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

[whedon]

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:

HTML: <a href="https://joss.theoj.org/papers/1a2ae4a7df2dc0623752782decfe2b86"><img src="https://joss.theoj.org/papers/1a2ae4a7df2dc0623752782decfe2b86/status.svg"></a>
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:

1. Make sure you're logged in to your GitHub account
2. 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @finsberg, @SirSharpest it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[meg-simula]

@finsberg @SirSharpest Thanks again for agreeing to review. Reviewer checklists have been generated for each you above - take a look and dig in at will.

[finsberg]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[fcooper8472]

@finsberg looks as though the markdown list I put in with the new instructions hasn't rendered nicely. It's just a standard list in the source - any ideas?

[finsberg]

I am not sure, but one thing you could try is to add a new line between each item. You can just execute the command @whedon generate pdf as a comment here to check the pdf afterwards.

[SirSharpest]

I have started to review, but from this submission I cannot see what specifically is different from https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002970 or https://www.sciencedirect.com/science/article/pii/S0010465509002604.

If it is a specific recent addition to this existing and established software, then could the submission be made to reflect this?

Otherwise I would need @meg-simula to verify if established and published software is an issue / needs to be taken into account in this review?

[fcooper8472]

Hi @SirSharpest. The paper you mention was published in 2009, and there has been a vast quantity of development since then.

This paper references that publication, and another (from 2013), but this will serve as an updated reference with details about Chaste as it exists now (rather than 6 or 10 years ago).

Almost every element of the software has been substantially changed, and information on the installation and example usage reflects the current release of the software:

• All three of the examples of functionality relate to new functionality since the 2009 paper you reference
• Information on how to run the examples reflects a completely new build system
• Installation instructions reflect new functionality including Docker

As this is a software paper (which will allow the citing of the software) I think it would not be useful to highlight how the current version is different from previous versions, but simply (as is presented) what the current version of the software offers.

Certainly happy to hear any input from @meg-simula on this though.

[finsberg]

@meg-simula I am now done with my review, and I think that Chaste more than qualifies for publication in JOSS. Its seems to have an active community of maintainers and it also has a very nice test suite as well a good documentation with a lot of tutorials. It was also very easy to use together with the provided docker image. I have added a final suggestion to add a section for benchmarks which I think would be a very nice addition.

[meg-simula]

Otherwise I would need @meg-simula to verify if established and published software is an issue / needs to be taken into account in this review?

Thanks for the due diligence @SirSharpest! In this case, the difference between the aforementioned published papers and the current submission, in terms of target audience, scope and new development seems substantial and warrants review. But please do feel free to add a pointer in your review if you would like this point to be addressed more clearly in the manuscript.

[meg-simula]

Thanks for the reviewing @finsberg! There is one checkbox (state of the art) unchecked in your list - is that on purpose?

[finsberg]

Thanks for the reviewing @finsberg! There is one checkbox (state of the art) unchecked in your list - is that on purpose?

There is a reason for this. The question in the checkbox says " Do the authors describe how this software compares to other commonly-used packages?" and I cannot see that they have any comparison with other commonly-used packages. Thats said, I think adding a section with benchmarks would be a good solution to address this question. However, in my opinion I think Chaste qualifies for publication also without this benchmark section.

[meg-simula]

Ok, thanks for the clarification. I would then advise @fcooper8472 to add a discussion on comparison with other packages (in addition to the optional benchmark comparison).

[SirSharpest]

@meg-simula Could I ask to be removed as a reviewer? I have ethical concerns over this which make it so that I cannot be fully objective.

[mirams]

It would be good to get some clarification on this (I’m one of the authors of the Chaste paper).

As I understood it, the central motivation for a JOSS paper is to give all the authors that have contributed to a certain version of an open source scientific code some credit and citations for their work, and to provide a short summary of the capabilities and science the software has enabled.

We’ve listed all the authors that have committed more than once or twice to the git repository (also some svn before that) since the last (2013) paper. We would be planning to submit another new updated paper in a year or two with a new set of authors who have contributed code from now until then, if this isn’t allowed or encouraged by JOSS that would be useful to know.

[meg-simula]

I will discuss the matter with the JOSS editorial board and get back to you all.

[meg-simula]

I've consulted with the editorial board and the main points are as follows:

(1) As the previous papers are published in Software "tracks" e.g. PLOS Computational Biology: Software and a special issue of Computer Physics Communications focused on high quality software and indeed focus on software aspects of the project, these papers do indeed document the Chaste software.

(2) A JOSS paper is admissible if and only if the software has substantial new additions since the previous papers.

Thus, if it is the case as @fcooper8472 states that "Almost every element of the software has been substantially changed", I would consider this to constitute substantial new additions and thus that this paper is admissible. I would however encourage the authors to present the main additions compared to the previous versions in the current paper.

@mirams: The same thus applies for future versions - substantial new additions since previous papers required. Hope this clarifies, please let me know if not.

@SirSharpest: would you still like to be removed as reviewer? If so, no problem, just let me know.

[labarba]

@fcooper8472 — it looks like the handling editor is waiting for a reply from you. Can you update this thread with your assessment and how you wish this to move forward?

[fcooper8472]

@labarba thanks - sorry for the delay.

I will update the paper shortly with clarification that it is substantially different, and will address the remaining point from finsberg's review.

[meg-simula]

Thanks @fcooper8472, glad to hear that you are working on the matter.

I'm working on finding a replacement second reviewer, but it is taking some time - thanks for your patience on this matter.

[meg-simula]

Thanks @IgorBaratta for agreeing to review this submission. I'll generate a review checklist for you above shortly.

[meg-simula]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to accept the paper and deposit with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[meg-simula]

@whedon add @IgorBaratta as reviewer

[whedon]

OK, @IgorBaratta is now a reviewer

[meg-simula]

@whedon remove @SirSharpest as reviewer

[whedon]

OK, @SirSharpest is no longer a reviewer

[meg-simula]

@IgorBaratta reviewer checklist ready for you above whenever you are. Thanks again for agreeing to review.

[whedon]

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

[IgorBaratta]

Hi @meg-simula, I have completed my review.

Yet, there are still two boxes unchecked, both concerning the software paper:

• State of the field – As previosly noted by @finsberg, a comparison to other commonly-used packages is missing.
• References – There seem to be some inconsistencies in the citation format in the section “Recent publications enabled by Chaste”.

But in any case, I recommend this submission for publication in JOSS.

The software is exceptionally documented and is a great resource. I was able to follow the tutorials of the core functionality smoothly. Also tried with success the three tutorials presented in the text: cardiac, cell-based, and lung Chaste.

_Minor Remark:_
Installation went well following the “Users of the Ubuntu package” tutorial in a brand new Ubuntu installation. However, I had some issues with a previously installed PETSc that complied with the Dependency Version guide.
It didn’t work with PETSc compiled with complex numbers. So, I think that this incompatibility, if confirmed, could be mentioned in the documentation in https://chaste.cs.ox.ac.uk/trac/wiki/InstallGuides/DependencyVersions or https://chaste.cs.ox.ac.uk/trac/wiki/InstallPetscAndMpi.

[danielskatz]

👋 @meg-simula - can you help this process move forward?

[fcooper8472]

Sorry for the delay on my end - I'll have a revised version that addresses the two outstanding points shortly.

[fcooper8472]

@whedon generate pdf

[whedon]

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

[fcooper8472]

@IgorBaratta @finsberg @meg-simula please see the latest version, which addresses the following points:

1. Information on the extent of changes since 2013, when the most recent previous paper about Chaste was published
2. A new section with comparison to similar software

Two things I see when looking at the proof:

1. The table (in the new comparison section) is badly formatted due to lengthy references.
2. All cases with multiple refs in one place are not formatted correctly. The syntax [@ref1, @ref2] does not seem to work.

Any ideas on these formatting issues?

[finsberg]

@IgorBaratta @finsberg @meg-simula please see the latest version, which addresses the following points:

1. Information on the extent of changes since 2013, when the most recent previous paper about Chaste was published
2. A new section with comparison to similar software

Great! I have now checked off the final tick mark and can recommend this for publication.
I don't know if it is possible to change the reference style to use numbers instead? See e.g
https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_styles

[fcooper8472]

@finsberg Great, thanks!

My mistake on the multiple refs - syntax is ; rather than , separation.

For the table, I have just changed it to have the refs below in the caption, which is probably the easiest solution for the time being.

[fcooper8472]

@whedon generate pdf

[whedon]

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

[whedon]

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/TBME.2010.2078817 is OK
- 10.1016/j.procs.2011.04.087 is OK
- 10.1177/1094342012474997 is OK
- 10.1016/j.pbiomolbio.2011.05.002 is OK
- 10.1137/11082796X is OK
- 10.1073/pnas.1304382110 is OK
- 10.3389/fphys.2017.00278 is OK
- 10.1115/1.1583758 is OK
- 10.1007/s10439-010-0051-1 is OK
- 10.1016/j.cam.2015.02.008 is OK
- 10.1371/journal.pone.0092792 is OK
- 10.1371/journal.pone.0202410 is OK
- 10.1242/jcs.211656 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
- 10.1152/ajpheart.01170.2010 is OK
- 10.1039/C2IB00100D is OK
- 10.1038/srep42492 is OK
- 10.1098/rsos.150499 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
- 10.2165/11591950-000000000-00000 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
- 10.1109/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
- 10.1161/01.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
- 10.1039/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
- 10.1146/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
- 10.1007/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
- 10.1109/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
- 10.1111/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
- 10.1016/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

- https://doi.org/10.1109/iembs.2010.5626338 may be missing for title: Shock-induced arrhythmogenesis in the human heart: A computational modelling study
- https://doi.org/10.1109/iembs.2010.5625979 may be missing for title: Integrated approach for the study of anatomical variability in the cardiac purkinje system: from high resolution MRI to electrophysiology simulation
- https://doi.org/10.1371/journal.pone.0144105 may be missing for title: Development and analysis of patient-based complete conducting airways models
- https://doi.org/10.3389/fphys.2017.00597 may be missing for title: Quantitative comparison of effects of dofetilide, sotalol, quinidine, and verapamil between human ex vivo trabeculae and in silico ventricular models incorporating inter-individual action potential variability
- https://doi.org/10.1080/21681163.2015.1023358 may be missing for title: A combined image-modelling approach assessing the impact of hyperinflation due to emphysema on regional ventilation–perfusion matching
- https://doi.org/10.1093/europace/euw346 may be missing for title: Human ventricular activation sequence and the simulation of the electrocardiographic QRS complex and its variability in healthy and intraventricular block conditions
- https://doi.org/10.1109/iembs.2010.5626614 may be missing for title: A novel biophysically-detailed mathematical model of rabbit Purkinje cell electrophysiology.
- https://doi.org/10.1201/b10407-7 may be missing for title: Multiscale modeling of colonic crypts and early colorectal cancer
- https://doi.org/10.1098/rstb.2015.0519 may be missing for title: Mechanocellular models of epithelial morphogenesis
- https://doi.org/10.1109/tbme.2012.2205575 may be missing for title: The secrets to the success of the Rush–Larsen method and its generalizations
- https://doi.org/10.1016/0022-5193(79)90042-0 may be missing for title: Simple chemical reaction systems with limit cycle behaviour
- https://doi.org/10.1007/978-3-642-21028-0_9 may be missing for title: Estimation of activation times in cardiac tissue using graph based methods
- https://doi.org/10.1007/978-3-642-21028-0_32 may be missing for title: Simulating drug-induced effects on the heart: from ion channel to body surface electrocardiogram
- https://doi.org/10.1109/tbme.2012.2205575 may be missing for title: The secrets to the success of the Rush–Larsen method and its generalizations

INVALID DOIs

- 1098/rsif.2017.0340 is INVALID
- 2012.10.1137/11082796X is INVALID
- 10.​1152/​ajpheart.​00668.​2011 is INVALID
- 10.1109/EMBC.2015 is INVALID

[meg-simula]

@fcooper8472 Could you take a look at the references missing DOIs as reported by Whedon above?

[meg-simula]

Also @fcooper8472, please consider the following minor issue in the paper:
a) The python post-processing terminal command spills over the page, please fix.

[fcooper8472]

@whedon generate pdf

[fcooper8472]

@whedon check references

[whedon]

PDF failed to compile for issue #1848 with the following error:

Can't find any papers to compile :-(

[whedon]

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
- 10.1109/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
- 10.1016/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]

@meg-simula I have fixed the DOIs and the formatting issue.

No idea why whedon can't generate a new pdf - I only changed a single line in the paper.md - it's definitely still there! (And the references were found and checked fine!)

[meg-simula]

@whedon generate pdf

[meg-simula]

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

[fcooper8472]

@whedon generate pdf

[whedon]

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

[fcooper8472]

@meg-simula looks to be OK this morning!

[meg-simula]

Lovely, thanks @fcooper8472.

[meg-simula]

@whedon check references

[meg-simula]

@whedon generate pdf

[whedon]

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

[meg-simula]

@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]

@whedon check references

[whedon]

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]

@whedon generate pdf

[whedon]

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

[fcooper8472]

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

[fcooper8472]

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

[meg-simula]

@whedon generate pdf

[meg-simula]

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

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

[whedon]

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

[meg-simula]

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]

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]

@whedon generate pdf

[whedon]

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

[meg-simula]

Looks good to me, thanks @fcooper8472!

[fcooper8472]

@meg-simula the metadata is correct now.

[meg-simula]

@whedon set 10.5281/zenodo.3702736 as archive

[whedon]

OK. 10.5281/zenodo.3702736 is the archive.

[meg-simula]

@whedon set release_2019.1 as version

[whedon]

OK. release_2019.1 is the version.

[meg-simula]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

: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]

👋 @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]

@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]

@whedon generate pdf

[whedon]

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

[danielskatz]

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]

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]

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]

@whedon generate pdf

[whedon]

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

[meg-simula]

/ooo March 12 until March 27

[ooo[bot]]

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

[finsberg]

/ooo March 12 until March 27

[ooo[bot]]

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

[fcooper8472]

@whedon generate pdf

[whedon]

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

[fcooper8472]

@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]

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

[fcooper8472]

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.

[danielskatz]

Thanks - please let me know when that is done

[danielskatz]

@whedon set 10.5281/zenodo.3708497 as archive

[whedon]

OK. 10.5281/zenodo.3708497 is the archive.

[mirams]

@danielskatz I have updated the Zenodo metadata to match the paper title and authors.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

: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/1369

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1369, 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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1370
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01848
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[danielskatz]

Thanks to @finsberg & @IgorBaratta for reviewing!
And to @meg-simula for editing!

[ooo[bot]]

:wave: Hey @danielskatz...

Letting you know, @finsberg is currently OOO until Friday, March 27th 2020. :heart:

[ooo[bot]]

:wave: Hey @danielskatz...

Letting you know, @meg-simula is currently OOO until Friday, March 27th 2020. :heart:

[danielskatz]

Congratulations to @fcooper8472!
And again, apologies for your getting penalized with some extra work as we changed our guidelines.

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01848/status.svg)](https://doi.org/10.21105/joss.01848)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01848">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01848/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01848/status.svg
   :target: https://doi.org/10.21105/joss.01848

This is how it will look in your documentation:

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