Publishing Code in Aperture Neuro

[layerfMRI]

Title

Publishing Code in Aperture Neuro

Short description and the goals for the OHBM BrainHack

Aperture Neuro is a new journal from the OHBM community for the OHBM community.

In a new initiative, Aperture Neuro aims to expand the formats of submissions beyond traditional PDF papers found in conventional journals, by including code submissions.

In the dynamic field of neuroimaging, researchers derive new insights into the brain through the application and development of innovative software and analysis tools. While these insights can be described in conventional PDF papers, many other aspects of researchers' work often do not go through a similar publication procedure, lacking peer review and full citability. These research outputs, collectively known as research objects, hold significant value for the neuroimaging community.
Examples of such research objects include:

• Code
• Code wrappers
• Pipelines
• Toolboxes
• Toolbox plugins
• Code notebooks

Although these research objects are typically not subject to peer review and are not indexed in standardized publication systems, they deserve to be citable in a manner that recognizes the author's contribution and aids in the assessment of their scholarly impact, such as their h-index.

In a special initiative, Aperture Neuro wants to invite members of the neuroimaging community to submit their research objects in the form of code.

This invitation is specifically aimed to code that fulfills the following criteria:

• High quality
• Open
• Useful to the community
• Not previously published as a peer-review paper

The goal of this hackathon project is to:

• Identify codes that are used in the field of neuroimaging but are not citable via PubMed listed publications.
• Build a database of code repositories that are widely used. This list of code could be given to the Aperture Editorial Board to invite authors for submissions.
• Have a discussion on whether the submission guidelines from Aperture Neuro need to be revised to incorporate these codes.

Resources:

• Journal website: https://apertureneuro.org/
• Flyer (pdf)
• Draft of call for papers with submission guidelines
• Table that is aimed to be extended.

This project is lead via online-attendees.

Link to the Project

https://docs.google.com/spreadsheets/d/1eeWxKzl-dCffbMSaciWRC-0wPJwVAD2MtceT7hqEXr0/edit?usp=sharing

Image for the OHBM brainhack website

https://drive.google.com/file/d/1VQR-Mo1lXrSJIXVLQVGSM0dP9SgaOchj/view?usp=sharing

Project lead

Discord handle: renzohuber Twitter @layerfMRI

Main Hub

Montreal

Other Hub covered by the leaders

• Montreal
• Asia / Pacific
• Europe / Middle East / Africa
• Americas

Skills

No specific skills required

Recommended tutorials for new contributors

• Set up a brainhack friendly computing environment
• A introduction to Bash
• Python: Writing a script
• Python: Data analysis with Python
• Python: Visualisation
• Machine learning basics
• BIDS
• Machine learning for neuroimaging
• VCS: Using Git and Github
• VCS: Data management with Datalad
• Virtualization
• High Performance Computing: Oracle cloud resource

Good first issues

Go through the methods section of the last few papers that you have been reading and see if all the code that has been used is cited with a PubMed listed reference.
If there is code that looks relevant to a wider community and is only referring to github, add it to the list of valuable code.

Twitter summary

Community discussions on publishing code in the OHBM journal Aperture.
There is lots of good code out there that is waiting to be peer-reviewed and published. Let's identify it and make it citable.
@ApertureOHBM
#OHBMHackathon #Brainhack #OHBM2023

Short name for the Discord chat channel (~15 chars)

Code-Aperture

Please read and follow the OHBM Code of Conduct

• I agree to follow the OHBM Code of Conduct during the hackathon

[ufangYang]

hi @layerfMRI can you provide the content and/or figure for this project to be added to Brainhack Proceeding 2023 by 15th May? Also, please don't forget to fill out your team member's details using this form: https://forms.gle/Ku3AVHcXvpUqVVkV7 . Cheers

[layerfMRI]

Thanks @ufangYang,

I filled out the form and agreed with my co-authors to include a brief pitch in of our project. Whats the best way to get the content to you?

Below is everything copy-pasted.

Best regards,
Renzo

Authors:
Renzo Huber 1, M. Mallar Chakravarty 2, Peter Bandettini 1

1 National Institute of Mental Health
Bethesda, MD, USA

2 McGill University & Douglas Research Centre
Montreal, Canada

Body text:
In the dynamic field of neuroimaging, researchers derive new insights into the brain through the application and development of innovative software and analysis tools. While the scientific findings can be described in conventional PDF papers, many other aspects of researchers' work often do not go through a similar publication procedure, lacking peer review and full citability. These research outputs hold significant value for the neuroimaging community. Examples include: Code, code wrappers, pipelines, toolboxes, toolbox plugins, and code notebooks.
Although these research objects are typically not subject to peer review and are not indexed in standardized publication systems, the quality of research outputs is directly dependent on the quality of these tools. Hence, it is critical that these objects are citable in a manner that recognizes the author's contribution and to aid in the assessment of scholarly impact, such as their h-index, and to promote a dynamic and reproducible research enterprise.
At the time of the Brainhack July 2023, the OHBM Journal Aperture Neuro aimed to broaden the range of submission formats, surpassing the constraints of traditional PDFs, by incorporating code submissions. In a special initiative, Aperture Neuro wanted to change this and invite members of the neuroimaging community to submit their research objects in the form of code.
The purpose of the brain hack project 2023 was to discuss this initiative with members of the OHBM coding community and find a community consensus of most suitable publication mechanisms. As part of this brainchack project:

• We compiled a list of most impactful previously unpublished codes.
• We defined the focus of Aperture Neuro’s Code submissions with respect to: Openness, novelty, utility to the community, scientific need, coding style, reproducible executability, etc.
• And we evaluated the compromise of competing views of research output of time-less doi printed document vs. dynamic continuously developing code.

Ever since the brain hack project in July 2023, Aperture Neuro has launched the call for submission https://apertureneuro.org/pages/533-code. And multiple code submissions have been published already.
In this mechanism publication mechanism, each code publication is undergoing assessment by field experts, and when accepted, is aimed to be subject to a corresponding PubMed-listed index, DOI, and citable reference.

Figure:

Caption:
Aperture Neuro logo