Dear Dr. Swetnam,

Thank you very much for submitting your manuscript "CyVerse: Cyberinfrastructure for Open Science" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Thank you for your submission, and my apologies that it has been difficult to secure reviews. Based on the review comments and my own reading of the text, I am content to recommend this for minor revisions, with amendments as suggested by Reviewer 1.

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Dan Stowell

Academic Editor

PLOS Computational Biology

Jason Papin

Editor-in-Chief

PLOS Computational Biology

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Thank you for your submission, and my apologies that it has been difficult to secure reviews. Based on the review comments and my own reading of the text, I am content to recommend this for minor revisions, with amendments as suggested by Reviewer 1.

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Comments and significant suggested edits

1) I commend the authors and their team for providing a valuable resource to the scientific community, and for their dedication to enabling its use through innovation and training.

2) The web re-design (not new I know) is an attractive improvement in form and functionality, especially the DE.

3) Supplemental - Are the metadata AVU triplets indexed for searching? If so, this would be good to include. If not, this is necessary to address specifically. Also, where do these metadata 'fit' in the description of metadata on page 20 of the supplemental material?

4) Supplemental - Page 15 - Data Commons - What is the process for curating datasets? Is there expert curation? Who performs this and how are curations quality controlled? A brief explanation would be helpful.

5) Is there a process to quality control public Apps supplied by users?

6) Fig S10 - What is 'porklock'? Is a citation needed? As written this is mysteriously uninformative.

7) Line 80 - Deployment in a matter of hours is only possible with the necessary experience and expertise. Could this statement be reworded to clarify that fast deployment does require necessary knowledge and skills and is not an 'out of the box' possibility for the majority of users? For instance, not all users can access all layers of the 'cake' stack as specified in the following section.

8) Line 147 - Are there any data (counts) available to include for the number of workshop attendees who used CyVerse as part of successful proposals and the other examples listed?

9) Scientific Impacts - an impressive section!

Minor suggested edits

1) Supplemental - Page 9 - User Portal - It may be good to specify that users must request and be approved to be powered by CyVerse. As written, it appears as though the choice is entirely in the hands of the users.

2) Line 38 - 'compliments' can work, but 'components' may be easier for a broad audience to understand

3) Line 51 - fame is less of a factor than capability - suggest changing to say something like, '...best equipped and well funded...'

4) Line 96 - Should 'CyVerse' be possessive here? 'CyVerse's featured software stack...'?

5) Line 155 - perhaps just say 'outside' or 'beyond' life sciences?

6) Be consistent with use of 'R1' and 'Research 1'

7) Supplemental - Page 20 - How challenges are met - Should this section be moved to the main manuscript? Especially the first paragraph. The last 2 paragraphs appear a little awkwardly fitted in.

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Reviewer #1: Yes

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Reviewer #1: No

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Review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.

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Dear Dr. Swetnam,

We are pleased to inform you that your manuscript 'CyVerse: Cyberinfrastructure for Open Science' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Jason Papin

Editor-in-Chief

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: This is an excellent manuscript describing a valuable resource. I have no other recommendations.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data and code should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No