[PRE REVIEW]: Pore2Chip: All-in-One Python Tool for Soil Microstructure Analysis and Micromodel Design #7546

editorialbot · 2024-12-02T18:49:59Z

Submitting author: @aramyxt (Aramy Truong)
Repository: https://github.com/EMSL-Computing/Pore2Chip
Branch with paper.md (empty if default branch):
Version: 0.1.0
Editor: @cheginit
Reviewers: Pending
Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/43f8e0e986bc30fc3e2b81220c6db0e0"><img src="https://joss.theoj.org/papers/43f8e0e986bc30fc3e2b81220c6db0e0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/43f8e0e986bc30fc3e2b81220c6db0e0/status.svg)](https://joss.theoj.org/papers/43f8e0e986bc30fc3e2b81220c6db0e0)

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editorialbot · 2024-12-02T18:50:03Z

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editorialbot · 2024-12-02T18:50:21Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (456.0 files/s, 292977.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              5              0              0          17563
Python                          16            616           1099           1929
Markdown                         8            164              0            481
Jupyter Notebook                 7              0           2882            479
TeX                              1             39              0            381
TOML                             1              4              0             30
YAML                             1              1              0             19
Bourne Shell                     1              5              5              5
-------------------------------------------------------------------------------
SUM:                            40            829           3986          20887
-------------------------------------------------------------------------------

Commit count by author:

    51	Mudunuru, Maruti K
     7	aramyxt
     4	Aramy Truong
     1	Maruti Kumar Mudunuru
     1	mlmamud

editorialbot · 2024-12-02T18:50:25Z

Paper file info:

📄 Wordcount for paper.md is 1383

✅ The paper includes a Statement of need section

editorialbot · 2024-12-02T18:50:28Z

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot · 2024-12-02T18:50:52Z

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

✅ OK DOIs

- 10.1016/0167-1987(84)90005-9 is OK
- 10.1128/msystems.00913-22 is OK
- 10.1016/j.orggeochem.2017.10.012 is OK
- 10.1016/j.enggeo.2020.105921 is OK
- 10.1016/j.still.2018.04.017 is OK
- 10.1016/j.still.2019.104567 is OK
- 10.1890/10-2246.1 is OK
- 10.1109/MCSE.2016.49 is OK
- 10.21105/joss.01296 is OK
- 10.1038/s41586-018-0463-x is OK
- 10.2136/vzj2011.0185 is OK
- 10.1016/j.soilbio.2012.04.002 is OK
- 10.1016/j.scitotenv.2021.146572 is OK
- 10.1016/j.geoderma.2021.115170 is OK
- 10.1016/j.still.2018.01.001 is OK
- 10.1128/aem.54.6.1472-1480.1988 is OK
- 10.1016/j.still.2020.104855 is OK
- 10.3390/ijerph191710582 is OK
- 10.1007/s11242-009-9412-3 is OK
- 10.1016/j.geoderma.2021.115674 is OK
- 10.1038/s41467-017-01320-x is OK
- 10.1002/jeq2.20256 is OK
- 10.1029/2003GB002041 is OK
- 10.1071/WF15037 is OK
- 10.1007/s11104-012-1470-6 is OK
- 10.3390/soilsystems2040066 is OK
- 10.1111/gcb.15365 is OK
- 10.1007/s11242-022-01852-x is OK
- 10.1007/s10596-014-9424-0 is OK
- 10.1117/12.2611234 is OK
- 10.21105/joss.03764 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Microfluidic model porous media: Fabrication and a...
- No DOI given, and none found for title: The D ual A rrhenius and M ichaelis–M enten kineti...

❌ MISSING DOIs

- 10.2136/vzj2011.0072 may be a valid DOI for title: A review of micromodels and their use in two-phase...
- 10.1016/j.egyr.2022.04.071 may be a valid DOI for title: Fluid–rock interactions and its implications on EO...
- 10.1021/acs.est.1c03899.s001 may be a valid DOI for title: Microfluidics as an emerging platform for explorin...
- 10.1016/j.matdes.2022.111517 may be a valid DOI for title: Development of glass-based microfluidic devices: A...
- 10.1029/2009wr008424 may be a valid DOI for title: Excluded-volume expansion of Archie’s law for gas ...
- 10.1016/j.soilbio.2016.11.025 may be a valid DOI for title: Differences in soluble organic carbon chemistry in...
- 10.5194/bg-15-5031-2018 may be a valid DOI for title: Diffusion limitations and Michaelis–Menten kinetic...

❌ INVALID DOIs

- None

editorialbot · 2024-12-02T18:51:31Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-12-02T18:52:15Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kthyng · 2024-12-02T18:55:12Z

Hi @aramyxt and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

OSI-approved license
Installation instructions
Documentation exists at all
Tests of some sort
Check paper (make sure compiles, read through, check for length 250-1000 words)
Substantial scholarly effort
Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

kthyng · 2024-12-02T23:17:35Z

@aramyxt I consulted with a license expert from our editorial team about your license and was told:

It's not an OSI-approved license. It's a mash-up, borrowing phrases from different licenses with unclear implications on compatibility. It could be submitted to OSI for approval, but I expect it would be declined since that would contribute to license proliferation without adding clarity or semantic value.

Note that having an OSI-approved license is a requirement for JOSS to review your submission.

aramyxt · 2024-12-04T16:18:45Z

Thank you for the response! I will talk to my team about the license issue.

maruti-iitm · 2024-12-04T17:06:17Z

@kthyng, can you please give us a couple of days to discuss this with our team and potentially change it to an MIT license?

kthyng · 2024-12-04T17:11:50Z

@aramyxt, @maruti-iitm Yes, no problem.

maruti-iitm · 2024-12-04T21:44:05Z

@kthyng We have removed the disclaimer and have updated the LICENSE.md, which now follows the BSD 2-Clause License.

Please see the updated license here: https://github.com/EMSL-Computing/Pore2Chip/blob/main/LICENSE.md

Let me know if you need further information on the LICENSE.md

maruti-iitm · 2024-12-04T23:02:04Z

10.2136/vzj2011.0072 may be a valid DOI for title: A review of micromodels and their use in two-phase...

10.1016/j.egyr.2022.04.071 may be a valid DOI for title: Fluid–rock interactions and its implications on EO...

10.1021/acs.est.1c03899.s001 may be a valid DOI for title: Microfluidics as an emerging platform for explorin...

10.1016/j.matdes.2022.111517 may be a valid DOI for title: Development of glass-based microfluidic devices: A...

10.1029/2009wr008424 may be a valid DOI for title: Excluded-volume expansion of Archie’s law for gas ...

10.1016/j.soilbio.2016.11.025 may be a valid DOI for title: Differences in soluble organic carbon chemistry in...

10.5194/bg-15-5031-2018 may be a valid DOI for title: Diffusion limitations and Michaelis–Menten kinetic...

@editorialbot and @kthyng incorporated these inputs in the latest paper.bib at:https://github.com/EMSL-Computing/Pore2Chip/blob/main/paper/paper.bib

maruti-iitm · 2024-12-04T23:14:21Z

@kthyng

Potential/Suggested reviewers:

Piyoosh Jaysaval (GitHub: pjaysaval; Piyoosh Jaysaval email
Habiba Akter (GitHub: ha06; Habiba Akter email)
Pratanu Roy (GitHub: pratanuroy; Pratanu Roy email)
Daniel Hirmas (GitHub: danielhirmas; Affiliation: Texas Tech University; Daniel Hirmas email)
Devin Rippner (GitHub: daripp; Affiliation: ARS; Devin Rippner email)
Sara E. Acevedo (GitHub: Saryace; Profile: https://reviewers.joss.theoj.org/reviewers/3687))
Joshua Larsen (GitHub: jlarsen-usgs; Profile: https://reviewers.joss.theoj.org/reviewers/2182))

Additional Suggested Reviewers:

Steffen Schluter (Affiliation: Hemholtz-Center for Environmental Research; Steffen Schluter Email)
Xia Hu (Affiliation: Beijing Normal University; Xia Hu Email)
Renming Ma (Affiliation: Shenyang Agricultural University; Renming Ma Email)
Dorte Wildenschild (Affiliation: Oregon State University; Dorte Wildenschild Email)

maruti-iitm · 2024-12-09T16:34:03Z

@kthyng, do you have any input or feedback on the next steps? Please advise.

kthyng · 2024-12-12T21:02:10Z

@editorialbot check repository

editorialbot · 2024-12-12T21:02:41Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (444.6 files/s, 278768.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              5              0              0          17563
Python                          16            616           1099           1929
Markdown                         9            160              0            481
Jupyter Notebook                 7              0           2882            479
TeX                              1             39              0            388
TOML                             1              4              0             30
YAML                             1              1              0             19
Bourne Shell                     1              5              5              5
-------------------------------------------------------------------------------
SUM:                            41            825           3986          20894
-------------------------------------------------------------------------------

Commit count by author:

    54	Mudunuru, Maruti K
     7	aramyxt
     4	Aramy Truong
     1	Maruti Kumar Mudunuru
     1	mlmamud

editorialbot · 2024-12-12T21:02:52Z

Paper file info:

📄 Wordcount for paper.md is 1383

✅ The paper includes a Statement of need section

editorialbot · 2024-12-12T21:02:56Z

License info:

🟡 License found: Other (Check here for OSI approval)

kthyng · 2024-12-12T22:54:57Z

@maruti-iit, @aramyxt The license still isn't following just one license. It has three clauses and the text above the clauses is mostly borrowed from MIT, not any of the BSD licenses. Is there something preventing you from adopting a single license type?

maruti-iitm · 2024-12-13T15:07:38Z

@kthyng, we just got approval to change it to an MIT license.

Here is the updated license text in the repo: https://github.com/EMSL-Computing/Pore2Chip/blob/main/LICENSE.md

kthyng · 2024-12-18T18:57:29Z

@aramyxt @maruti-iitm ok thanks. Do you have documentation outside of the readme file for guiding users?

maruti-iitm · 2024-12-18T21:49:13Z

@kthyng current documentation includes a readme file along with extensive Jupyter Notebooks and a video tutorial: https://www.youtube.com/watch?v=_DTLtYBAZSo

Additional resources for Pore2Chip users to develop lab-on-chip using the software and other user-related applications are here: https://www.emsl.pnnl.gov/science/instruments-resources/terraforms-pore2chip

These are all in the Pore2Chip readme file.

kthyng · 2025-01-08T21:03:59Z

@maruti-iitm @aramyxt

Please reduce to length of your paper to up to about 1000 words. Paper format information here: https://joss.readthedocs.io/en/latest/paper.html. You can check paper length (and a few other items) with the command @editorialbot check repository though note it needs to be the first item in a comment to run correctly. Currently it is 1383 words.
Check your bib in detail — Davidson et al looks weird and check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

kthyng · 2025-01-09T14:33:54Z

@cheginit Can you edit this? They need to fix up their paper but then it would be ready to review.

kthyng · 2025-01-09T14:34:03Z

@editorialbot invite @cheginit as editor

editorialbot · 2025-01-09T14:34:06Z

Invitation to edit this submission sent!

cheginit · 2025-01-09T14:42:28Z

@kthyng Yes, I can.

👋🏼 @maruti-iitm @aramyxt, I will be the editor for your submission. Once you addressed the issues with the paper, please let me know so I can go ahead with finding reviewers.

cheginit · 2025-01-09T14:42:46Z

@editorialbot assign @cheginit as editor

editorialbot · 2025-01-09T14:42:50Z

Assigned! @cheginit is now the editor

aramyxt · 2025-01-10T17:59:00Z

@editorialbot check repository

editorialbot · 2025-01-10T17:59:28Z

Software report:

github.com/AlDanial/cloc v 1.98  T=0.10 s (568.0 files/s, 301601.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              7              1              1          22611
Python                          18            645           1129           2030
Markdown                         9            161              0            491
Jupyter Notebook                 7              0           2786            487
TeX                              1             39              0            389
reStructuredText                10            127            126            137
YAML                             2              4              0             44
TOML                             1              4              0             30
DOS Batch                        1              8              1             26
Text                             1              0              0             19
make                             1              4              7              9
Bourne Shell                     1              5              5              5
-------------------------------------------------------------------------------
SUM:                            59            998           4055          26278
-------------------------------------------------------------------------------

Commit count by author:

    55	Mudunuru, Maruti K
    15	aramyxt
    10	Aramy Truong
     1	Maruti Kumar Mudunuru
     1	mlmamud

editorialbot · 2025-01-10T17:59:34Z

Paper file info:

📄 Wordcount for paper.md is 1122

✅ The paper includes a Statement of need section

editorialbot · 2025-01-10T17:59:37Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

aramyxt · 2025-01-10T20:08:33Z

@editorialbot check repository

editorialbot · 2025-01-10T20:09:04Z

Software report:

github.com/AlDanial/cloc v 1.98  T=0.10 s (565.5 files/s, 300214.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              7              1              1          22611
Python                          18            645           1129           2030
Jupyter Notebook                 7              0           2786            487
Markdown                         9            161              0            484
TeX                              1             39              0            389
reStructuredText                10            127            126            137
YAML                             2              4              0             44
TOML                             1              4              0             30
DOS Batch                        1              8              1             26
Text                             1              0              0             19
make                             1              4              7              9
Bourne Shell                     1              5              5              5
-------------------------------------------------------------------------------
SUM:                            59            998           4055          26271
-------------------------------------------------------------------------------

Commit count by author:

    55	Mudunuru, Maruti K
    16	aramyxt
    10	Aramy Truong
     1	Maruti Kumar Mudunuru
     1	mlmamud

editorialbot · 2025-01-10T20:09:10Z

Paper file info:

📄 Wordcount for paper.md is 935

✅ The paper includes a Statement of need section

editorialbot · 2025-01-10T20:09:13Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

aramyxt · 2025-01-10T20:12:09Z

@cheginit @kthyng @maruti-iitm

Hello, I have reduced the wordcount of the paper to 935 words and also fixed the strange formatting error with one of the references. Please reach out to me if there are any more changes that I need to make to be compliant with JOSS formatting requirements. Thank you!

cheginit · 2025-01-13T15:09:08Z

@editorialbot generate pdf

editorialbot · 2025-01-13T15:10:37Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2025-01-13T15:11:28Z

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cheginit · 2025-01-13T15:23:41Z

👋🏼 @maruti-iitm @aramyxt thanks for addressing the issue with the paper. I went through the list of potential reviewers that you provided, but unfortunately none of them appear to work in a related field and have experience with Python. Also, please note that they should have a GitHub account and have no the conflict of interest, e.g., working in the same institution as yours. You can review JOSS's policy on this here. You can use JOSS' tool to search for reviewers in addition to other people in your own network that have the required expertise.

maruti-iitm · 2025-01-13T16:45:57Z

Hi @cheginit, Thank you so much! Happy New Year! The potential reviewers suggested here are not co-authors (in any of our previous research work/papers): #7546 (comment)

They have experience with software-based experimental design and Python programming (e.g., Pratanu Roy and Habiba Akter). @aramyxt can correct me if I am wrong.

Sure, moving forward, we will use the JOSS tool to search for additional reviewers and get back to you as soon as we can. Is that okay?

editorialbot added pre-review Track: 6 (ESE) Earth Sciences and Ecology labels Dec 2, 2024

editorialbot added Python TeX Shell labels Dec 2, 2024

editorialbot assigned cheginit Jan 9, 2025

[PRE REVIEW]: Pore2Chip: All-in-One Python Tool for Soil Microstructure Analysis and Micromodel Design #7546

[PRE REVIEW]: Pore2Chip: All-in-One Python Tool for Soil Microstructure Analysis and Micromodel Design #7546

Comments

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kthyng commented Dec 12, 2024

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maruti-iitm commented Jan 13, 2025

editorialbot commented Dec 2, 2024 •

edited

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