[REVIEW]: Chaste: Cancer, Heart and Soft Tissue Environment

whedon commented 5 years ago

Submitting author: @fcooper8472 (Fergus Cooper) Repository: https://github.com/Chaste/Chaste Version: release_2019.1 Editor: @meg-simula Reviewers: @finsberg, @IgorBaratta Archive: 10.5281/zenodo.3708497

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1a2ae4a7df2dc0623752782decfe2b86/status.svg)](https://joss.theoj.org/papers/1a2ae4a7df2dc0623752782decfe2b86)

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

@finsberg & @SirSharpest, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @finsberg

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@fcooper8472) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @IgorBaratta

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@fcooper8472) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @SirSharpest

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[ ] Repository: Is the source code for this software available at the repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@fcooper8472) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

meg-simula commented 4 years ago

@whedon generate pdf

meg-simula commented 4 years ago

@fcooper8472 Whedon seems to be having some difficulties indeed, I'll investigate.

fcooper8472 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

fcooper8472 commented 4 years ago

@meg-simula looks to be OK this morning!

meg-simula commented 4 years ago

Lovely, thanks @fcooper8472.

meg-simula commented 4 years ago

@whedon check references

meg-simula commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

meg-simula commented 4 years ago

@fcooper8472 Looks like there is still a few references missing dois/link for instance some of the Spiteri papers - could you take another look? (Sorry to keep niggling about this.)

fcooper8472 commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1098/rsta.2010.0170 is OK
- 10.1088/1741-2560/10/2/026019 is OK
- 10.1007/s11538-017-0377-z is OK
- 10.1016/j.jcp.2012.01.037 is OK
- 10.1242/dev.126359 is OK
- 10.1016/j.celrep.2014.07.019 is OK
- 10.1016/j.vascn.2013.04.004 is OK
- 10.1109/CIC.2008.4749143 is OK
- 10.1098/rsta.2008.0309 is OK
- 10.1109/IEMBS.2010.5626338 is OK
- 10.1109/TBME.2010.2078817 is OK
- 10.1016/j.procs.2011.04.087 is OK
- 10.1177/1094342012474997 is OK
- 10.1109/IEMBS.2010.5625979 is OK
- 10.1016/j.pbiomolbio.2011.05.002 is OK
- 10.1137/11082796X is OK
- 10.1371/journal.pone.0144105 is OK
- 10.1073/pnas.1304382110 is OK
- 10.3389/fphys.2017.00278 is OK
- 10.3389/fphys.2017.00597 is OK
- 10.1115/1.1583758 is OK
- 10.1007/s10439-010-0051-1 is OK
- 10.1080/21681163.2015.1023358 is OK
- 10.1016/j.cam.2015.02.008 is OK
- 10.1371/journal.pone.0092792 is OK
- 10.1093/europace/euw346 is OK
- 10.1371/journal.pone.0202410 is OK
- 10.1242/jcs.211656 is OK
- 10.1137/17M1137061 is OK
- 10.1109/MCSE.2007.74 is OK
- 10.1016/j.pbiomolbio.2011.06.002 is OK
- 10.1016/j.pbiomolbio.2011.06.003 is OK
- 10.1016/j.procs.2013.05.235 is OK
- 10.3389/fphys.2014.00511 is OK
- 10.1016/j.bpj.2015.12.012 is OK
- 10.1137/16M1092246 is OK
- 10.1016/j.mbs.2015.12.005 is OK
- 10.1098/rsta.2010.0083 is OK
- 10.1109/IEMBS.2010.5626614 is OK
- 10.1152/ajpheart.01170.2010 is OK
- 10.1039/C2IB00100D is OK
- 10.1038/srep42492 is OK
- 10.1098/rsos.150499 is OK
- 10.1098/rsif.2017.0340 is OK
- 10.1016/j.pbiomolbio.2018.05.011 is OK
- 10.1016/j.drudis.2016.02.003 is OK
- 10.1103/PhysRevE.87.042724 is OK
- 10.1016/j.jtbi.2011.12.013 is OK
- 10.1371/journal.pcbi.1002515 is OK
- 10.1371/journal.pone.0080516 is OK
- 10.1091/mbc.E15-12-0854 is OK
- 10.1007/978-3-642-21028-0_3 is OK
- 10.1016/j.pbiomolbio.2016.01.008 is OK
- 10.1016/j.pbiomolbio.2017.02.007 is OK
- 10.1016/j.vascn.2013.04.007 is OK
- 10.1098/rsfs.2012.0081 is OK
- 10.15252/embj.2018100072 is OK
- 10.1201/b10407-7 is OK
- 10.2165/11591950-000000000-00000 is OK
- 10.1016/j.jtbi.2012.01.021 is OK
- 10.1016/j.pbiomolbio.2013.09.003 is OK
- 10.1142/S0218202515400187 is OK
- 10.1098/rstb.2015.0519 is OK
- 10.1109/EMBC.2015.7318511 is OK
- 10.1529/biophysj.104.041459 is OK
- 10.1016/j.aml.2008.06.051 is OK
- 10.1007/s10439-014-1021-9 is OK
- 10.1109/TBME.2015.2412533 is OK
- 10.1002/wsbm.63 is OK
- 10.1137/11082796X is OK
- 10.1161/01.RES.0000016960.61087.86 is OK
- 10.1038/s41540-017-0020-5 is OK
- 10.1103/PhysRevLett.69.2013 is OK
- 10.1109/TBME.2016.2606563 is OK
- 10.1016/j.bpj.2017.03.036 is OK
- 10.1371/journal.pcbi.1006049 is OK
- 10.1007/s10237-014-0639-8 is OK
- 10.1016/j.cpc.2015.03.005 is OK
- 10.1113/JP272015 is OK
- 10.1145/1089014.1089020 is OK
- 10.1016/S0022-5193(80)80021-X is OK
- 10.1039/C3IB40141C is OK
- 10.1016/j.yjmcc.2015.11.018 is OK
- 10.1016/j.jtbi.2014.06.001 is OK
- 10.1371/journal.pcbi.1004679 is OK
- 10.1016/j.jcp.2017.05.048 is OK
- 10.1016/j.jtbi.2018.01.020 is OK
- 10.1063/1.5012848 is OK
- 10.1109/TBME.2014.2327025 is OK
- 10.1016/j.media.2015.03.006 is OK
- 10.1063/1.5019367 is OK
- 10.1093/europace/euy226 is OK
- 10.1038/srep26744 is OK
- 10.1109/TBME.2012.2205575 is OK
- 10.1039/C7TX00141J is OK
- 10.1046/j.0960-7722.2001.00216.x is OK
- 10.1111/j.1749-6632.2011.06324.x is OK
- 10.1093/cvr/cvr044 is OK
- 10.1111/j.1476-5381.2012.02020.x is OK
- 10.1016/j.jtbi.2012.08.002 is OK
- 10.1371/journal.pcbi.1002970 is OK
- 10.1016/j.vascn.2014.07.002 is OK
- 10.1113/JP271671 is OK
- 10.1088/1478-3975/8/1/015017 is OK
- 10.1093/cvr/cvv196 is OK
- 10.5194/ars-10-85-2012 is OK
- 10.1098/rsif.2018.0037 is OK
- 10.1103/PhysRevE.80.031912 is OK
- 10.1016/j.bpj.2010.05.016 is OK
- 10.1088/1478-3975/8/2/026011 is OK
- 10.1152/ajpheart.00477.2017 is OK
- 10.1080/13642810108205772 is OK
- 10.1186/1752-0509-8-66 is OK
- 10.1098/rsta.2011.0139 is OK
- 10.1098/rsta.2010.0173 is OK
- 10.4137/CIN.S19332 is OK
- 10.1371/journal.pcbi.1005387 is OK
- 10.1016/j.yjmcc.2015.09.003 is OK
- 10.3389/fphys.2017.00668 is OK
- 10.1088/1478-3975/6/3/036001 is OK
- 10.1007/s10439-009-9663-8 is OK
- 10.1093/qjmam/hbq014 is OK
- 10.1016/j.pbiomolbio.2010.05.006 is OK
- 10.1002/cnm.2467 is OK
- 10.1002/cnm.1438 is OK
- 10.1002/cnm.2467 is OK
- 10.1002/cnm.2615 is OK
- 10.1155/2015/720575 is OK
- 10.1371/journal.pone.0014790 is OK
- 10.1098/rsta.2008.0096 is OK
- 10.1016/j.cpc.2009.07.019 is OK
- 10.1016/j.bpj.2011.09.060 is OK
- 10.1126/scitranslmed.aac4296 is OK
- 10.1038/clpt.2010.95 is OK
- 10.4137/CIN.S19965 is OK
- 10.1038/ncomms6069 is OK
- 10.1016/j.celrep.2015.06.018 is OK
- 10.1152/ajpheart.00668.2011 is OK
- 10.1146/annurev.physiol.68.040504.094718 is OK
- 10.1007/s10439-013-0949-5 is OK
- 10.1109/EMBC.2015.7318643 is OK
- 10.1109/TBME.2015.2444384 is OK
- 10.1109/EMBC.2015.7320264 is OK
- 10.1016/0022-5193(79)90042-0 is OK
- 10.1007/s11693-012-9095-x is OK
- 10.1183/1393003.congress-2017.PA2476 is OK
- 10.1016/j.jocs.2010.03.010 is OK
- 10.1016/j.jocs.2011.11.002 is OK
- 10.1152/ajpheart.00109.2006 is OK
- 10.7554/eLife.12094 is OK
- 10.1111/j.1365-2184.2009.00627.x is OK
- /10.1109/ACCESS.2018.2853624 is OK
- 10.1007/978-3-642-21028-0_9 is OK
- 10.1109/TBME.2012.2193398 is OK
- 10.1016/j.media.2013.10.006 is OK
- 10.1016/j.bpj.2011.11.3230 is OK
- 10.1007/978-3-642-38899-6_27 is OK
- 10.1371/journal.pone.0056359 is OK
- 10.1016/j.jtbi.2014.10.029 is OK
- 10.1016/j.vascn.2015.05.002 is OK
- 10.3389/fphys.2019.00259 is OK
- 10.1007/978-3-319-67552-7_8 is OK
- 10.1007/978-3-642-21028-0_32 is OK
- 10.1111/j.1476-5381.2012.02200.x is OK
- 10.1093/europace/euu122 is OK
- 10.1161/CIRCRESAHA.115.307836 is OK
- 10.1371/journal.pbio.1002491 is OK
- 10.1109/EMBC.2018.8513223 is OK
- 10.1137/17M1137061 is OK
- 10.1016/j.cam.2015.09.015 is OK
- 10.1137/18M1201421 is OK
- 10.1016/B978-0-12-388403-9.00013-8 is OK
- 10.1093/bioinformatics/btt772 is OK
- 10.1093/bioinformatics/bts659 is OK
- 10.1093/bioinformatics/btq437 is OK
- 10.1371/journal.pcbi.1005991 is OK
- 10.1093/bioinformatics/btu498 is OK
- 10.1104/pp.110.167619 is OK
- 10.1093/bioinformatics/btv527 is OK

MISSING DOIs

- None

INVALID DOIs

- None

fcooper8472 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

fcooper8472 commented 4 years ago

@meg-simula There are now DOIs for all references other than the Computing in Cardiology articles, which don't appear to have DOIs.

fcooper8472 commented 4 years ago

Hi @meg-simula - what's the next step on this?

meg-simula commented 4 years ago

@whedon generate pdf

meg-simula commented 4 years ago

Hi @meg-simula - what's the next step on this?

@fcooper8472 I'll check the references and then we are good to go!

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

meg-simula commented 4 years ago

Ok, looks great @fcooper8472!

At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

fcooper8472 commented 4 years ago

Thanks @meg-simula

When checking the Zenodo metadata @mirams found one of the author affiliations was incorrect so I have made a new commit fixing that. It might be worth checking the proof again just in case something has gone wrong.

In terms of the other information you requested:

Make a tagged release of your software, and list the version tag of the archived version here.

Tagged as release_2019.1 (link)

Archive the reviewed software in Zenodo or a similar service

Done: https://zenodo.org/record/3702736

Please list the DOI of the archived version here.

10.5281/zenodo.3702736

The Zenodo metadata will be updated shortly.

meg-simula commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

meg-simula commented 4 years ago

Looks good to me, thanks @fcooper8472!

fcooper8472 commented 4 years ago

@meg-simula the metadata is correct now.

meg-simula commented 4 years ago

@whedon set 10.5281/zenodo.3702736 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3702736 is the archive.

meg-simula commented 4 years ago

@whedon set release_2019.1 as version

whedon commented 4 years ago

OK. release_2019.1 is the version.

meg-simula commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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

. Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1366

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1366, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

👋 @fcooper8472 - as the AEiC currently on duty, I have some requests before this goes into the final acceptance processing

[ ] please remove a large number of the reference related to use of Chaste - you do not need to cite all papers in which Chaste has been used, just a selection showing its breadth, perhaps 5-10. This paper is far longer than a JOSS paper is recommended to be, and while some of this is because it is a complex package, we can reduce some of the length and number of references by doing this.
[ ] please fix paper and journal titles - e.g., I see both PLoS one and PLOS ONE, where the latter is correct, and Computing in cardiology, rather than Computing in Cardiology. Also re titles, I see one lgr+ that should be Lgr5+, for example.

fcooper8472 commented 4 years ago

@danielskatz, please see responses inline:

please remove a large number of the reference related to use of Chaste - you do not need to cite all papers in which Chaste has been used, just a selection showing its breadth, perhaps 5-10.

We added a comprehensive list of research using/enabled by Chaste because that was listed on the JOSS website under "What should my paper contain?", which included:

"Mention (if applicable) of any past or ongoing research projects using the software and recent scholarly publications enabled by it."

The paper is longer than the recommended limit of 1000 words because that seemed necessary in order to hit all of the submission requirements. I notice that, since yesterday, the JOSS website has changed, and the new instructions are to:

"Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it."

In light of the fact that we submitted our paper to JOSS before the requirements changed, it doesn't seem appropriate to make substantial changes at this stage.

please fix paper and journal titles - e.g., I see both PLoS one and PLOS ONE, where the latter is correct, and Computing in cardiology, rather than Computing in Cardiology. Also re titles, I see one lgr+ that should be Lgr5+, for example.

I have gone thoroughly through the bibliography file and checked journal names and titles. They should now be correct.

The issue with Computing in cardiology, rather than Computing in Cardiology appears to be a JOSS problem - all instances of Cardiology in the bibliography file were already capitalised, and they became lowercase when converted to PDF. I have tried to circumvent this by wrapping in an extra layer of {} which will hopefully mean they are displayed verbatim.

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

In light of the fact that we submitted our paper to JOSS before the requirements changed, it doesn't seem appropriate to make substantial changes at this stage.

I disagree - please make the changes I requested.

I have gone thoroughly through the bibliography file and checked journal names and titles. They should now be correct.

Thank you

The issue with Computing in cardiology, rather than Computing in Cardiology appears to be a JOSS problem - all instances of Cardiology in the bibliography file were already capitalised, and they became lowercase when converted to PDF. I have tried to circumvent this by wrapping in an extra layer of {} which will hopefully mean they are displayed verbatim.

Rather than a problem with JOSS, we could call this a feature that comes from pandoc - titles, including booktitles, are changed to only an initial capital letter.

mirams commented 4 years ago

Hi, I am one of the authors of the Chaste paper, I have spent a while trying to shorten it down as requested. I would ask that you take another look, for a couple of reasons.

Firstly in my draft I've had to remove all the citations to similar software that feature in the comparison table we added (as requested before), this seems against the spirit of JOSS in giving credit to these people for developing their software.

Secondly, the section on "Recent Publications..." gives a very good indication to readers of what Chaste can be used for, and where they can find more information on this, which is a far wider range of things than the limited examples in the paper can hope to cover.

If you would still like to chop it down we're happy to oblige, but personally I think it makes the paper less useful.

danielskatz commented 4 years ago

The original request I made was "you do not need to cite all papers in which Chaste has been used, just a selection showing its breadth, perhaps 5-10." - I did not mean that you should remove references to things that Chaste depends on, or those to similar software, just to reduce the number of references in the section "Recent Publications enabled by Chaste" to a representative 5 to 10 rather than every paper that has used Chaste. You can still say that Chaste can be used in a variety of fields without referencing papers from each of them.

I apologize if this was confusing.

Also, when you make changes, you can ask whedon to create a new PDF by putting the command @whedon generate pdf in this issue as a new comment

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

meg-simula commented 4 years ago

/ooo March 12 until March 27

ooo[bot] commented 4 years ago

:+1: Marked @meg-simula as OOO from Thursday, March 12th 2020 to Friday, March 27th 2020. :calendar:

finsberg commented 4 years ago

/ooo March 12 until March 27

ooo[bot] commented 4 years ago

:+1: Marked @finsberg as OOO from Thursday, March 12th 2020 to Friday, March 27th 2020. :calendar:

fcooper8472 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

fcooper8472 commented 4 years ago

@danielskatz here is the substantially lighter version.

Please let me know if you would like any further changes. We will need to generate a new archive & DOI reflecting these changes before publication.

danielskatz commented 4 years ago

looks good - thanks - let me know the new archive and doi when you have them

fcooper8472 commented 4 years ago

The new Zenodo archive is: https://zenodo.org/record/3708497

with DOI: 10.5281/zenodo.3708497

@mirams will be able to update the title and author list at that new Zenodo archive to match this JOSS paper.

openjournals / joss-reviews