Pre-submission enquiry

[matsvanes]

Dear Editorial Board,

I would like to enquire about to possibility to submit to JOSS, as well as its format. We are interested in submitting a software tool that enables researchers to easily produce reproducible code and accompanying data. This is highly sought after in the field of neuroimaging, where the datasets are large, and analyses are complex. Data and code sharing is not standard, and even if they are shared, often reproducibility of published results is still limited.
The tool is not a standalone repository (which I believe is most common for JOSS submissions), but is integrated in the widely adopted open-source FieldTrip Toolbox. It is therefore unclear to me whether it would be considered for publication in JOSS.
Additionally, we have developed tutorials to help people get started with the tool. Currently, these are incorporated in the pre-print of the tool, but could potentially be added to the FieldTrip website. I would like to ask if and how I could best incorporate the tutorials in the journal submission.

Many thanks for your help,

Mats W.J. van Es, PhD

[arfon]

@matsvanes – we have reviewed and published papers where the functionality is associated with a larger submission (in this case FieldTrip Toolbox) but it depends on a few things such as:

• Are there other papers about the 'parent' package?
• How significant/substantial is the contribution for this submission? Do they pass our substantial scholarly effort criterion?
• Are the authors of the parent package happy for a paper to be published for a part of their overall work?

[matsvanes]

@arfon Thank you for the information. To answer your questions:

1. The parent package is described in
   Robert Oostenveld, Pascal Fries, Eric Maris, and Jan-Mathijs Schoffelen. [FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data.](https://doi.org/10.1155/2011/156869) Computational Intelligence and Neuroscience, 2011; 2011:156869.
   There are other papers about the parent package, for example containing an example pipeline:
   Popov, T., Oostenveld, R., & Schoffelen, J. M. (2018). FieldTrip made easy: an analysis protocol for group analysis of the auditory steady state brain response in time, frequency, and space. Frontiers in neuroscience, 12, 711.
   None of them contain any information about the proposed tool however.

2. Based on my estimation the contribution does pass the substantial scholarly effort criterion, including having over 300 LOC, a substantial number of commits as well as authors, the parent package being well established, and the new contribution is likely to be cited in the field.

3. two out of four of the authors of the parent package are authors on the current contribution. They are also the main developers of the toolbox, and the owner of the repository is the senior author on the current contribution. We don't foresee problems in getting approval from the remaining two authors of the parent package if this is required.

[arfon]

OK thanks @matsvanes.

Based on my estimation the contribution does pass the substantial scholarly effort criterion, including having over 300 LOC, a substantial number of commits as well as authors, the parent package being well established, and the new contribution is likely to be cited in the field.

Is there a way to take a peek at the JOSS-specific contributions you'd be proposing for review here?

[matsvanes]

This is the question I had regarding the format of submission, i.e. how do we submit part of the parent toolbox for review? Is it helpful to list the functions that underwent changes for the implementation of the tool (and of course, entirely new function)? Also, would the documentation (outlined in the preprint) be of use, e.g. when incorporated in fieldtrip/website? Currently the tutorial code is available at https://github.com/matsvanes/reproducescript
I believe the modified/added functions are the following:

• utilities/private/reproducescript.m
• ft_reproducescript.m
• utilities/private/ft_preamble_init.m
• utilities/private/ft_preamble_loadvar.m
• private/savevar.m
• utilities/private/savevar.m
• utilities/private/ft_postamble_savevar.m
• utilities/private/ft_postamble_savefig.m
• utilities/private/isplottingfunction.m
• utilities/private/make_or_fetch_inputfile.m
• utilities/private/save_large_cfg_fields.m
• private/ignorefields.m
• fileio/private/ignorefields.m
• utilities/private/ignorefields.m
• contrib/misc/private/ignorefields.m

[matsvanes]

Hi @arfon - any news on this front?

[arfon]

This is the question I had regarding the format of submission, i.e. how do we submit part of the parent toolbox for review? Is it helpful to list the functions that underwent changes for the implementation of the tool (and of course, entirely new function)?

Yes, please make it clear in the submission form but also document this in the paper for completeness too. Thanks!