Dear Professor Jiranek,

Thank you very much for submitting your manuscript "An off-lattice discrete model to characterise filamentous yeast colony morphology" 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.

Please ensure you address the main points raised by the referees, especially the major concerns of reviewer 1 on the lack of modelling nutrients.

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,

Attila Csikász-Nagy

Academic Editor

PLOS Computational Biology

Daniel Beard

Section 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:

Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #1: Please see attached document.

Reviewer #2: The paper is interesting the described methods are elegant. It communicates the motivation of the work, the applied methods and the results clearly. The text is also well written.

Questions, comments:

- What were the reasons behind using the two mentioned yeast strains?

- Figure 1.3: What were the experimental conditions (strain, nutrient level) of the colonies shown at the image?

- Figure 2.1 shows 5 budding sites at the end of the cell, while line 122 mentions 3 sites. Which value was used in the model?

- Can filaments cross each other in the model? Would it possible or useful to extend the model into 3D?

- What were the typical cell numbers in the simulations?

- What kinds of computational resources were used for the presented work? How much time a typical does a typical simulation required?

- Is there any cell death in the model? How could it influence the results?

- Line 222 states: “we only counted a quarter of the colony’s branches”. Could you elaborate on this (e.g.: which quarter was counted)?

- How were the initial values of the parameters defined at the parameter inference?

- Figure 3.1: Were the differences between the showed metrics statistically significant?

- Could be any difference in the cell sizes, shapes or cell growths (division intensities) between the studied strains? - - Could these influence the differences between their colonies (on top of the studied parameters)?

- Link for the supporting materials is missing from the “Supporting Material” section. (It appears at the end of the manuscript.)

- Most of the references are older. Are there more state of the art publications on the topic?

Minor suggestions:

- Line 3: Yeasts (typo)

- Line 144: Figure1.3g

- IB is both called branch count and sub-branch index

- Line 284: means, deviations, statistics

- Figure 3.1: concentrations, strains

- Figure 3.2: statistics, areas

- Line 328: is in the

- Line 376: Credit (capital letters)

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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: None

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: No

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.

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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.

Attachments

Attachment

Submitted filename: review-PCOMPBIOL-D-24-01245.pdf

Dear Professor Jiranek,

Thank you very much for submitting your manuscript "An off-lattice discrete model to characterise filamentous yeast colony morphology" 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.

Referee 1 still have concerns mainly about the way nutrient levels are handled in the model. Please address these concerns in a revised version!

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,

Attila Csikász-Nagy

Academic Editor

PLOS Computational Biology

Daniel Beard

Section Editor

PLOS Computational Biology

***********************

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:

Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #1: I thank the authors for responding to each of my original comments. While I do find many of the responses reasonable, I feel that none of my original concerns were actually properly addressed (but rather, rebutted). The comments, in particular, that I feel need to be addressed are as follows.

1. The authors claim very early on that "initial nutrient concentration" among other features, was a key determining feature that determines the shape and structure of the colony, however they do not explicitly model nutrients. They do have experimental information that could give insight into this (two experiments with the same strain, with a 10-fold difference in nutrient concentration), with which they could do a statistical test (for instance) to determine if key parameters are different. How do the authors reconcile the 10-fold difference in nutrient concentration with similar values of n^* (as per the posterior distributions in Fig. 8)? Presumably, the authors could, for instance, use a fit to AWRI 50uM data to test their hypothesis that nutrient concentration is proportional to cell-count to predict AWRI 500uM data.

In short, I am of the view that the authors cannot state any conclusions relating to nutrient concentration without either: (1) performing some kind of statistical demonstratation to discuss how n^* is different between 50uM and 500uM measurements; (2) performing some kind of validation for the nutrient-cell count assumption; or (3) explicitly modelling the nutrient concentration.

2. I accept that ABC has known convergence issues, however the parameter space is relatively small (only five parameters). For example, ABC MCMC or even ABC SMC can give good results even for relatively uninformative priors. Investigating the effect of prior choice on at least one of the conditions would significantly strengthen the paper.

3. (relatively minor) In response to original minor comment 3, the authors state that they initialise the colonies from a single cell. Is this actually how the experiments are initiated? This could significantly impact the effect of the nutrient-cell count model, since a colony that is initiated with a set nutrient count at a size that is not zero would have additional biomass not accounted for by nutrient consumption.

Reviewer #2: Thank you for your answers and your clarifications in the manuscript. I accept them.

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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

Reviewer #2: 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: No

Reviewer #2: No

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 Professor Jiranek,

We are pleased to inform you that your manuscript 'An off-lattice discrete model to characterise filamentous yeast colony morphology' 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,

Attila Csikász-Nagy

Academic Editor

PLOS Computational Biology

Daniel Beard

Section Editor

PLOS Computational Biology

Feilim Mac Gabhann

Editor-in-Chief

PLOS Computational Biology

Jason Papin

Editor-in-Chief

PLOS Computational Biology

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