[REVIEW]: FrESCO: Framework for Exploring Scalable Computational Oncology #5345

editorialbot · 2023-04-06T03:51:06Z

Submitting author: @aspannaus (Adam Spannaus)
Repository: https://github.com/DOE-NCI-MOSSAIC/FrESCO
Branch with paper.md (empty if default branch): JOSS
Version: v0.2.4
Editor: @jmschrei
Reviewers: @gabeerion, @anupamajha1
Archive: 10.5281/zenodo.8325993

Status

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Markdown: [![status](https://joss.theoj.org/papers/8d4ad516cb5201cb643ef46d22067692/status.svg)](https://joss.theoj.org/papers/8d4ad516cb5201cb643ef46d22067692)

Reviewers and authors:

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Reviewer instructions & questions

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

Checklists

📝 Checklist for @gabeerion

📝 Checklist for @anupamajha1

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-04-06T03:51:07Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2023-04-06T03:51:20Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.49 s (57.6 files/s, 12989.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18           1134           1133           3432
Markdown                         2             35              0            212
TeX                              2             41             36            162
YAML                             3             12             16            103
JSON                             3              0              0              3
-------------------------------------------------------------------------------
SUM:                            28           1222           1185           3912
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-04-06T03:51:25Z

Wordcount for paper.md is 842

editorialbot · 2023-04-06T03:52:38Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

jmschrei · 2023-04-06T03:56:11Z

Howdy @gabeerion and @SimonBiggs!

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
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Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

SimonBiggs · 2023-04-06T03:57:20Z

Review checklist for @SimonBiggs

Conflict of interest

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

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 https://code.ornl.gov/mossaic/fresco?
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 (@aspannaus) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
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?

editorialbot · 2023-04-06T03:58:41Z

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

OK DOIs

- None

MISSING DOIs

- Errored finding suggestions for "Combating Label Noise in Deep Learning using Abste...", please try later
- 10.1371/journal.pone.0232840 may be a valid DOI for title: Using case-level context to classify cancer pathology reports
- Errored finding suggestions for "Automatic extraction of cancer registry reportable...", please try later
- Errored finding suggestions for "PyTorch: An Imperative Style, High-Performance Dee...", please try later
- Errored finding suggestions for "Pyhealth: A python library for health predictive m...", please try later
- 10.21105/joss.04943 may be a valid DOI for title: FuseMedML: a framework for accelerated discovery in machine learning based biomedicine
- Errored finding suggestions for "Med7: A transferable clinical natural language pro...", please try later
- Errored finding suggestions for "Clinical deployment environments: Five pillars of ...", please try later
- Errored finding suggestions for "ECP-Candle", please try later

INVALID DOIs

- https://doi.org/10.1016/j.artmed.2019.101726 is INVALID because of 'https://doi.org/' prefix

gabeerion · 2023-04-09T07:55:11Z

Review checklist for @gabeerion

Conflict of interest

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

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 https://code.ornl.gov/mossaic/fresco?
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 (@aspannaus) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
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?

jmschrei · 2023-05-03T16:23:58Z

Hi @SimonBiggs @gabeerion, how are the reviews coming?

SimonBiggs · 2023-05-04T03:12:50Z

Hi @jmschrei,

Not yet begun. I'm hoping to be able to earmark some time next week.

gabeerion · 2023-05-06T22:05:07Z

@jmschrei actively working on my review over last week and the coming one, thanks!

SimonBiggs · 2023-05-10T06:14:00Z

Hi @aspannaus,

I was hoping to be able to report an issue, however your issue list is locked down in such a way that I cannot create an account through the web interface.

Would it be possible for you to make a fork of this repository on GitHub where I can access the code without needing an ornl.gov account?

aspannaus · 2023-05-10T14:18:28Z

Hi @SimonBiggs,

Let me take a look at the permissions. Someone outside of the organization was able to access the repo earlier this week, so I'm not sure what the issue is. I'll also look into the possibility of creating an open fork on Github. Thanks

I created a fork at https://code.ornl.gov/3t6/fresco that should be completely open. Check it out and let me know if you encounter any issues.

SimonBiggs · 2023-05-10T22:42:25Z

Hi @aspannaus,

I can confirm that cloning is now working. But I cannot raise an issue there either:

aspannaus · 2023-05-11T13:52:20Z

Hi @SimonBiggs,

Apologies for the continued issue. We've got an internal ticket filed to sort this out; I'll post here once I have some resolution.

Update: we're going to move the repo over to GitHub, but this won't be instantaneous. I'll update here with the new url. Thanks

aspannaus · 2023-05-15T14:43:01Z

Hi @SimonBiggs, @gabeerion and @jmschrei,

We've moved the repo over to: https://github.com/DOE-NCI-MOSSAIC/FrESCO/tree/JOSS to address the issue noted above about not being able to create a git issue without registering.

Thanks again for your patience.

jmschrei · 2023-05-20T22:37:42Z

@SimonBiggs @gabeerion how are the reviews coming?

SimonBiggs · 2023-05-21T05:46:56Z

@jmschrei, just waiting on the following before I continue:

We will finish internal testing with the reorganization to make the repo pip-installable and push the changes early next week.

DOE-NCI-MOSSAIC/FrESCO#1 (comment)

aspannaus · 2023-05-25T13:33:55Z

Just posting here for completeness, we updated the repository based on @gabeerion comments and suggestions.

https://github.com/DOE-NCI-MOSSAIC/FrESCO/issues/1#issuecomment-1561201091

SimonBiggs · 2023-06-05T23:30:35Z

Thanks @aspannaus,

I took a few small bites off the review this morning and have left two PRs on your repo for your review.

Cheers,
Simon

aspannaus · 2023-06-06T16:37:14Z

Hey @SimonBiggs,

Thanks for taking a look, we'll start working on the PRs.

aspannaus · 2023-06-26T16:52:38Z

Hi @SimonBiggs and @gabeerion,

Just checking in on the status of the review, if there's anything else you need from us.

Thanks!

gabeerion · 2023-06-26T17:09:21Z

Hi, so sorry for the delay! I appreciate the ping and will work on this again tomorrow. Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: aspannaus ***@***.***> Sent: Monday, June 26, 2023 12:52:48 PM To: openjournals/joss-reviews ***@***.***> Cc: Gabriel Erion ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [REVIEW]: FrESCO: Framework for Exploring Scalable Computational Oncology (Issue #5345) Hi @SimonBiggs<https://github.com/SimonBiggs> and @gabeerion<https://github.com/gabeerion>, Just checking in on the status of the review, if there's anything else you need from us. Thanks! — Reply to this email directly, view it on GitHub<#5345 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA2QE6PWCSUCUQ3WFDVAH33XNG46BANCNFSM6AAAAAAWU3YZIQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

aspannaus · 2023-08-28T12:32:39Z

@jmschrei, no worries. Glad to have it through and accepted. Thanks again for all the assistance!

Kevin-Mattheus-Moerman · 2023-09-04T10:56:03Z

@aspannaus I am the AEiC for this track and here to help with final steps. Apologies for the delay, I was out of the office for a bit.

I have checked your repository, the paper, this review, and the archive, and have a few points the need your attention:

I have just looked at archive link provided: https://doi.org/10.11578/dc.20230227.2. That link does not seem to archive the actual software. Can you clarify if you've archived the software (full content of your software repository)? This is what is required for JOSS.
In your paper's affiliations, please spell out USA as United States of America
It looks like you can add a DOI (https://doi.org/10.48550/arXiv.2211.02701) for the paper "MONAI: An open-source framework for deep learning in healthcare"
It looks like you can add a DOI (https://doi.org/10.48550/arXiv.2204.06604) for the paper "Ehrkit: A python natural language processing toolkit for electronic health record texts."
It looks like you can add a DOI (https://doi.org/10.48550/arXiv.2101.04209) for the paper "PyHealth: A Python Library for Health Predictive Models."

aspannaus · 2023-09-05T12:32:50Z

@editorialbot generate pdf

editorialbot · 2023-09-05T12:34:15Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

aspannaus · 2023-09-05T12:36:46Z

@editorialbot generate pdf

editorialbot · 2023-09-05T12:38:50Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

Kevin-Mattheus-Moerman · 2023-09-07T09:10:32Z

@aspannaus I see the DOIs seem fixed. However, are you also able to address the issue with the archiving link? ☝️

aspannaus · 2023-09-07T14:07:41Z

Hi @Kevin-Mattheus-Moerman, we are working on getting Zenodo connected to the repo and expect to have that completed by tomorrow. Thanks

aspannaus · 2023-09-07T15:07:26Z

Hi @Kevin-Mattheus-Moerman,

The archive link is here: https://zenodo.org/record/8325994. Let us know if there's anything else you need from us. Thanks!

Kevin-Mattheus-Moerman · 2023-09-10T07:41:05Z

@editorialbot set 10.5281/zenodo.8325993 as archive

editorialbot · 2023-09-10T07:41:07Z

Done! archive is now 10.5281/zenodo.8325993

Kevin-Mattheus-Moerman · 2023-09-10T07:42:26Z

Kevin-Mattheus-Moerman · 2023-09-10T07:44:39Z

@editorialbot set v0.2.4 as version

editorialbot · 2023-09-10T07:44:41Z

Done! version is now v0.2.4

Kevin-Mattheus-Moerman · 2023-09-10T07:46:37Z

@aspannaus thanks for posting that archive link. The above checkbox set ☝️ shows some remaining action items. In particular the authors listed, the title, and the license listed for the archive need to be amended. You can do this manually.

aspannaus · 2023-09-11T12:19:32Z

Hi @Kevin-Mattheus-Moerman , we've taken care of the above items. Let us know if you need anything else. Thanks again

Kevin-Mattheus-Moerman · 2023-09-11T12:34:00Z

@aspannaus nearly there. The archive title should match the paper title FrESCO: Framework for Exploring Scalable Computational Oncology, so please amend accordingly.

aspannaus · 2023-09-11T12:47:56Z

@Kevin-Mattheus-Moerman , thanks for catching that. I've amended the software archive title to match the manuscript title.

Kevin-Mattheus-Moerman · 2023-09-11T12:56:39Z

@aspannaus thanks. All looks good now.

Kevin-Mattheus-Moerman · 2023-09-11T12:56:44Z

@editorialbot accept

editorialbot · 2023-09-11T12:56:46Z

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

editorialbot · 2023-09-11T12:58:31Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Spannaus
  given-names: Adam
  orcid: "https://orcid.org/0000-0002-2521-3657"
- family-names: Gounley
  given-names: John
- family-names: Shekar
  given-names: Mayanka Chandra
- family-names: Fox
  given-names: Zachary R.
- family-names: Mohd-Yusof
  given-names: Jamaludin
- family-names: Schaefferkoetter
  given-names: Noah
- family-names: Hanson
  given-names: Heidi A.
contact:
- family-names: Spannaus
  given-names: Adam
  orcid: "https://orcid.org/0000-0002-2521-3657"
doi: 10.5281/zenodo.8325993
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Spannaus
    given-names: Adam
    orcid: "https://orcid.org/0000-0002-2521-3657"
  - family-names: Gounley
    given-names: John
  - family-names: Shekar
    given-names: Mayanka Chandra
  - family-names: Fox
    given-names: Zachary R.
  - family-names: Mohd-Yusof
    given-names: Jamaludin
  - family-names: Schaefferkoetter
    given-names: Noah
  - family-names: Hanson
    given-names: Heidi A.
  date-published: 2023-09-11
  doi: 10.21105/joss.05345
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5345
  title: "FrESCO: Framework for Exploring Scalable Computational
    Oncology"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05345"
  volume: 8
title: "FrESCO: Framework for Exploring Scalable Computational Oncology"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

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editorialbot · 2023-09-11T12:58:36Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-09-11T12:58:36Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05345 joss-papers#4546
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05345
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

aspannaus · 2023-09-11T13:08:09Z

Thanks to @Kevin-Mattheus-Moerman and @jmschrei for editorial assistance and @gabeerion @anupamajha1 for the constructive feedback and reviews.

Kevin-Mattheus-Moerman · 2023-09-11T13:29:43Z

@aspannaus congratulations on this publication!

Thanks for editing @jmschrei !

And a special thanks to the reviewers: @gabeerion, @anupamajha1 !!

editorialbot · 2023-09-11T13:29:45Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Apr 6, 2023

editorialbot assigned jmschrei Apr 6, 2023

editorialbot mentioned this issue Apr 6, 2023

[PRE REVIEW]: FrESCO: Framework for Exploring Scalable Computational Oncology #5274

Closed

editorialbot added accepted published Papers published in JOSS labels Sep 11, 2023

Kevin-Mattheus-Moerman closed this as completed Sep 11, 2023

[REVIEW]: FrESCO: Framework for Exploring Scalable Computational Oncology #5345

[REVIEW]: FrESCO: Framework for Exploring Scalable Computational Oncology #5345

Comments

editorialbot commented Apr 6, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Apr 6, 2023

editorialbot commented Apr 6, 2023

editorialbot commented Apr 6, 2023

editorialbot commented Apr 6, 2023

jmschrei commented Apr 6, 2023

SimonBiggs commented Apr 6, 2023 • edited

Review checklist for @SimonBiggs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented Apr 6, 2023

gabeerion commented Apr 9, 2023 • edited

Review checklist for @gabeerion

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jmschrei commented May 3, 2023

SimonBiggs commented May 4, 2023

gabeerion commented May 6, 2023

SimonBiggs commented May 10, 2023

aspannaus commented May 10, 2023 • edited

SimonBiggs commented May 10, 2023

aspannaus commented May 11, 2023 • edited

aspannaus commented May 15, 2023

jmschrei commented May 20, 2023 • edited

SimonBiggs commented May 21, 2023

aspannaus commented May 25, 2023

SimonBiggs commented Jun 5, 2023

aspannaus commented Jun 6, 2023

aspannaus commented Jun 26, 2023

gabeerion commented Jun 26, 2023 via email

aspannaus commented Aug 28, 2023

Kevin-Mattheus-Moerman commented Sep 4, 2023 • edited

aspannaus commented Sep 5, 2023

editorialbot commented Sep 5, 2023

aspannaus commented Sep 5, 2023

editorialbot commented Sep 5, 2023

Kevin-Mattheus-Moerman commented Sep 7, 2023

aspannaus commented Sep 7, 2023

aspannaus commented Sep 7, 2023

Kevin-Mattheus-Moerman commented Sep 10, 2023

editorialbot commented Sep 10, 2023

Kevin-Mattheus-Moerman commented Sep 10, 2023 • edited

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Kevin-Mattheus-Moerman commented Sep 10, 2023

editorialbot commented Sep 10, 2023

Kevin-Mattheus-Moerman commented Sep 10, 2023

aspannaus commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023 • edited

aspannaus commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

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aspannaus commented Sep 11, 2023

Kevin-Mattheus-Moerman commented Sep 11, 2023

editorialbot commented Sep 11, 2023

editorialbot commented Apr 6, 2023 •

edited

SimonBiggs commented Apr 6, 2023 •

edited

gabeerion commented Apr 9, 2023 •

edited

aspannaus commented May 10, 2023 •

edited

aspannaus commented May 11, 2023 •

edited

jmschrei commented May 20, 2023 •

edited

Kevin-Mattheus-Moerman commented Sep 4, 2023 •

edited

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edited

Kevin-Mattheus-Moerman commented Sep 11, 2023 •

edited