babs

BIDS App Bootstrap (BABS)

https://github.com/pennlinc/babs

Science Score: 67.0%

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

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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 6 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

BIDS App Bootstrap (BABS)

Basic Info

Host: GitHub
Owner: PennLINC
License: mit
Language: Python
Default Branch: main
Homepage: https://pennlinc-babs.readthedocs.io
Size: 2.22 MB

Statistics

Stars: 9
Watchers: 11
Forks: 7
Open Issues: 33
Releases: 15

Created over 4 years ago · Last pushed 12 months ago

Metadata Files

Readme License Citation

README.rst

BABS: BIDS App Bootstrap
========================

.. image:: https://readthedocs.org/projects/pennlinc-babs/badge/?version=latest
:target: http://pennlinc-babs.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://circleci.com/gh/PennLINC/babs/tree/main.svg?style=svg
:target: https://circleci.com/gh/PennLINC/babs/tree/main
.. image:: https://codecov.io/gh/PennLINC/babs/branch/main/graph/badge.svg
:target: https://codecov.io/gh/PennLINC/babs
:alt: Code Coverage
.. image:: https://zenodo.org/badge/456981533.svg
:target: https://zenodo.org/badge/latestdoi/456981533
:alt: DOI

Full documentation at https://pennlinc-babs.readthedocs.io

About
-----

BIDS App Bootstrap (BABS) is a reproducible, generalizable, and
scalable Python package for BIDS App analysis of large datasets.
It uses `DataLad `_ and adopts
the `FAIRly big framework `_.
Currently, BABS supports job submissions and audits on SLURM
high performance computing (HPC) clusters.

Citing BABS
-----------

If you use BABS, please cite it using the metadata from the `CITATION.cff `_ file,
as well as the following papers:

Zhao, C., Jarecka, D., Covitz, S., Chen, Y., Eickhoff, S. B., Fair, D. A., ... & Satterthwaite, T. D. (2024).
A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections
using BIDS Apps. *Imaging Neuroscience*, 2, 1-19. doi:10.1162/imag_a_00074.

Zhao, C., Chen, Y., Jarecka, D., Ghosh, S., Cieslak, M., & Satterthwaite, T. D. (2024).
BABS in Action: Merging Reproducibility and Scalability for Large-Scale Neuroimaging Analysis With BIDS Apps.
*Biological Psychiatry*, 95(10), S21-S22. doi:10.1016/j.biopsych.2024.02.056.

BABS programs
-------------

.. image:: https://github.com/PennLINC/babs/raw/main/docs/_static/babs_cli.png
.. Note: this image is taken from the main branch, so it's normal that docs built from branches is not up-to-date.
.. If using relative path, e.g., `_static/babs_cli.png`, although readthedocs front page would look good, GitHub front page cannot find that image!!!

Schematic of BABS workflow
--------------------------

.. image:: https://github.com/PennLINC/babs/raw/main/docs/_static/babs_workflow.png
.. Note: this image is taken from the main branch, so it's normal that docs built from branches is not up-to-date.

Background and Significance
---------------------------

Neuroimaging research faces a crisis of reproducibility.
With massive sample sizes and greater data complexity, this problem becomes more acute.
The BIDS Apps - the software operating on BIDS data - have provided a substantial advance.
However, even using BIDS Apps, a full audit trail of data processing is a necessary prerequisite for fully reproducible research.
Obtaining a faithful record of the audit trail is challenging - especially for large datasets.
Recently, the `FAIRly big framework `_
was introduced as a way to facilitate reproducible processing of large-scale data
by leveraging `DataLad `_ - a version control system for data management.
However, the current implementation of this framework remains challenging to general users.

BABS was developed to address these challenges
and to facilitate the reproducible application of BIDS Apps to large-scale datasets.

Owner

Name: Lifespan Informatics and Neuroimaging Center
Login: PennLINC
Kind: organization

Website: www.pennlinc.io
Repositories: 59
Profile: https://github.com/PennLINC

The Lifespan Informatics and Neuroimaging Center at the University of Pennylvannia

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  BABS : BIDS App Bootstrap
message: >-
  If you use this software, please cite it using the
  metadata from this file, as well as the
  Imaging Neuroscience (doi:10.1162/imag_a_00074) and
  Biological Psychiatry (doi:10.1016/j.biopsych.2024.02.056) papers.
type: software
authors:
  - given-names: Chenying
    family-names: Zhao
    orcid: "https://orcid.org/0000-0001-7878-6259"
  - given-names: Dorota
    family-names: Jarecka
  - given-names: Sydney
    family-names: Covitz
    affiliation: Stanford University
    orcid: "https://orcid.org/0000-0002-7430-4125"
  - given-names: Yibei
    family-names: Chen
  - given-names: Simon B.
    family-names: Eickhoff
  - given-names: Damien
    family-names: Fair
    affiliation: University of Minnesota
    orcid: "https://orcid.org/0000-0001-8602-393X"
  - given-names: Alexandre R.
    family-names: Franco
  - given-names: Yaroslav O.
    family-names: Halchenko
  - given-names: Timothy J.
    family-names: Hendrickson
  - given-names: Felix
    family-names: Hoffstaedter
  - given-names: Audrey
    family-names: Houghton
  - given-names: Gregory
    family-names: Kiar
  - given-names: Austin
    family-names: Macdonald
  - given-names: Kahini
    family-names: Mehta
    email: kahini.mehta@pennmedicine.upenn.edu
    affiliation: Columbia University
    orcid: "https://orcid.org/0000-0001-9466-100X"
  - given-names: Michael P.
    family-names: Milham
  - given-names: Taylor
    family-names: Salo
    email: salot@pennmedicine.upenn.edu
    affiliation:Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
    orcid: "https://orcid.org/0000-0001-9813-3167"
  - given-names: Michael
    family-names: Hanke
  - given-names: Satrajit S.
    family-names: Ghosh
  - given-names: Brooke L.
    family-names: Sevchik
    affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
  - given-names: S. Parker
    family-names: Singleton
    affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
    orcid: "https://orcid.org/0000-0002-7102-7820"
  - given-names: Tien
    family-names: Tong
    affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
    orcid: 'https://orcid.org/0000-0002-1940-3198'
  - given-names: Matthew
    family-names: Cieslak
    email: matthew.cieslak@pennmedicine.upenn.edu
    affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
    orcid: "https://orcid.org/0000-0002-1931-4734"
  - given-names: Steven
    family-names: Meisler
    orcid: "https://orcid.org/0000-0002-8888-1572"
    affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
  - given-names: Theodore
    family-names: Satterthwaite
    affiliation: Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
    orcid: "https://orcid.org/0000-0001-7072-9399"
identifiers:
  - type: doi
    value: 10.5281/zenodo.8184642
    description: The Zenodo DOI
repository-code: "https://github.com/PennLINC/babs"
url: "https://pennlinc-babs.readthedocs.io/"
abstract: >-
  BIDS App Bootstrap (BABS) is a reproducible, generalizable, and scalable
  Python package for BIDS App analysis of large datasets.
  It uses DataLad and adopts the FAIRly big framework.
  Currently, BABS supports jobs submissions and audits on SLURM
  high performance computing (HPC) clusters.
keywords:
  - BIDS-App
  - Neuroimaging
license: MIT
version: 0.0.10
date-released: "2025-03-24"

GitHub Events

Total

Create event: 85
Release event: 7
Issues event: 95
Watch event: 5
Delete event: 57
Member event: 2
Issue comment event: 89
Push event: 432
Pull request review event: 46
Pull request review comment event: 30
Pull request event: 137
Fork event: 3

Last Year

Create event: 85
Release event: 7
Issues event: 95
Watch event: 5
Delete event: 57
Member event: 2
Issue comment event: 89
Push event: 432
Pull request review event: 46
Pull request review comment event: 30
Pull request event: 137
Fork event: 3

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 162
Total pull requests: 212
Average time to close issues: 7 months
Average time to close pull requests: 17 days
Total issue authors: 14
Total pull request authors: 11
Average comments per issue: 1.44
Average comments per pull request: 0.69
Merged pull requests: 169
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 50
Pull requests: 151
Average time to close issues: 25 days
Average time to close pull requests: 1 day
Issue authors: 11
Pull request authors: 9
Average comments per issue: 0.72
Average comments per pull request: 0.42
Merged pull requests: 119
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

zhao-cy (82)
tsalo (19)
tientong98 (9)
smeisler (7)
mattcieslak (6)
yarikoptic (6)
asmacdo (6)
yibeichan (5)
audreycluo (4)
Michael-Sun (4)
singlesp (3)
B-Sevchik (2)
djarecka (1)
jacobsanz97 (1)

Pull Request Authors

mattcieslak (72)
zhao-cy (45)
tsalo (31)
tientong98 (22)
singlesp (12)
smeisler (10)
asmacdo (7)
djarecka (4)
yibeichan (4)
yarikoptic (3)
B-Sevchik (2)

Top Labels

Issue Labels

enhancement (29) bug (24) documentation (10) roadmap (8) breaking-change (6) container (2) maintenance (1) scheduler (1)

Pull Request Labels

documentation (22) refactor (18) enhancement (15) breaking-change (15) bug (11) examples-enhancement (1) container (1) bids-app (1)

Packages

Total packages: 1
Total downloads:
- pypi 174 last-month

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

pypi.org: babs

BABS: BIDS App BootStrap

Homepage: https://github.com/pennlinc/babs
Documentation: https://pennlinc-babs.readthedocs.io/en/stable/
License: MIT License Copyright (c) 2022- Lifespan Informatics and Neuroimaging Center Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Latest release: 0.5.2
published about 1 year ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 174 Last month

Rankings

Dependent packages count: 7.1%

Forks count: 15.7%

Average: 21.7%

Dependent repos count: 31.5%

Stargazers count: 32.5%

Maintainers (3)

mcieslak tsalo zhao-cy