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[REVIEW]: Chaste: Cancer, Heart and Soft Tissue Environment #1848

Closed whedon closed 4 years ago

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

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @IgorBaratta

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @SirSharpest

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 5 years ago

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:

watching

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

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 commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

meg-simula commented 5 years ago

@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 commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

fcooper8472 commented 5 years ago

@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 commented 5 years ago

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.

AoifeHughes commented 5 years ago

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 commented 5 years ago

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:

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 commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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

finsberg commented 5 years ago

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 commented 5 years ago

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).

AoifeHughes commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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

meg-simula commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

@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 commented 4 years ago

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 commented 4 years ago

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

meg-simula commented 4 years ago

@whedon commands

whedon commented 4 years ago

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 commented 4 years ago

@whedon add @IgorBaratta as reviewer

whedon commented 4 years ago

OK, @IgorBaratta is now a reviewer

meg-simula commented 4 years ago

@whedon remove @SirSharpest as reviewer

whedon commented 4 years ago

OK, @SirSharpest is no longer a reviewer

meg-simula commented 4 years ago

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

whedon commented 4 years ago

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

IgorBaratta commented 4 years ago

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

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

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 commented 4 years ago

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

fcooper8472 commented 4 years ago

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

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

@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 commented 4 years ago

@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 commented 4 years ago

@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 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

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/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 commented 4 years ago

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

meg-simula commented 4 years ago

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 commented 4 years ago

@whedon generate pdf

fcooper8472 commented 4 years ago

@whedon check references

whedon commented 4 years ago

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

Can't find any papers to compile :-(

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
- 10.1109/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 commented 4 years ago

@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!)