[PRE REVIEW]: MiNAA: Microbiome Network Alignment Algorithm

[editorialbot]

Submitting author: @crsl4 (Claudia Solis-Lemus)
Repository: https://github.com/solislemuslab/minaa
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @graciellehigino
Reviewers: @Becheler, @waynebhayes
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b4d9f26021065b1759d50413f60aa9c3/status.svg)](https://joss.theoj.org/papers/b4d9f26021065b1759d50413f60aa9c3)

Author instructions

Thanks for submitting your paper to JOSS @crsl4. Currently, there isn't a JOSS editor assigned to your paper.

@crsl4 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (839.2 files/s, 122737.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              6            248            440           1626
Python                           1             37             12            229
Markdown                         4             85              0            184
TeX                              1             27              0            180
JSON                             1              0              0             98
C/C++ Header                     5             13              0             52
R                                1              5              3             35
make                             1              5              0             24
YAML                             1              1              4             18
Bourne Shell                     1              2             14             11
DOS Batch                        1              1              0             10
-------------------------------------------------------------------------------
SUM:                            23            424            473           2467
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1671

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1093/sysbio/syy023 is OK
- 10.48550/ARXIV.0910.4067 is OK
- 10.13140/RG.2.1.3572.3287 is OK

MISSING DOIs

- 10.1109/icfhr.2014.76 may be a valid DOI for title: Real-time segmentation of on-line handwritten arabic script
- 10.1109/socpar.2014.7008025 may be a valid DOI for title: Fast classification of handwritten on-line Arabic characters
- 10.1371/journal.pcbi.1004226 may be a valid DOI for title: Sparse and compositionally robust inference of microbial ecological networks
- 10.1109/bibm49941.2020.9313552 may be a valid DOI for title: GPPIAL: A New Global PPI Network Aligner Based on Orthologs
- 10.1016/j.csbj.2020.09.011 may be a valid DOI for title: A review of protein–protein interaction network alignment: From pathway comparison to global alignment
- 10.1101/2020.07.15.195248 may be a valid DOI for title: NetCoMi: network construction and comparison for microbiome data in R
- 10.1186/s12864-019-5471-1 may be a valid DOI for title: Meta-network: optimized species-species network analysis for microbial communities
- 10.4016/12159.01 may be a valid DOI for title: Topological network alignment uncovers biological function and phylogeny
- 10.1002/nav.20053 may be a valid DOI for title: The Hungarian method for the assignment problem
- 10.1093/bioinformatics/btt202 may be a valid DOI for title: NETAL: a new graph-based method for global alignment of protein–protein interaction networks
- 10.1093/bioinformatics/btv130 may be a valid DOI for title: L-GRAAL: Lagrangian graphlet-based network aligner
- 10.1093/bioinformatics/btq091 may be a valid DOI for title: Biological network comparison using graphlet degree distribution
- 10.1186/1471-2105-12-24 may be a valid DOI for title: GraphCrunch 2: software tool for network modeling, alignment and clustering
- 10.18637/jss.v071.i10 may be a valid DOI for title: Computation of graphlet orbits for nodes and edges in sparse graphs
- 10.4137/cin.s680 may be a valid DOI for title: Uncovering biological network function via graphlet degree signatures

INVALID DOIs

- None

[crsl4]

Should we fix the invalid DOIs now or do we wait for more instructions?

[Kevin-Mattheus-Moerman]

@crsl4 thanks for this submission. I am the AEiC for this track and here to help check if this work is in scope, and if so, to help recruit a handling editor.

• On the DOI's yes you may fix those now. You can call @editorialbot check references here to check them again.
• Furthermore, can you please add the city, (and perhaps state), and country information for all affiliations? Please spell out USA as United States of America.

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@crsl4 I have just assigned the query scope label to get help from the editorial board to review if this work is deemed in scope. The work looks well written and useful to me but since it is on the small end of the spectrum in terms of lines of code I would like to get some opinions from those in this domain to see if this conforms to our substantial scholarly effort criteria. This scope review is usually completed within about 2 weeks.

[crsl4]

Thanks @Kevin-Mattheus-Moerman ! We will work on the DOIs and affiliations in the meantime.

[crsl4]

@Kevin-Mattheus-Moerman Fixed DOIs and added more details to affiliations in this commit.

[crsl4]

Fixed silly error in paper.bib here.

[danielskatz]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/bibm49941.2020.9313552 is OK
- 10.18637/jss.v071.i10 is OK
- 10.1098/rsif.2010.0063 is OK
- 10.1186/1471-2105-12-24 is OK
- 10.1002/nav.20053 is OK
- 10.1016/j.csbj.2020.09.011 is OK
- 10.1093/bioinformatics/btv130 is OK
- 10.4137/cin.s680 is OK
- 10.1093/bioinformatics/btt202 is OK
- 10.1101/2020.07.15.195248 is OK
- 10.13140/RG.2.1.3572.3287 is OK
- 10.1093/bioinformatics/btq091 is OK
- 10.1186/s12864-019-5471-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@editorialbot generate pdf

(@crsl4 - note that you can use these same commands)

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@crsl4 our board has determined this work may be in scope for JOSS. I have therefore removed the query-scope label. We will now proceed to seek a handling editor.

[Kevin-Mattheus-Moerman]

@editorialbot invite @graciellehigino as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot invite @graciellehigino as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@graciellehigino 👋 do you think you can help with this one? Thanks.

[graciellehigino]

Oops, I didn't get the first invite... Thanks, @Kevin-Mattheus-Moerman - count me in! =D

[graciellehigino]

@editorialbot assign @graciellehigino as editor

[editorialbot]

Assigned! @graciellehigino is now the editor

[graciellehigino]

@gabrielspadon @evadelmas Hey! Would you be interested in reviewing this paper? =D

[Kevin-Mattheus-Moerman]

@graciellehigino thanks for editing this submission. Let me know if you need help finding more reviewers.

[graciellehigino]

Hi @Kevin-Mattheus-Moerman ! Yes, I'm having a bit of trouble finding reviewers for this one. I'll send a couple more messages this week, but then I'm afraid I'm out of options...

[graciellehigino]

@adavidzh @vc1492a Hey! Would you be interested in reviewing this paper? =D

[adavidzh]

Would you be interested in reviewing this paper? =D

Thanks for the invite. After looking through the summary, the subject matter does not intersect enough with my expertise.

[vc1492a]

The biology aspect and graph alignment aspect is outside of my expertise.

[Kevin-Mattheus-Moerman]

@graciellehigino can you pick this up again?

[Kevin-Mattheus-Moerman]

@crsl4 would you be able to help suggest some reviewers here too? You can mention their github handles, but leave out the @ symbols, so they are not tagged. Thanks!

[Kevin-Mattheus-Moerman]

@graciellehigino I tried to help find potential reviewers (but this is not my field of expertise, so review them yourself). Perhaps: Becheler (who forked this software), perhaps some of the folks working on / using : https://github.com/taowenmicro/ggClusterNet e.g. rsiani, lindanimoyo (who starred the previous), or some of the folks behind/starring/forking https://github.com/microbiome/OMA e.g. HenrikEckermann, artur-sannikov.

[graciellehigino]

@editorialbot add @Becheler as reviewer

[editorialbot]

@Becheler added to the reviewers list!

[crsl4]

We can recommend other reviewers as well:

• Connections with GRAAL algorithm: okuchaiev, Vessy, waynebhayes
• Connections with MAGNA algorithm: vhxs
• Connections with ORCA algorithm: thocevar, janezd

[graciellehigino]

Thank you, @crsl4 and @Kevin-Mattheus-Moerman ! That's really helpful =D

[graciellehigino]

@editorialbot add @waynebhayes as reviewer

[editorialbot]

@waynebhayes added to the reviewers list!

[graciellehigino]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #5448.

[arfon]

@editorialbot generate pdf

[editorialbot]

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

[arfon]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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