[PRE REVIEW]: kinisi: Bayesian analysis of mass transport from molecular dynamics simulations

[editorialbot]

Submitting author: !--author-handle-->@arm61<!--end-author-handle-- (Andrew McCluskey) Repository: https://github.com/bjmorgan/kinisi/ Branch with paper.md (empty if default branch): Version: 0.7.0 Editor: !--editor-->@zhubonan<!--end-editor-- Reviewers: @hmacdope, @dengzeyu Managing EiC: George K. Thiruvathukal

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Software report:

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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 739

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/PhysRevB.47.558 is OK
- 10.1103/PhysRevB.49.14251 is OK
- 10.21105/joss.01864 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.25080/majora-629e541a-00e is OK
- 10.1002/jcc.21787 is OK
- 10.21105/joss.02214 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1103/physrevlett.112.145901 is OK
- 10.1021/acs.chemmater.0c03738 is OK
- 10.1038/s41563-022-01316-z is OK
- 10.1016/j.sbi.2009.03.004 is OK
- 10.1002/jcc.21939 is OK
- 10.1021/acs.chemmater.9b01824 is OK
- 10.1021/la901314b is OK
- 10.1039/c5cp03414k is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[arm61]

Suitable reviewers that come to mind include:

• hmacdope
• shyuep
• richardjgowers

Both have experience developing diffusion analysis packages, as parts of MDAnalysis and pymatgen, respectively.

[arm61]

Also, just to note. The title of the paper has changed to the more descriptive “kinisi: Bayesian analysis of mass transport from molecular dynamics simulations”.

[zhubonan]

@Kevin-Mattheus-Moerman I can probably edit this one.

[Kevin-Mattheus-Moerman]

@editorialbot assign @zhubonan as editor

[editorialbot]

Assigned! @zhubonan is now the editor

[zhubonan]

Hi @richardjgowers @rangsimanketkaew @masrul @hmacdope, would you be interested and available to review this JOSS submission? It is about using Bayesian analysis to obtain mass-transports coefficients and their error bars from MD simulation trajectories, which I think are relevant to your areas of expertise.

The manuscript can be viewed here 👉 View article proof on GitHub Software repository 👉 https://github.com/bjmorgan/kinisi/ The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

[hmacdope]

I can :)

[arm61]

Some other potential reviewers include pdebuyl and malramsay64, who develop the tidynamics package. Also, @zhubonan is there anything required to ensure that the change of title (mentioned here https://github.com/openjournals/joss-reviews/issues/5797#issuecomment-1703849989) is carried out?

[zhubonan]

Thanks for the suggestion. I have also changed the title of the issue. But maybe it needs to be changed else where as well.

[arm61]

Great cheers, it has been updated in the paper header so that should be fine now.

[zhubonan]

Hi @pdebuyl and @malramsay64, would you be interested and available to review this JOSS submission? It is about using Bayesian analysis to obtain mass-transports coefficients and their error bars from MD simulation trajectories, which I think are relevant to your areas of expertise.

The manuscript can be viewed here 👉 View article proof on GitHub Software repository 👉 https://github.com/bjmorgan/kinisi/ The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

[malramsay64]

Unfortunately I don't have availability to review.

[Kevin-Mattheus-Moerman]

@zhubonan could you continue your search for reviewers again?

[zhubonan]

Hi @dengzeyu, @shyuep would you be interested to review this JOSS submission? It is about using Bayesian analysis to obtain mass-transports coefficients and their error bars from MD simulation trajectories, which I think are relevant to your areas of expertise.

The manuscript can be viewed here 👉 View article proof on GitHub Software repository 👉 https://github.com/bjmorgan/kinisi/ The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

[zhubonan]

@editorialbot set @denzeyu as reviewer

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[zhubonan]

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[zhubonan]

@editorialbot add @denzeyu as reviewer

[editorialbot]

@denzeyu added to the reviewers list!

[zhubonan]

@editorialbot add @hmacdope as reviewer

[editorialbot]

@hmacdope added to the reviewers list!

[zhubonan]

@editorialbot start-review

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[zhubonan]

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[zhubonan]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5984.

[zhubonan]

@editorialbot add @dengzeyu as reviewer

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@dengzeyu added to the reviewers list!

[zhubonan]

@editorialbot remove @denzeyu from reviewers

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