[PRE REVIEW]: ratesb_python: Rate Law Analysis for SBML and Antimony

[editorialbot]

Submitting author: @longxf21 (Longxuan Fan)
Repository: https://github.com/sys-bio/ratesb_python
Branch with paper.md (empty if default branch):
Version: v0.2.6
Editor: @RMeli
Reviewers: @ayush9pandey, @dilawar
Managing EiC: Kevin M. Moerman

Status

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

⚠️ An error happened when generating the pdf.

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (2478.1 files/s, 113993.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            351            500           1669
XML                             62              8             10            686
reStructuredText                 8            122             98            278
JSON                             8              1              0            274
Markdown                         2             79              0            220
TeX                              1              3              0             50
YAML                             2              7              0             44
DOS Batch                        1              8              1             26
TOML                             1              0              0             21
Dockerfile                       1              5              7             20
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            98            588            623           3297
-------------------------------------------------------------------------------

Commit count by author:

    44	Aldrich Fan
     2	longxf
     1	Joseph Hellerstein

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 863

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[Kevin-Mattheus-Moerman]

@longxf21 Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps.
The paper compilation error above seems to relate to the fact that the paper lacks the required YAML content. Please update the paper as per our guidelines and include the required YAML content.

[Kevin-Mattheus-Moerman]

@longxf21 👋

[longxf21]

Hi Kevin, Thanks! I will revise it soon. Longxuan

…

On Thu, Sep 26, 2024 at 08:54 Kevin Mattheus Moerman < ***@***.***> wrote: @longxf21 <https://github.com/longxf21> 👋 — Reply to this email directly, view it on GitHub <#7268 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AY2M7DBQUEKU3533XZ4HCFTZYQU33AVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZXGM2TGOBUGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Kevin-Mattheus-Moerman]

@longxf21 have you updated the paper yet?

[longxf21]

Hi Kevin, I apologize that I didn't get back to you. I took some time to review the submission guidelines and followed the Docker one. I compiled it with Docker and it works fine now. Thanks Longxuan

…

On Mon, Oct 14, 2024 at 03:18 Kevin Mattheus Moerman < ***@***.***> wrote: @longxf21 <https://github.com/longxf21> have you updated the paper yet? — Reply to this email directly, view it on GitHub <#7268 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AY2M7DEV6VLRFSFKCQJ64WLZ3OK6LAVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJQG4YTEMRSHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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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.

[Kevin-Mattheus-Moerman]

@longxf21 thanks for updating the paper. That compiled now and I had a quick look, and have some comments below:

• Please add the country (in full, please do not use acronyms) to the affiliations.
• Check expressiona that should probably read expressions

[Kevin-Mattheus-Moerman]

@editorialbot invite @ppxasjsm as editor

[editorialbot]

Invitation to edit this submission sent!

[ppxasjsm]

I don't think I can do this one I am afraid. My next few weeks are very busy with teaching.

[Kevin-Mattheus-Moerman]

@longxf21 please see my comments above ☝️

[longxf21]

Hi Kevin, Thanks for your comments, but I thought having a commit after the first review would be better. Next time I would let you know first! Thanks! Longxuan

…

On Fri, Nov 1, 2024 at 08:24 Kevin Mattheus Moerman < ***@***.***> wrote: @longxf21 <https://github.com/longxf21> please see my comments above ☝️ — Reply to this email directly, view it on GitHub <#7268 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AY2M7DDBL2WGPW3TCSBDMC3Z6OMK5AVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJSGA3DIMJXGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[longxf21]

If you would like me to make a commit before further review, please let me know, I would be happy to do that! Longxuan

…

On Fri, Nov 1, 2024 at 09:19 sparrow 123 ***@***.***> wrote: Hi Kevin, Thanks for your comments, but I thought having a commit after the first review would be better. Next time I would let you know first! Thanks! Longxuan On Fri, Nov 1, 2024 at 08:24 Kevin Mattheus Moerman < ***@***.***> wrote: > @longxf21 <https://github.com/longxf21> please see my comments above ☝️ > > — > Reply to this email directly, view it on GitHub > <#7268 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AY2M7DDBL2WGPW3TCSBDMC3Z6OMK5AVCNFSM6AAAAABOWF7MB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJSGA3DIMJXGA> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> >

[Kevin-Mattheus-Moerman]

@longxf21 yes please do commit and update as requested on a rolling bases.

[Kevin-Mattheus-Moerman]

@longxf21 apologies for the delays encountered so far. Many editors have been preoccupied handling other submissions. I hope to be able to invite one today so hopefully that will work out and we'll be able to move on from there.

[Kevin-Mattheus-Moerman]

@editorialbot invite @RMeli as editor

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

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Submitting author: @davidtourigny
Handling editor: @marcosvital (Active)
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Similarity score: 0.7250

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
Submitting author: @ayush9pandey
Handling editor: @csoneson (Active)
Reviewers: @Farnazmdi, @Robaina
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BASICO: A simplified Python interface to COPASI
Submitting author: @fbergmann
Handling editor: @marcosvital (Active)
Reviewers: @ayush9pandey, @jguhlin, @darogan
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ChemPy: A package useful for chemistry written in Python
Submitting author: @bjodah
Handling editor: @kyleniemeyer (Active)
Reviewers: @bryanwweber
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Heta compiler: a software tool for the development of large-scale QSP models and compilation into simulation formats
Submitting author: @metelkin
Handling editor: @fboehm (Active)
Reviewers: @martinmodrak, @elimillera
Similarity score: 0.7008

⚠️ 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.

[longxf21]

@Kevin-Mattheus-Moerman Apologies for the delay, I've checked the compiled paper pdf and the problems are fixed! Thanks!

[Kevin-Mattheus-Moerman]

@editorialbot assign @RMeli as editor

[editorialbot]

Assigned! @RMeli is now the editor

[Kevin-Mattheus-Moerman]

@RMeli thanks for still agreeing to be editor. I'll tag @lucydot @rkurchin @HaoZeke @mbarzegary to see if they can help suggest reviewers too in case you are stuck. Let me know if I can help too.

[Kevin-Mattheus-Moerman]

@longxf21 we've now assigned an editor @RMeli who will be the point of contact from now on. They will be looking for a set of reviewers now. If at this point you'd like to suggest any reviewers, please feel free to mention their GitHub handles here. But please do leave out the @ symbol so they are not tagged. Thanks!

[RMeli]

Hi @ayush9pandey 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

Thank you in advance!

[RMeli]

Hi @bjodah 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

Thank you in advance!

[ayush9pandey]

Happy to review this submission for JOSS.

[RMeli]

@editorialbot add @ayush9pandey as reviewer

Thank you very much @ayush9pandey!

[editorialbot]

@ayush9pandey added to the reviewers list!

[RMeli]

Hi @davidtourigny 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

Thank you in advance!

[davidtourigny]

I won't be able to, sorry!

[RMeli]

No worries @davidtourigny, thank you for letting me know!

[RMeli]

Hi @dilawar 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

[RMeli]

Hi @jrybarczyk 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

[dilawar]

Hi @dilawar 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

Hi @RMeli, I'd love to if timelines are not tight.

[RMeli]

@editorialbot set @dilawar as reviewer.

Thank you @dilawar! We usually aim for 6 weeks from the start of the review, but it is not too strict.

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[RMeli]

@editorialbot add @dilawar as reviewer.

[editorialbot]

@dilawar added to the reviewers list!

[RMeli]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7618.

[jrybarczyk]

Hi @jrybarczyk 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #7268.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

Hi @RMeli ! Thank you for the invitation, I accept.

[RMeli]

@jrybarczyk, thank you very much for willing to review! Unfortunately, we already found two reviewers for this paper. I'll keep you in mind when a similar paper pops up.