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I wish to provide codes and data to reviewer along with manuscript at the time of submission. I can upload the codes on a public repository, but it will bring it in public domain, I want to provided the codes only when the paper is accepted.

What is the standard practice?

My search directs me towards repositories: Dryad, Figshare and Zenodo. Which one of them provides secure code upload OR limited access?

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    What's wrong with general purpose file sharing tools (like Dropbox or Google Drive)?
    – MJeffryes
    Commented Jan 11, 2018 at 11:40
  • @MJeffryes, I do not know? I do not know what is the practice?
    – pkj
    Commented Jan 11, 2018 at 11:42
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    Many, if not all, journals allow the authors to upload confidential materials to the reviewers along with the manuscript.
    – FBolst
    Commented Jan 11, 2018 at 12:08
  • Did you ask the editor or contact person at the journal about that?
    – Dirk
    Commented Jan 11, 2018 at 12:25
  • 3
    Possible duplicate of How can I anonymously store supplemental research data that I submit with papers?
    – Ben
    Commented Apr 15, 2019 at 5:03

3 Answers 3

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As others have mentioned, some venues offer an option of submitting additional material.

If not, you have two options.

  1. Include your code as a single file into your submission in the PDF/A-3 format. (I do not recommend this option that much, though, since special software is required.)

  2. Put your code on a public site as a password-protected archive. Most compressors such as zip and rar allow you to encrypt and compress. Put the archive on a public site but give the password only along with the submission. E.g.

    Bibliography

    [S18] Smith, J., Example codes, 2018, http://www.example.com/example.zip, protected with the password example_password.

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Edit: This gives away the reviewer's identity. (Not Suitable)

I am not sure if this is the standard practice but it might be of interest to you:

Assuming you have a CS (or related) background and also that your reviewer also would be in a CS related field:

GitHub does provide the ability to have private repositories. You can also add collaborators, to whom you want to grant access to, via their GitHub username or email. (Also, GitHub also provides free private repositories for as long as you are a student. See GitHub Student Pack)

If you are not a student, you can use BitBucket, another version control system that offers free private repositories.

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  • How would you preserve reviewer anonymity with this?
    – Wrzlprmft ♦
    Commented Jan 13, 2018 at 10:53
  • Correct. I now realize this does give away the reviewer's identity. This should not be done. I have edited my answer. Thanks, @Wrzlprmft.
    – code
    Commented Jan 13, 2018 at 11:36
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The presented method is a little bit more complex but, in my personal opinion, very close to an optimal solution as it solves additional issues. Since you may have a CS or related background, this may be technically viable for you.

This question has two components:

  1. How to permanently publish material
  2. How to limit access to this material during review

The first question is especially difficult to solve since the costs, URLs, and availability of services like Dropbox may be subjected to change. Perhaps not this year, but let's say in a few years. However, you want your material to be available permanently but cannot update the URL in the paper.

Limiting access during review is solved by using an encrypted file or by some sort of login/password, before downloading is allowed. If you have several large datasets, the "encrypted file" solution is often not viable, since you do not want to have a link for each (encrypted) dataset in the paper (e.g., you have 10 datasets, each 50MB => 10 links). In this case you also do not want to have a large 500MB file that someone has to download, just to look into a single dataset.

All in all, I was not satified with the available services and solutions since they did not guarantee that the URLs are permanent and the did not have a "login" feature.

I came up with an own solution:

  • The URL in the paper points to one of my (personal) URLs. This is also safe in case of changing institutions. However, you can still have your dataset at some other domain, the URL in the paper is just a forwarder/redirect. If the location of the data changes, you can simply update the target of the forwarder/redirect.
  • During review, I uploaded the files to a server and enabled a simple login (htaccess-based). The files are all listed in this folder, but to get access to the folder you need the login.
  • In the paper, I added the following note:

We provide supplementary material at https://science.[mydomain].de/paperXYZ

The material includes all required scripts for experiments ABC and XYZ.

Restricted access during review:

Username: review Password: [password]

I explicitily state that the restricted access only applies to review, so we are willing to publish this data together with the paper.

While this comes with some effort, this method worked very well during review and also afterwards as the paper is publicly available, now.

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  • If you have access to the server logs, they would revel the IP adress of anyone downloading the files, which could refeal the identity of the reviewer. It could also raise doubts by the reviewers that you might change the files during the review process. Better to ask the editor to post a copy of your files on a server that they control.
    – JeffE
    Commented Jan 14, 2018 at 5:13

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