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Ten-year reproducibility challenge: friction coefficients of mixed globular/chain molecules (1995) #26

Closed charlestonchas closed 4 years ago

charlestonchas commented 4 years ago

Original article: Charles H. Robert. "Estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes." Biophys. J. 69 (Sept. 1995), pp. 840–848 https://doi.org/10.1016/S0006-3495(95)79957-X

PDF URL: revised MS https://github.com/charlestonchas/rehydro-rescience-submit/blob/master/tex/article.pdf

Metadata URL:
https://github.com/charlestonchas/rehydro-rescience-submit/blob/master/tex/metadata.yaml

Code URL:
[https://zenodo.org/record/3878075](version 1.0.2 https://zenodo.org/record/3878075)

Scientific domain: Structural Biology, Hydrodynamics

Programming language: Mathematica

Suggested editor:
Konrad Hinsen

khinsen commented 4 years ago

Thanks for your submission! I will start looking for a reviewer.

khinsen commented 4 years ago

@ChrisRackauckas Can you review this submission? I know it's not fully in your field of expertise, but it isn't terribly remote either. And I can help out with the biophysics aspects myself. What I am mainly looking for is Mathematica expertise.

mstimberg commented 4 years ago

What I am mainly looking for is Matlab expertise.

Probably just a typo, but note that the paper is using Mathematica, not Matlab.

khinsen commented 4 years ago

@mstimberg Thanks for pointing this out, it was indeed a typo!

ChrisRackauckas commented 4 years ago

Sorry, I will not have adequate time to properly review this.

khinsen commented 4 years ago

@ChrisRackauckas OK, thanks for the quick feedback!

charlestonchas commented 4 years ago

I updated the initial submission post to link to the zenodo code entry (rehydro) containing additional pdf versions of the Mathematica notebooks that were omitted in the original version.

Here it is as well: https://doi.org/10.5281/zenodo.3747007

khinsen commented 4 years ago

Activity note: I am contacting potential reviewers outside of the GitHub universe. Silence should not be interpreted as absence of progress!

khinsen commented 4 years ago

Gerald Kneller kindly accepted to review this article. Since he doesn't have a GitHub account, I transmit his review received by mail:

Report on manuscript

[Rp] Reproducibility report: Estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes. [Biophys J 69, 840-848 (1995)]

By Charles ROBERT

The paper describes a reproducibility study concerning an article published in 1995 [Biophys J, 69, 840-848 (1995)], dealing with the estimation of friction coefficients of mixtures of macromolecules with open chain and globular form, respectively. The calculations for this article have been performed with Wolfram's Mathematica Package for symbolic and numerical calculations and the targets for the reproducibility study are four Mathematica Notebooks, named Figure2.nb - Figure5.nb, which produce essentially figures and tables. The original notebooks from 1995 cannot be used any more, because of the transition from 32 bit to 64 bit technology, and test notebooks are provided for Mathematica 5.2 (2005) and 12.0 (2019).

I performed the test runs with Mathematica 12.0 for both series of targets which ran properly after a modification of the code to read in the s6.1_repro.m and extra.m libraries. From all I could see, the figures and tables were reproduced, where the figures were checked by visual inspection and the tables were spot-checked.

khinsen commented 4 years ago

@charlestonchas Would it be possible to include the reproduced figures and tables in the text of your submission? That would permit every reader to judge similarity with the originals, not only those who have access to Mathematics.

charlestonchas commented 4 years ago

Thanks to Gerald Kneller and yourself for taking the time to review the manuscript and provide feedback. I'll modify the MS to add the tables and figures generated by Mathematica as soon as possible; it will indeed be better to include them in the article itself.

charlestonchas commented 4 years ago

@khinsen I added the requested figures to the MS, along with a corresponding table, and took the opportunity to improve the clarity of the presentation (an advantage of leaving the MS alone for a few weeks). I also added the tex to the github repository to facilitate diffs. The pdf, metadata, and code links at the top of this issue have been updated accordingly.

The original article figures were created with the aid of additional software that is no longer available, so I added new Mathematica 12 code to take the reproduced values (the calculations themselves were untouched) and produce figures that closely match the original formatting. These files were updated in the software distribution in the Zenodo repository (rehydro version 1.0.2).

Please let me know any additional steps needing to be made.

khinsen commented 4 years ago

@charlestonchas Thanks for the update! I'd say this looks good and... I proclaim this submission accepted!

I will start the publication process, which may or may not involve further requests to you, depending on how it goes.

khinsen commented 4 years ago

@charlestonchas Could you please review the metadata updates at https://github.com/ReScience/submissions/issues/26? I can then generate the final PDF myself because you have used our template.

charlestonchas commented 4 years ago

That's good news! I updated the metadata.yaml (using one of your articles as a reference!), but there are a few things missing, notably in the "contributors" section. Please check my work!

khinsen commented 4 years ago

@charlestonchas Looks good overall, but requires two more corrections:

  1. DOIs in our metadata are DOIs, not URLs pointing to a DOI resolver.
  2. Under "contributors", the "editor" entry is required for publication.
charlestonchas commented 4 years ago

Sorry; done!

khinsen commented 4 years ago

The article has been published (http://doi.org/10.5281/zenodo.3886412) and will soon be listed on the ReScience Web site!

khinsen commented 4 years ago

@charlestonchas The final metadata and PDF are at https://github.com/charlestonchas/rehydro-rescience-submit/pull/1 - just accept the pull request and your repository is up to date!

charlestonchas commented 4 years ago

Great! Pull request acccepted

On 9 Jun 2020, at 10:54, Konrad Hinsen notifications@github.com wrote:

The article has been published (http://doi.org/10.5281/zenodo.3886412 http://doi.org/10.5281/zenodo.3886412) and will soon be listed on the ReScience Web site!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ReScience/submissions/issues/26#issuecomment-641136883, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFNPTO436TOTSOMZGWN6TGLRVX2D5ANCNFSM4MFQWMWQ.

rougier commented 4 years ago

It's online