[REVIEW]: Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

[editorialbot]

Submitting author: !--author-handle-->@ayush9pandey<!--end-author-handle-- (Ayush Pandey) Repository: https://github.com/biocircuits/bioscrape/ Branch with paper.md (empty if default branch): joss-paper Version: v1.2.2 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @Farnazmdi, @Robaina Archive: 10.5281/zenodo.7677726

Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@Farnazmdi & @Robaina, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @csoneson know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @Robaina

📝 Checklist for @Farnazmdi

[csoneson]

@editorialbot set v1.2.2 as version

[editorialbot]

Done! version is now v1.2.2

[csoneson]

@editorialbot set 10.5281/zenodo.7677726 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7677726

[csoneson]

Thanks @ayush9pandey, this looks good. Only one minor thing: the license in the Zenodo record doesn't match the one in the GitHub repository. Could you please change that in the metadata on Zenodo? Then I'm going to hand over to the track EiC for the final steps.

[ayush9pandey]

Done! Thanks for noticing that!

[csoneson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1093/bioinformatics/btl485 is OK
- 10.1093/bioinformatics/btac770 is OK
- 10.1093/bioinformatics/btv363 is OK
- 10.1371/journal.pcbi.1006220 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1016/j.cell.2012.01.002 is OK
- 10.1109/tcbb.2011.63 is OK
- 10.1098/rsfs.2011.0047 is OK
- 10.1073/pnas.1200161109 is OK
- 10.1126/science.1105809 is OK
- 10.1186/1471-2105-10-343 is OK
- 10.1109/mcse.2010.118 is OK
- 10.1371/journal.pone.0079345 is OK
- 10.1073/pnas.1013171108 is OK
- 10.1101/071100 is OK
- 10.1002/rnc.6013 is OK
- 10.48550/arXiv.1202.3665 is OK
- 10.1021/acssynbio.2c00534 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3998, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

I checked the repo, the archive, and the paper, and all looks good to proceed.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4038
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05057
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@ayush9pandey congratulations on this JOSS publication!

Thank you @csoneson for editing!

And, also a special thanks to the reviewers @Farnazmdi and @Robaina !

[editorialbot]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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