biobb-amber

Biobb_amber is a BioBB category for AMBER MD package.

https://github.com/bioexcel/biobb_amber

Science Score: 67.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: nature.com, zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (6.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Biobb_amber is a BioBB category for AMBER MD package.

Basic Info

Host: GitHub
Owner: bioexcel
License: apache-2.0
Language: Python
Default Branch: master
Homepage: https://mmb.irbbarcelona.org/biobb/
Size: 28.7 MB

Statistics

Stars: 13
Watchers: 6
Forks: 3
Open Issues: 3
Releases: 0

Created about 5 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation

biobb_amber

Introduction

biobbamber is a BioBB category for AMBER MD package. biobbamber allows setup and simulation of atomistic MD simulations using AMBER MD package and its associated AMBER tools. 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_amber>=5.1.0"
```
Usage: Python API documentation

Using ANACONDA:

Installation:

conda install -c bioconda "biobb_amber>=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_amber:5.1.0--pyhdfd78af_0

Usage:

docker run quay.io/biocontainers/biobb_amber: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_amber.sif https://depot.galaxyproject.org/singularity/biobb_amber:5.1.0--pyhdfd78af_0

Usage:

singularity exec biobb_amber.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)"
    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

GitHub Events

Total

Issues event: 1
Watch event: 4
Issue comment event: 1
Push event: 100
Pull request review event: 1
Pull request event: 5
Fork event: 1
Create event: 6

Last Year

Issues event: 1
Watch event: 4
Issue comment event: 1
Push event: 100
Pull request review event: 1
Pull request event: 5
Fork event: 1
Create event: 6

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 138
Total Committers: 7
Avg Commits per committer: 19.714
Development Distribution Score (DDS): 0.254

Top Committers

Name	Email	Commits
gbayarri	g**i@i**g	103
Adam Hospital	a**l@i**g	23
Pau Andrio	a**u@g**m	7
Adam Hospital Gasch	h**l@u**s	2
Nazanin Donyapour	n**r@g**m	1
Adam Hospital Gasch	h**l@A**l	1
Adam Hospital Gasch	h**l@p**s	1

Committer Domains (Top 20 + Academic)

irbbarcelona.org: 2 prttl-adam.mmb.pcb.ub.es: 1 ub247037.ub.es: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 8
Total pull requests: 2
Average time to close issues: 5 months
Average time to close pull requests: 11 days
Total issue authors: 7
Total pull request authors: 2
Average comments per issue: 2.38
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 22 days
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

adamhospital (2)
rahul2512 (1)
ndonyapour (1)
ademariag (1)
gbayarri (1)
GregorySchwing (1)
AndyDanian (1)

Pull Request Authors

ndonyapour (1)
PabloNA97 (1)

Top Labels

Issue Labels

stale (5) bug (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 294 last-month
Total docker downloads: 8

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 17
Total maintainers: 3

pypi.org: biobb-amber

Biobb_amber is a BioBB category for AMBER MD package.

Homepage: https://github.com/bioexcel/biobb_amber
Documentation: http://biobb-amber.readthedocs.io/en/latest/
License: Apache Software License
Latest release: 5.1.0
published 9 months ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 294 Last month
Docker Downloads: 8

Rankings

Docker downloads count: 4.0%

Dependent packages count: 10.1%

Average: 17.2%

Stargazers count: 21.5%

Dependent repos count: 21.6%

Forks count: 22.6%

Downloads: 23.1%

Maintainers (3)

andriopau gbayarri adam.hospital

Last synced: 7 months ago

Dependencies

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_amber/docs/requirements.txt pypi

recommonmark *
sphinx_rtd_theme *

.github/workflows/fair-software.yml actions

fair-software/howfairis-github-action 0.2.1 composite

.github/workflows/citation.yaml actions

actions/checkout v3 composite
peter-murray/workflow-application-token-action v3 composite

.github/workflows/pr-tests.yml actions

actions/checkout v4 composite
actions/github-script v6 composite
mamba-org/setup-micromamba v2.0.0 composite

biobb-amber

Science Score: 67.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

biobb_amber

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-amber

Rankings

Maintainers (3)

Dependencies