-mutations

Lysozyme + Mutations workflow built using BioBB Based on the official Gromacs tutorial: http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html

Homepage: https://github.com/bioexcel/biobb_md
Documentation: http://biobb_wf_mutations.readthedocs.io/en/latest/
License: Apache Software License
Latest release: 0.0.6
published about 7 years ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 42 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 16.8%

Stargazers count: 20.3%

Average: 21.1%

Dependent repos count: 21.6%

Downloads: 36.9%

Maintainers (2)

andriopau gbayarri

Last synced: 8 months ago

Dependencies

biobb_md/docs/requirements.txt pypi

docutils ==0.17.1

setup.py pypi

biobb_common ==3.7.0

biobb-md

Science Score: 54.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

biobb_md

Introduction

Version

Installation

Copyright & Licensing

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: biobb-md

Rankings

Maintainers (2)

pypi.org: biobb-wf-mutations

Rankings

Maintainers (2)

Dependencies