[PRE REVIEW]: pymgpipe: microbiome metabolic modeling in Python

[editorialbot]

Submitting author: !--author-handle-->@ym2877<!--end-author-handle-- (Yoli Meydan) Repository: https://github.com/korem-lab/pymgpipe Branch with paper.md (empty if default branch): joss-paper Version: v0.15.0 Editor: !--editor-->@fboehm<!--end-editor-- Reviewers: @cumbof, @ammaraziz Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @ym2877. Currently, there isn't a JOSS editor assigned to your paper.

@ym2877 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (218.5 files/s, 306880.6 lines/s)
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Python                          21            435            120           2264
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 925

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1007/s13105-015-0390-3 may be a valid DOI for title: Gut microbiota: a key player in health and disease. A review focused on obesity
- 10.1038/s41467-019-10927-1 may be a valid DOI for title: Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences
- 10.1101/318485 may be a valid DOI for title: The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
- 10.1101/361907 may be a valid DOI for title: MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota
- 10.1093/bioinformatics/btac003 may be a valid DOI for title: MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data
- 10.1038/nprot.2009.203 may be a valid DOI for title: A protocol for generating a high-quality genome-scale metabolic reconstruction
- 10.1038/s41587-022-01628-0 may be a valid DOI for title: Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
- 10.1093/nar/gkz1054 may be a valid DOI for title: BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
- 10.1093/nar/gky537 may be a valid DOI for title: Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
- 10.1101/2021.06.14.448190 may be a valid DOI for title: Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome
- 10.1186/s40168-019-0689-3 may be a valid DOI for title: Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
- 10.2139/ssrn.3305554 may be a valid DOI for title: Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in Parkinson’s disease
- 10.1186/1752-0509-7-74 may be a valid DOI for title: COBRApy: constraints-based reconstruction and analysis for python
- 10.21105/joss.00139 may be a valid DOI for title: Optlang: An algebraic modeling language for mathematical optimization.
- 10.1186/s12859-020-03711-2 may be a valid DOI for title: VFFVA: dynamic load balancing enables large-scale flux variability analysis
- 10.1016/j.ymben.2003.09.002 may be a valid DOI for title: The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
- 10.4161/gmic.22370 may be a valid DOI for title: Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

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:

[Kevin-Mattheus-Moerman]

@ym2877 thanks for this submission. I am the AEiC on this track, and here to help process initial steps. For the moment, please can you check the above potentially missing DOIs? :point_up: You can update the .bib file and paper and use: @editorialbot check references, to check those DOIs again, and use @editorialbot generate pdf to update the paper.

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@ym2877 - I'll serve as editor for your submission. Please feel free to notify me of questions or concerns by using my github user name in a comment (preceded by @). The next task is to find reviewers for your submission. Do you have suggestions on who might be suitable reviewers? Please reply to in this comment thread with 4 or 5 names and github user names. Thank you!

[ym2877]

Awesome @fboehm @Kevin-Mattheus-Moerman , thank you so much! I will update that bib and get you a list of suitable reviewers asap.

[ym2877]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/s13105-015-0390-3 is OK
- 10.1038/s41586-020-2896-2 is OK
- 10.1038/s41467-019-10927-1 is OK
- 10.1101/318485 is OK
- 10.1101/361907 is OK
- 10.1093/bioinformatics/btac003 is OK
- 10.1038/nbt.1614 is OK
- 10.1038/nprot.2009.203 is OK
- 10.1038/s41587-022-01628-0 is OK
- 10.1093/nar/gkz1054 is OK
- 10.1093/nar/gky537 is OK
- 10.1101/2021.06.14.448190 is OK
- 10.1186/s40168-019-0689-3 is OK
- 10.1080/19490976.2021.1915673 is OK
- 10.2139/ssrn.3305554 is OK
- 10.1186/s12915-020-00775-7 is OK
- 10.1186/1752-0509-7-74 is OK
- 10.21105/joss.00139 is OK
- 10.1186/s12859-020-03711-2 is OK
- 10.1016/j.ymben.2003.09.002 is OK
- 10.4161/gmic.22370 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ym2877]

@editorialbot generate pdf

[editorialbot]

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

[ym2877]

@fboehm , here is the list of individuals we believe would be suitable reviewers. Please don't hesitate to let me know if you have any further questions!

• Christian Diener (cdiener)
• Marco Fondi (mfondi)
• Claudio Angione (claudioangione)
• Eric Franzosa (franzosa)
• Marouen Ben Guebila (marouenbg)

I also want to note that Marouen is listed in our acknowledgments.

[fboehm]

@cdiener @mfondi - would you be willing to review this submission for JOSS? Our reviews differ from those of many journals in that we use pre-specified checklists as the focus of the review. The review is also iterative and open, where we encourage communications between the reviewers and authors. Thank you for considering this invitation!

[fboehm]

@claudioangione @franzosa - would you be willing to review this submission for JOSS? Our reviews differ from those of many journals in that we use pre-specified checklists as the focus of the review. The review is also iterative and open, where we encourage communications between the reviewers and authors. Thank you for considering this invitation!

[cdiener]

Sorry, I'm on vacation and won't be available for a while. Best of luck.

[fboehm]

Sorry, I'm on vacation and won't be available for a while. Best of luck.

Thanks for letting me know. I hope that we can work together in the future.

[fboehm]

@editorialbot list reviewers

[editorialbot]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[fboehm]

@amoeba @nicoguaro @rougier - would you be willing to review this submission for JOSS? I'd really appreciate reviews from someone with your python expertise. Thank you for considering this invitation.

[amoeba]

Hi @fboehm, I have another JOSS review about to become in progress and I don't think I have capacity at the moment.

[fboehm]

Thanks for getting back to me, @amoeba. And thanks for your continued involvement with JOSS. i hope that we can work together in the future.

[fboehm]

@cumbof @ManavalanG @flekschas - would you be willing to review this submission for JOSS? Our reviews differ from those of many journals in that we use pre-specified checklists as the focus of the review. The review is also iterative and open, where we encourage communications between the reviewers and authors. Thank you for considering this invitation!

[fboehm]

@mbhall88 @ammaraziz - would you be willing to review this submission for JOSS? Our reviews differ from those of many journals in that we use pre-specified checklists as the focus of the review. The review is also iterative and open, where we encourage communications between the reviewers and authors. Thank you for considering this invitation!

[cumbof]

@cumbof @ManavalanG @flekschas - would you be willing to review this submission for JOSS? Our reviews differ from those of many journals in that we use pre-specified checklists as the focus of the review. The review is also iterative and open, where we encourage communications between the reviewers and authors. Thank you for considering this invitation!

Hi @fboehm, I would be happy to review this submission. Thanks

[fboehm]

Thank you, @cumbof ! I'll add you to the list of reviewers. Once we find a second reviewer, we can start the review. Thanks again!

[fboehm]

@editorialbot add @cumbof as reviewer

[editorialbot]

@cumbof added to the reviewers list!

[flekschas]

@cumbof @ManavalanG @flekschas - would you be willing to review this submission for JOSS? Our reviews differ from those of many journals in that we use pre-specified checklists as the focus of the review. The review is also iterative and open, where we encourage communications between the reviewers and authors. Thank you for considering this invitation!

@fboehm I don't have any expertise in microbiome research or metabolomic modeling so I don't think I'm suited to review this submission

[fboehm]

@flekschas - thanks for the reply. I hope that we can work together on a future submission.

[ammaraziz]

I would be happy to review this submission but I also don't have much experience with modelling microbiomes. As long as this is acceptable, happy to review.

[fboehm]

Thanks so much, @ammaraziz ! Yes, it's ok that you don't have experience with modeling microbiomes. If you find that you can't evaluate some aspects of the software, please let me know. I'm confident that your python skills will be quite useful for the review.

[fboehm]

@editorialbot add @ammaraziz as reviewer

[editorialbot]

@ammaraziz added to the reviewers list!

[fboehm]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5545.