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[REVIEW]: SCONE: Open Source Software for Predictive Simulation of Biological Motion #1421

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @tgeijten (Thomas Geijtenbeek) Repository: https://github.com/opensim-org/SCONE Version: v1.0.0 Editor: @Kevin-Mattheus-Moerman Reviewer: @modenaxe, @demotu Archive: 10.5281/zenodo.3245810

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Reviewers and authors:

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

Reviewer instructions & questions

@modenaxe & @demotu, 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 @Kevin-Mattheus-Moerman know.

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

Review checklist for @modenaxe

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @demotu

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. @modenaxe, it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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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:

Kevin-Mattheus-Moerman commented 5 years ago

@modenaxe, @demotu thanks for agreeing to review this work. Can you give an indication as to when you can finish this review work? Thanks again

modenaxe commented 5 years ago

@Kevin-Mattheus-Moerman I will try to do it by the end of next week, my apologies for the delay!

Kevin-Mattheus-Moerman commented 5 years ago

@modenaxe great thanks, let me know if you have questions.

modenaxe commented 5 years ago

@tgeijten I installed SCONE in the past and used it, but now, after I uninstalled it completely and reinstalled v1.0.0, I cannot run it after installation. I am prompted the following error:

image

I have already tried uninstalling again, removing all installation files and resources, restarting the machine and reinstalling but it doesn't seem to work, same error that I have reported above. I have already check if the issue comes from the antivirus blocking the executable, but it doesn't seem so. Any idea on what could be the cause and how to fix it? My computer runs Windows 10 Pro (64-bit), let me know if you need more details of my system.

tgeijten commented 5 years ago

@modenaxe sorry for the trouble! It seems you have an old configuration file that's no longer valid. You can delete to following folder to reset the configuration:

C:\Users\<UserName>\AppData\Local\SCONE

After that, everything should work fine.

modenaxe commented 5 years ago

that worked, thank you!

modenaxe commented 5 years ago

First of all, I want to congratulate @tgeijten for the quality of this software. Graphical interface and visualisation window in particular are truly remarkable for a research tool. I think that SCONE is an ambitious project with huge potential and creating the conditions for interested researchers of learning how to use it will be of paramount importance for its long-term success.

Software paper

A statement of need

While the motivation for SCONE is well explained, and numerous examples of use are mentioned, the target audience seems very broad in scope, i.e. the paper mentions researchers interested in biological movement. As explained in more details in the Documentation comments, the SCONE user is assumed to be familiar with advanced concepts in order to build his/her own scenarios, and this already stratifies users, in a sense. I think that the target audience could be better identified specifying their intended level of computational skills, for example. Multiple typologies of users could also be identified, e.g. researchers in the field of computational biomechanics and neuromechanics, interested in developing new SCONE scenarios, controllers etc. and other researchers focusing on more clinical applications, e.g. using existing scenarios to investigate interventions outcomes by modifying just the model etc.

Functionality

“The ability to simultaneously optimize both model and control parameters” is listed as one of the features of SCONE. What aspects of the model can be optimised? Muscle parameters or also the musculoskeletal geometry? I would list some example. What is the "thin API layer" needed to connect SCONE to a musculoskeletal simulation package doing? Implementing methods to read in models and input data from a specific specific format? I would add few words about this feature.

Documentation

A statement of need

The same comment about the software paper applies to the documentation, since the description of the software in the SCONE website is identical the submitted paper.

Functionality documentation

Considering the broad audience of the project, the users will have variable background in terms of computer skills. The documentation is currently minimal, probably sufficient for a developer but surely not enough for a clinician or someone not belonging to a computational field of research. Also, the concepts of "model, controller, objective, and optimization strategy" are given for granted in the documentation. I would include in the documentation appropriate links and references to help the users to gather at least some basic information about these main conceptual components of SCONE and specify how the documentation will grow in the future (if there is a plan in this respect). Also, in my opinion, few additional points could be added in the current documentation:

  1. It is not explained how to stop the simulations before the optimization is complete. Is it enough to use “Abort Optimizations”? Can the optimizations of the scenario be restarted from that point at another time?
  2. Can any OpenSim model be used in a scenario or just 2D models? Is there any guideline on how to build scenarios with new models?
  3. In my machine, the "Optimization Results" window does not update while I am optimizing the scenario, when the optimization is concluded or when I abort the optimization. It updates only if I restart the application, is this a bug or a feature to document?

Minor note: In the first tutorial, "File>open scenario" does not correspond to the software, where there is only “open”

Community guidelines

It seems that feature requests and bug tracking at the moment are done via github and not via the the simtk.org links provide on the SCONE website. Maybe it is worth including the github links together with simtk?

tgeijten commented 5 years ago

Thank you @modenaxe for the great feedback. I will add the suggested content to the documentation in the upcoming days. It is indeed our plan to develop a user base outside core developers, and feedback like this is essential to achieve that.

In general, the plan is to continuously improve the website and documentation based on user feedback. Funding has been secured to enable this until at least the end of 2020; we are currently investigating various options to extend funding after that.

The link to the issue tracker and the tutorial inconsistency have already been fixed.

Concerning your issue of the Optimization Results not updating, this is indeed a software issue (one I have not encountered before). It would be highly appreciated if you can report the issue so we can tackle it properly.

modenaxe commented 5 years ago

you're welcome @tgeijten! I realised I have another comment about functionality. Can SCONE be used also with just torque actuators acting at the joints? That would make the software of interest also for robotics. (This is more of a personal curiosity than a comment related to the software manuscript.)

tgeijten commented 5 years ago

Yes -- that's a good point. It can work with any actuator, although there is somewhat of a focus on neuromuscular control strategies. But it can definitely be used for robotics, especially assistive devices. I'll adapt the text to make that more clear.

tgeijten commented 5 years ago

@Kevin-Mattheus-Moerman do I need finish all suggested documentation updates first or can we proceed with the publication?

Kevin-Mattheus-Moerman commented 5 years ago

@tgeijten I would implement changes as soon as they are suggested. This keeps the reviewers happy and involved. So yeah start implementing those changes and alert the reviewers when you've done so.

tgeijten commented 5 years ago

@Kevin-Mattheus-Moerman thanks for the suggestion. @modenaxe, I have implemented all the changes suggested by you on the SCONE website -- I'm curious to hear if you agree. @demotu I am also eagerly awaiting your feedback!

tgeijten commented 5 years ago

@Kevin-Mattheus-Moerman we haven't heard from @demotu since the beginning of the review (May 1st). What to do?

Kevin-Mattheus-Moerman commented 5 years ago

@tgeijten I've e-mailed @demotu a reminder. If we do not hear back from him we'll proceed without his review.

Kevin-Mattheus-Moerman commented 5 years ago

@modenaxe thanks again for the awesome review efforts here! Can you review the changes implemented by @tgeijten?

modenaxe commented 5 years ago

Thanks @tgeijten, I am happy with the changes. In my opinion there are these few additional points to clarify to conclude the review process:

Other than this, I am ok with the rest, well done!

Kevin-Mattheus-Moerman commented 5 years ago

@tgeijten do you currently have community guidelines?

tgeijten commented 5 years ago

Thanks again @modenaxe for checking everything so thoroughly. I have addressed all points mentioned in your post, most of which have been added to the SCONE FAQ. In the paper, I replaced the 'features of SCONE' list with an 'intended users' list; I believe it works better that way, let me know if you agree.

Thanks @Kevin-Mattheus-Moerman for the suggestions and examples. I have added a CONTRIBUTING.md and updated the README.md, as well as some of the links on the website. I will consider adding a CODE_OF_CONDUCT.md later, even though I hope it won't be necessary ☺️

demotu commented 5 years ago

I installed SCONE and ran some examples and tutorials. The software runs perfect and the documentation is very well written. After the additions that have been made I don't have any critics to the paper. Congratulations for all the work.

modenaxe commented 5 years ago

@Kevin-Mattheus-Moerman for me the paper can be published. Congratulations @tgeijten!

Kevin-Mattheus-Moerman commented 5 years ago

@modenaxe great. Thanks a lot!

Kevin-Mattheus-Moerman commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- 10.1115/1.1392310 is OK
- 10.1371/journal.pcbi.1006223 is OK
- 10.1145/2508363.2508399 is OK

MISSING DOIs

- https://doi.org/10.1007/11007937_4 may be missing for title: The CMA evolution strategy: a comparing review

INVALID DOIs

- None
Kevin-Mattheus-Moerman 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:

Kevin-Mattheus-Moerman commented 5 years ago

@tgeijten can you check the following:

Kevin-Mattheus-Moerman 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:

Kevin-Mattheus-Moerman commented 5 years ago

@tgeijten looks like I broke both bullet lists. You need an enter between the text and the bullet lists, see https://github.com/opensim-org/SCONE/pull/64

Kevin-Mattheus-Moerman commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- 10.1115/1.1392310 is OK
- 10.1145/2508363.2508399 is OK

MISSING DOIs

- None

INVALID DOIs

- None
Kevin-Mattheus-Moerman 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:

Kevin-Mattheus-Moerman commented 5 years ago

@tgeijten at this point can you please do the following:

tgeijten 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:

tgeijten 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:

tgeijten commented 5 years ago

@whedon check references