Tennøe Hodne Haug Weltzien Einevoll Halnes

[simetenn]

AUTHOR

Dear @ReScience/editors,

I request a review for the following replication:

Original article

Title: Fast-Activating Voltage- and Calcium-Dependent Potassium (BK) Conductance Promotes Bursting in Pituitary Cells: A Dynamic Clamp Study
Author(s): J. Tabak, M. Tomaiuolo, A. Gonzalez-Iglesias, L. Milescu and R. Bertram
Journal (or Conference): Journal of Neuroscience
Year: 2011
DOI: 10.1523/JNEUROSCI.3235-11.2011
PDF: http://www.jneurosci.org/content/jneuro/31/46/16855.full.pdf

Replication

Author(s): Simen Tennøe, Kjetil Hodne, Trude M. Haug, Finn-Arne Weltzien, Gaute T. Einevoll, and Geir Halnes
Repository: https://github.com/simetenn/ReScience-submission/tree/tennøe-hodne-haug-weltzien-einevoll-halnes
PDF: https://github.com/simetenn/ReScience-submission/tree/tennøe-hodne-haug-weltzien-einevoll-halnes/article/tennøe-hodne-haug-weltzien-einevoll-halnes-2018.pdf
Keywords: Neuroscience, Python, Uncertainty quantification, Pituitary cells
Language: Python
Domain: Computational Neuroscience

Results

• Article has been fully replicated
• Article has been partially replicated
• Article has not been replicated

Potential reviewers

---

EDITOR

• Editor acknowledgment
• Reviewer 1 (@gdetor 23 November 2018)
• Reviewer 2 (@apdavison 03 December 2018)
• Review 1 decision accept (18 February 2019)
• Review 2 decision accept (11 March 2019)
• Editor decision accept (11 March 2019)

[rougier]

Thanks for your submission. An editor will be soon assigned!

@benoit-girard Could you handle this submission (I'll help with the publication step if necessary)

[benoit-girard]

@rougier : OK, I can do it.

[benoit-girard]

@stephanmg : are you familiar with Neuron? Do you think you could evaluate this work?
@ChristophMetzner : are you available and willing to evaluate this work?

[ChristophMetzner]

@benoit-girard I would be available and would really like to review this submission, however, I have an ongoing collaboration with Gaute Einevoll, which, I guess, constitutes a conflict of interest. Therefore, I think I have to decline.

[benoit-girard]

@ChristophMetzner I didn't know about that COI. Sorry.
@miladh : are you familiar with Neuron? Do you think you could evaluate this work?

[miladh]

Thanks for asking @benoit-girard, but Gaute Einevoll is my supervisor and I'm working closely with @simetenn in several projects, so I think I also have to decline due to COI.

[benoit-girard]

@stephanmg @gdetor : would you be interested in reviewing this submission?

[benoit-girard]

@apdavison : could you review this submission?

[apdavison]

@benoit-girard I'd be happy to.

I have a small potential conflict of interest, as Gaute Einevoll and I both receive funding under the Human Brain Project grant; however we do not collaborate directly (we are in different sub-projects).

Please let me know if this is a problem; otherwise I will go ahead and review the submission.

[benoit-girard]

I tend to think it is not a problem in that case, let's ask the bosses if they agree with me.
@rougier @khinsen : Do you agree?

[khinsen]

For me this is not a problem.

[gdetor]

@benoit-girard I can review this submission.

[benoit-girard]

Thank you @gdetor you are now reviewer number 1.
@rougier I am waiting for your feedback about @apdavison before validating him as reviewer number 2.

[rougier]

Fine for me as well.

[benoit-girard]

Then @apdavison you are reviewer 2! Thanks!

[benoit-girard]

@apdavison @gdetor : just a gentle reminder... Do you think you could provide a first evaluation mid-January?

[apdavison]

Yes, certainly.

[gdetor]

@benoit-girard Yes

[benoit-girard]

Dear @apdavison and @gdetor : a gentle reminder...

[gdetor]

@benoit-girard All my comments have been addressed properly. I have no further comments. I endorse the publication of this work.

[benoit-girard]

@apdavison Are you satisfied with the authors' reply and modifications?

[apdavison]

@benoit-girard I'm afraid I haven't had time to review the changes, but I will do so by the end of this week.

[apdavison]

My apologies for the delay. I am very satisfied by the reply and the additional exploration of the remaining discrepancies. Many thanks to the authors for this very nice replication.

[benoit-girard]

Given the positive feedback from both reviewers, the paper is accepted, I will now have to take care of the publishing steps (I may not be able to do it this week...).
@rougier : Is the publishing process as tough as it used to be, or have some steps evolved?

[rougier]

The new process is far more easier (because authors do all the hard work) but it is not yet online. But I can help you on this one if you want (as I promised at the top of this thread 😄).

[rougier]

@benoit-girard Do you need some help with the publishing process

[benoit-girard]

Indeed, what should I begin with (compared to the old procedure) ?

[rougier]

Well, in this specific case, you have to use the old procedure. Sorry for that.

[benoit-girard]

I have begun the process, I am now at the "Rebuild the PDF and check everything is OK" step.
I haven't build a "md" into a pdf in a while, I don't remember how to proceed. Where can I find a description of the process (including the bib processing, which, I vaguely remember, wasn't easy)? I thought it was somewhere in the ReScience repos, but couldn't find it...

[benoit-girard]

nevermind, I found it.

[benoit-girard]

This time, I am really stuck, at the "Merge the rescience branch into master" step.

I tried :
git add tennøe-hodne-haug-weltzien-einevoll-halnes-2018.md
git commit -m "Updated meta data fields"

but then, I don't know what to do... help ! @rougier

[rougier]

$ git checkout master
$ git merge rescience

If the branch is named rescience. Else you can try git branch to check what are the branch in your local repository.

By the way, @simetenn just told me (by email) that there is a small typo in the manuscript:

"The value of the parameter "c" (for NEURON) in Table 1 is written 1.6, but the correct value is 3.18. This mistake is only present in the manuscript".

Can you correct it while editing it ?

[rougier]

@benoit-girard I unlocked the conversation such that authors can comment (about the correction)

[simetenn]

@benoit-girard: Just tell me if you want me to submit a commit to this PR with the correction.

[benoit-girard]

I did that:

$ git checkout master
$ git merge rescience

then I modified the md so as to correct the error:

By the way, @simetenn just told me (by email) that there is a small typo in the manuscript:

"The value of the parameter "c" (for NEURON) in Table 1 is written 1.6, but the correct value is 3.18. This mistake is only present in the manuscript".

Can you correct it while editing it ?

but I get this when I try to push:

! [remote rejected] master -> master (permission denied)

This git thing is making me feel helpless once again...

[benoit-girard]

@rougier do I need more access rights to ReScience-Archive, or did I something wrong (again)?

[rougier]

You're right, I just changed your rights (you should have them all on the archives). Sorry for that.

[benoit-girard]

This submission has been accepted for publication.