-->PCOMPBIOL-D-26-01008

CRITERIA: A network decomposition and elementary flux mode translation-based tool for computing equilibria of biochemical systems

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: Review is uploaded as an attachment.

Reviewer #2: This is a referee report for "CRITERIA: A network decomposition and elementary flux mode translation-based tool for computing equilibria of biochemical systems" by Exequiel Jun V. Villejo, Aurelio A. de los Reyes V, Bryan S. Hernandez (PCOMPBIOL-D-26-01008).

This paper addresses the problem of computing steady state parametrizations for mass-action systems. In previous work, the authors utilized the network-based process of network translation to construct a MATLAB program called COMPILES. This work extends that program in a new direction by utilizing an elementary-flux-mode-based algorithm for determining network translations. The authors also swap the order of steady state determination and network recombination, leaving the algebraic step of steady state determination for the final step. The authors present a MATLAB program called CRITERIA which includes modules for both the translation and steady state parametrization portions of this workflow. The authors present documentation and a number of interesting worked out examples, including the EnvZ-OmpR signaling pathway and CRISPRi toggle switch.

The technical details utilized are mathematically sound and the program works incredibly well on all of the examples I checked. The program utilizes two recent theoretical advances which have not previously been implemented computationally in a widespread manner: Johnston and Burton's (2019) elementary flux mode approach to network translation, and Johnston, Muller, and Pantea's (2019) rational parametrization approach to weakly reversible networks. Implementing these theoretical formulas into a single computational package is highly non-trivial as it involves binary programming, convex polyhedral geometry, generalized inverses, and algebraic manipulation, among other steps. The computational test cases and worked-out examples presented in the paper are appropriate.

I expect that, once widely known, this program will be of profound benefit to the chemical reaction network and systems biology communities.

Suggestions/notes:

Line 11: "Analytically deriving equilibria, sometimes referred to as steady states, which often..." Remove "sometimes referred to as steady states"

Lines 55-56: "... since they characterize the long-term behavior of these systems." They "sometimes characterize" or "often characterize" the long-term behavior (limit cycles, chaos, and unbounded solutions are possible too)

Equation between lines 101-102: Perhaps a better example could be used here? I am not sure what the problem is here since XpY in the second equation could be substituted into the first equation and then you just have XD=0 or some equation for sigma1. If you had XD in the denominator or something like that, you would end up with a quadratic and the point might be more clear. That said, it seems like you are drawing from a real example, but I might suggest picking a more uncomfortable example than the one presented.

Line 61: "Recent research has focused on network-based approaches in DERIVERING analytic..." DELIVERING

Lines 97-98: "Second, there is a merging issue in COMPILES resulting TO interdependencies in the derived equilibrium parametrization." resulting in

Lines 163-164: "Several variations of the algorithm EXISTS." exist

Lines 241-242: "... while assigning to each of the source NODE of the edges..." nodes

Line 284: "It is WOTH noting here that all benchmark models are..." WORTH noting

Figure 1: "... the complex in parentheses is the kinetic complex associated IN that node." with

Line 324: "Now, it can be observed that..." "Now" is too colloquial for a journal paper. I would suggest simply "It can be observed that..."

Equation between lines 369 and 370: It is interesting and nonstandard that you allow conservation laws with negative coefficients. This also seems to be a feature of the computational package. This is particular interesting because there is an obvious second conservation law with positive coefficient for this example (Y+Yp+XpY+XDYp+XTYp=constant). Is it guaranteed that this will not lead to problems for positivity of the final parametrization? Is this just for show? At the very least, the possibility of conservation laws with negative coefficients should be noted in the paper.

Example in paragraph bound by lines 382 and 389: It is striking that you are able to show multistationarity as well as absolute concentration robustness for this example. To the best of my knowledge, this is the first time this has been shown for this model. This is very interesting!

General note on elementary flux modes: It should be noted that the elementary flux mode approach will only work if the coefficients of all the reactions in every elementary flux mode can be scaled to one. For example, the method will not work if one of the elementary flux modes has coefficients (1,2,1)---that is, one firing of the first reaction, two of the second, and one of the third are required to obtain stoichiometric balance. Since this limitation inherited from the underlying Johnston and Burton paper will be a limitation here as well, it should be mentioned.

Lines 433-434: "ACR suggests an intrinsic buffering mechanism wherein the EQULIBRIUM concentration of dCas9 remains..." equilibrium

Line 454: "... (see Fig 5 and its ACCOMPANIED discussion)." accompanying

Figure 4: "... thereby simplifying the analysis by focusing on smaller individual pieces rather than looking the network as a whole." rather than looking AT

Line 687: "In this subsection, we formally define the concept of a GCRN, which IS pioneered by..." was

Note on CRITERIA: The CRITERIA program works very well in the examples I checked. There are two notes I would like to make:

(1) It would be very nice if a user-friendly interface for implementing networks (like CRNTool or CoNtRol) could be developed. That said, the program is very well documented and I have no problem digging into the prebuilt MATLAB programs to change networks.

(2) For higher kinetic deficiency systems, the program does not seem to identify parameters generated from phantom edges (i.e., the sigmas) as free parameters. For example, when I run ModelL.m, it gives a parametrization including the parameter sigma1 but only says "Free parameters: XpY, Y".

Reviewer #3: Please refer to the attached PDF file for review comments.

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Attachments

Attachment

Submitted filename: PLOS review on CRITERIA paper.pdf

Attachment

Submitted filename: PCOMPBIOL-D-26-01008-review.pdf

Dear Dr. Hernandez,

We are pleased to inform you that your manuscript 'CRITERIA: A network decomposition and elementary flux mode translation-based tool for computing equilibria of biochemical systems' has been provisionally accepted for publication in PLOS Computational Biology.

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Best regards,

Sylvain Soliman

Academic Editor

PLOS Computational Biology

Pedro Mendes

Section Editor

PLOS Computational Biology

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Please take into account the remaining minor changes for the final version.

Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #1: Review is uploaded as an attachment.

Reviewer #2: The suggested edits have been made to my satisfaction.

Reviewer #3: The authors have adequately addressed all comments.

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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

Reviewer #3: Yes

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

Attachments

Attachment

Submitted filename: PLOS review for revised CRITERIA paper.pdf