Add CITATION.cff and update citations in README (#252)

Author: tsalo

CITATION.cff

@@ -0,0 +1,102 @@
+# 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: [email protected]
+    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: [email protected]
+    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: [email protected]
+    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"

README.rst

@@ -1,6 +1,6 @@
 
 BABS: BIDS App Bootstrap
-===============================
+========================
 
 .. image:: https://readthedocs.org/projects/pennlinc-babs/badge/?version=latest
   :target: http://pennlinc-babs.readthedocs.io/en/latest/?badge=latest
@@ -13,43 +13,50 @@ BABS: BIDS App Bootstrap
 
 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 <https://www.datalad.org/>`_ and adopts
 the `FAIRly big framework <https://doi.org/10.1038/s41597-022-01163-2>`_.
-Currently, BABS supports jobs submissions and audits on Sun Grid Engine (SGE) and Slurm
+Currently, BABS supports job submissions and audits on SLURM
 high performance computing (HPC) clusters.
 
-Please cite our paper if you use BABS:
 
-    Zhao, C., Jarecka, D., Covitz, S., Chen, Y., Eickhoff, S. B.,
-    Fair, D. A., Franco, A. R., Halchenko, Y. O., Hendrickson, T. J., Hoffstaedter, F.,
-    Houghton, A., Kiar, G., Macdonald, A., Mehta, K., Milham, M. P.,
-    Salo, T., Hanke, M., Ghosh, S. S., Cieslak, M. & Satterthwaite, T. D. (2024).
-    A reproducible and generalizable software workflow
-    for analysis of large-scale neuroimaging data collections using BIDS Apps.
-    *Imaging Neuroscience*. Accepted.
+Citing BABS
+-----------
+
+If you use BABS, please cite it using the metadata from the `CITATION.cff <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.
 
-Currently, the paper has been accepted for publication in *Imaging Neuroscience*.
-The *bioRxiv* version can be found `here <https://doi.org/10.1101/2023.08.16.552472>`_.
+  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.