[PRE REVIEW]: NeoViewer: Visualising Electrophysiology Data

[editorialbot]

Submitting author: !--author-handle-->@aopy<!--end-author-handle-- (Onur ATES) Repository: https://github.com/NeuralEnsemble/neo-viewer Branch with paper.md (empty if default branch): paper Version: 1.4.0 Editor: Pending Reviewers: Pending Managing EiC: Kyle Niemeyer

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Thanks for submitting your paper to JOSS @aopy. Currently, there isn't an JOSS editor assigned to your paper.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.28 s (217.8 files/s, 182305.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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JSON                             8              0              0          43255
JavaScript                      18            431             87           4499
CSS                              6            157             49           1145
HTML                             6             51             22            626
Python                          11            204            185            548
Markdown                         5            120              0            195
SVG                              2              1              2            141
YAML                             4             12              4            120
TeX                              1              1              0             15
INI                              1              1              0             14
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SUM:                            62            978            349          50558
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1282

[editorialbot]

:warning: An error happened when generating the pdf.

[kyleniemeyer]

Hi @aopy, thanks for your interest in JOSS. Since submissions that focus purely on visualization often fall outside our definition of research software, the editorial board is going to review your submission before it proceeds to review. This should hopefully take around a week.

[kyleniemeyer]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[appukuttan-shailesh]

While we wait and look forward to the decision of the review process, we are keen to highlight why we believe the present submission should satisfy the criteria required for submission to JOSS:

NeoViewer significantly contributes towards making scientific data more accessible. A large number of file formats currently are employed for storing neurophysiology data, a mix of proprietary and open formats. There exists currently a void with regards to a single service/tool that can help visualize and explore a multitude of such data formats. And this is what the NeoViewer offers.

We would also like to point out that the submission consists of two parts: (i) a web server providing a REST API , and (ii) and a web component. The REST API reads neurophysiology data files and makes the content available in JSON format. The API can be used by anyone to avail this functionality. The web component employs this API, to offer a free and easy to use scientific data visualization tool.

It fulfils the various criteria listed under 'Substantial scholarly effort', such as:

• Age of software: 4+ years (project started in Feb 2018)

• Number of commits: ~300 (master: 296, paper: 308)

• Number of authors: 5 authors

• Total lines of code: >50k

• Whether the software has already been cited in academic papers: Cited in a manuscript that is currently under review at a journal. Already available as preprint via OSF.

• Whether the software is sufficiently useful that it is likely to be cited by your peer group. Highly likely. The tool has been showcased in various Human Brain Project (HBP, now EBRAINS) Hackathons and CodeJams, and has had various adopters for in-house usage. It has now also seen uptake by other tool developers in the project, such as in the development of the EBRAINS Live Paper service (a multi-institute collaborative project for enabling ease in sharing scientific data). The more recent creation of the ReactJS version of the component was motivated by the interest of developers to incorporate this tool in their existing/new ReactJS projects.

Additionally, it satisfies other requirement such as:

• being feature-complete - extensions are certainly part of most tool development lifecycles, and that holds true for the NeoViewer as well
• the project is packaged as per standard API + JS conventions; made available via standard repos (e.g. npm)

[kyleniemeyer]

Hi @appukuttan-shailesh, thank you for the additional context. However, I am not concerned about the level of effort/size of the software, but instead whether it meets our requirement for research software:

This definition includes software that: solves complex modeling problems in a scientific context (physics, mathematics, biology, medicine, social science, neuroscience, engineering); supports the functioning of research instruments or the execution of research experiments; extracts knowledge from large data sets; offers a mathematical library, or similar. While useful for many areas of research, pre-trained machine learning models and notebooks are not in-scope for JOSS.

Generally an API does not meet our requirements, nor does a tool solely focused on visualization. If your software is doing additional analysis along with the visualization, that would likely help meet our requirements.

[apdavison]

Hi @kyleniemeyer, thank you for the clarification.

While I understand that general-purpose plotting tools, or visualization tools intended only for educational purposes, would not count as research software, I expect that software for the transformation and visualization of scientific data, intended for use as part of the scientific research process, would meet your requirement? (Examples: [1], [2])

[danielskatz]

@aopy - I'm sorry for the delay in getting back to you.

I'm sorry to say that after discussion amongst the JOSS editors, we have decided that this submission is not research software as defined by JOSS. This does not mean that it is not software that is useful in research, but just that JOSS does not consider it in scope for review as research software. Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your work.

[danielskatz]

@editorialbot reject

[editorialbot]

Paper rejected.