Dear Dr. Gameiro,

Thank you very much for submitting your manuscript "Rational design of complex phenotype via network models" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board, but in this case only one independent reviewer has submitted a written review. We are taking the unusual step of proceeding with an initial decision on the basis of a single review in order to expedite the process during a time when reviewing resources are stretched and because the review itself is from a known expert in this field who has chosen to reveal his identity. The reviewer has done an excellent job of highlighting the significance and potential interest of this submission, and I concur with his evaluation. He has, however, also brought up a number of important issues that should be addressed in a revised manuscript. Please pay particular attention to his suggestions for improving the presentation of the methodology, which in both his opinion and mine is not currently in a form that it can be understood by a general audience. I found his suggestions for a tutorial style presentation to be very appealing. In light of the reviews and these considerations, we would like to invite the resubmission of a significantly-revised version that takes them into account.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to additional reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

James R. Faeder

Associate Editor

PLOS Computational Biology

Mona Singh

Methods Editor

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: Attached

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Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

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.

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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: Yes: Leon Glass

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, PLOS recommends that you deposit laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions, please see http://journals.plos.org/compbiol/s/submission-guidelines#loc-materials-and-methods

Attachments

Attachment

Submitted filename: Mischaikow.pdf

Dear Dr. Gameiro,

Thank you very much for submitting your manuscript "Rational design of complex phenotype via network models" 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 an independent reviewer. The reviewer appreciated the attention to an important topic and your replies to his previous review. Based on the review, we plan to accept this manuscript for publication, but would ask that you consider modifying the manuscript according to the reviewer's recommendations. Once we receive your reply and revised manuscript we will proceed quickly to process your manuscript for publication.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

James R. Faeder

Associate Editor

PLOS Computational Biology

Mona Singh

Methods Editor

PLOS Computational Biology

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A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

[LINK]

Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #1: In this revised version, the authors have made several changes, primarily in Sections

4.1-4.4. The changes make the manuscript somewhat more self-contained though it will

still be rough going for the person who does not know this technique but would like to

understand how it can be used. I still have some issues with the revised manuscript.

1. Symmetry. Networks 1-4 all have the same state transition diagrams (an

example of which is now given in Fig. 6) and all have the same hysteresis scores

in Fig. 8. From a computational perspective, and a dynamics perspective these

seem to be the same network as classified by the symmetry under the 3-cube as

demonstrated initially in Glass (1975), Edwards and Glass (2000). The added

sentence in response to my earlier comment should be expanded to clarify so

that a clever reader who recognizes that the symmetry may be relevant would

realize that some aspects of symmetry in these networks have already been

investigated.

2. Multiple inputs to a node. The state transition diagrams will be very different

depending on how multiple inputs combine (e.g. for two positive inputs as an

AND or an OR function). Are the hysteresis scores independent of the type of

interaction? This would seem highly unlikely to me, but a clear statement about

the dependence of the hysteresis score on the implied function for multiple inputs

would be useful.

3. Dynamics of natural systems with hysteresis. As I pointed out in my first review,

there are several earlier papers identifying natural and man-made networks with

multiple steady states and hysteresis. It is great that the authors are collaborating

with synthetic biologists to generate robust networks based on their insights, but I

still believe that the authors should at least mention some of the earlier papers

that have demonstrated or analyzed multiple steady states and indicate how they

fit into the current scheme. For example, the current work would be strengthened

if the circuits for plant development from Elena Alvarez-Buylla’s group conformed

to their robust networks. If the networks did not conform, the authors could

predict that additional control elements should be present (a prediction almost

certain to be correct!).

4. Robustness. The authors now mention two earlier papers that deal with

robustness, but do not give a clear indication of how the current formulation

relates to the earlier ones. Although the current paper deals with hysteresis,

presumably it could also deal with limit cycle dynamics. If so, would the earlier

concept of stable attracting paths in the state transition diagram leading to robust

dynamics match the formulation of the current work?

The authors should correct the spelling of Kauffman’s name. Also, missing Section

numbers need to be corrected.

It would not be too difficult to implement any changes in response to these comments

and I would leave it up to the authors whether they wish to do so, or not.

Leon Glass

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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

**********

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: Yes: Leon Glass

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

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.

If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Dr. Gameiro,

We are pleased to inform you that your manuscript 'Rational design of complex phenotype via network models' 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,

James R. Faeder

Associate Editor

PLOS Computational Biology

Mona Singh

Methods Editor

PLOS Computational Biology

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