Joss-reviews: [PRE REVIEW]: MicroBenthos: a modeling framework for microbial benthic ecology

[whedon]

Submitting author: @achennu (Arjun Chennu)
Repository: https://github.com/achennu/microbenthos
Version: v0.8.2
Editor: @lheagy
Reviewers: @leouieda

Author instructions

Thanks for submitting your paper to JOSS @achennu. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@achennu if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @lheagy it looks like you're currently assigned as the editor for this paper :tada:

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[arfon]

👋 @lheagy - the submitting author suggested you as the handling editor.

[achennu]

@arfon Thanks for initiating the review. I just checked the proof. Noticed an error: There is a blank line in the bullet list of features.

@lheagy The software I submitted is useful in biogeochemistry. Based on your topical expertise and that simpeg relates to finite volume estimation, I figured you may be able to easily review my submission.

[lheagy]

@arfon, @achennu, I would be happy to edit this submission!

@achennu: do you have any suggestions for reviewers? I would like to find 2 here, biogeochemistry is outside of my main area of study

[achennu]

@lheagy Thanks for taking this on. I don't have other (specific) reviewers to suggest, but I suspect it would be directly within your reach. There is nothing critically specific to chemistry or biology to review. The software essentially is an interface for the user to create partial differential equations. Then these equations are solved, visualized in real time and saved. The benefit for a biogeochem user is that they can work at the abstractions of biomass, microbial group, etc.

There are tutorials in the source tree under docs/tutorials, each of which is runnable. While running with --show-eqns, the actual constructed PDE is shown. The --plot option visualizes the model domain as it happens. From a user perspective, one could try to edit the parameters in the definition file and confirm that these show up in the simulations.

If you could give this a try and let me know if you need more info, then I'd be happy to oblige.

[achennu]

@lheagy I noticed that there was a name clash within the modules. I've uploaded a new version (0.9) after refactoring the name change, updating tests. I also updated the tutorials having noticed some problem with parameters. I have checked again that the tutorials can be run with the given commands in it.

If you have cloned the earlier version, then please fetch the updates now.

[lheagy]

@leouieda has indicated that he is willing to help out with this submission. @leouieda: does it work with you if I put you down as the lead reviewer on this? I can jump in and help out as well.

[lheagy]

@whedon assign @leouieda as reviewer

[whedon]

OK, the reviewer is @leouieda

[lheagy]

@whedon start review magic-word=bananas

[whedon]

You didn't say the magic word! Try this:

@whedon start review magic-word=bananas

[lheagy]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/674. Feel free to close this issue now!

[leouieda]

@lheagy sorry for the late reply. Yes you can put me as reviewer.