reply2.txt

Title: Reversibility of Chemical Reactions
Reviewer: Ulrik Pagh Schultz

The paper is massively improved from the previous version, and the response to the authors shows that the comments from the reviewers have been carefully addressed. From a technical point of view the content seems fine, and the new structure and content improves significantly on the presentation. Nevertheless some a few issues still remain with writing and structuring of the paper, that must be resolved before the paper is in a publishable state. The comments follow below. Most of the comments concern typos but some rewriting/restructuring still remains to be done, in particular there is a very strong encouragement to add a new and separate Conclusion section in addition to the text that is already there (see comment below).

*** Higher-level editorial comments

Section 1. The whole block of text "Such biological processes require ... interesting examples of out-of-causal-order reversibility." was restructured in response to reviewer comments, but it however *still* detracts from the main flow of the text, and is thus confusing to the reader. One option would be to put this whole piece of text in a footnote (since it provides complementary information that can be ignored while reading). Otherwise delete it (as the text works fine without it).

SK> this has been rewritten

Section 1. The typography of the "Related Work" \subsubsection or \paragraph (not sure which it is) isn't working to tell the reader that the whole set of paragraphs that follow all belong to related work. Consider having a whole separate \section "Related Work" that comes after the "Paper organization" paragraph, or to use a \subsection* or similar that more clearly shows what is going on.

SK> I made these into subsections.

Section 1. The two paragraphs "Petri nets (PNs)..." and "Classical PNs and their extensions" feel a bit repetitive. The second paragraph does not seem like a continuation of the first, but feel like it was written independently and for this reason the two paragraphs come across as two independent discussion of the same area (petri nets).

A&K> We have rewritten slightly to make the transition smoother. One point that arises is whether a reference to the Bonding Calculus should be made in this section. There are references to CCB and RPNs (including some related work) but none to the Bonding Calculus.

Section 3.1. The figures 2,3,4,5 are all on one page. The vertical spacing however seems to be broken, as they flow together and it's hard to see where one figure stops and another continues. Could you perhaps move one or more of the figures to a separate page, to make it more readable? Moreover, in the caption of Fig. 4, part of the condition is apparently written in plain English i.e. "The condition (*) is 1. ..., and 2. ..." - why the use of plain English here as opposed to something more formal? Consider writing it formally instead, as it is a little hard to read, but perhaps more vertical space would have helped.

SK> I have rearranged the figures to be on separate pages and I have reworded the conditions. 

Section 3.3. The start of this section is not parallel with the other two subsections, as it gets into much more details about RPNs that in the parallel subsections 3.1 and 3.2 did because their background mateiral had already been covered. Indeed, there is a signifiant amount of related work here that really should have gone into the "Related Work" part of the paper, again to provide a clean and quick start of the subsection similar to the other two subsections.


A&K> We have moved discussion of related work to Section 1.2.

Section 4. This is not a conclusion in the usual sense. Normally a conclusion would sum up what we've read and provide perspective. There is far too much going on here. The last paragraph that introduces new information about software tools is nice but definitely does not have a concluding feel to it! I would strongly suggest to rename this section to "Analysis" or something similar and then add a new, short one-paragraph conclusion section that sums up the main results of the paper (rather than producing them, which is essentially what the current Section 4 is doing).


A&K> We propose to call the section "Evaluation".

*** Minor typos/fixes

General:

Nitpicking, but please consider to avoid using references as nouns. For example, try reading the text "The out-of-causal-order reversibility was first addressed in CCSK extended with controller processes in [28], and in the context of reversible event structures first in [27] and then in [26, 37]." aloud. The use of "[28]" is not ideal: contrast what you just read with "The out-of-causal-order reversibility was first addressed by Phillips et al. in CCSK extended with controller processes [28], and in the context of reversible..."

SK> I've tried to catch these all.

Author names:

Some author names include their Orcid IDs but not all, and the Orcid IDs take up a significant amound of visual space. Consider having Orcid IDs for all authors or none, and too use a less visually obtrusive display format see e.g. https://orcid.org/content/journal-article-display-guidelines

SK> The \orcidID{} notation is part of the Springer template, and it will probably be translated into links automatically (see other lncs papers for comparison). In any case, we should not come up with an individual solution per paper. We have therefore left the ORCIDS as they are to be dealt with by the publisher.

A&K plus IU > We have added our Orcid IDs.

Abstract:

"In this chapter we give an overview of some techniques developed for the modelling" -> "In this chapter we give an overview of techniques for modelling"

"This exercise demonstrates that the formalisms," -> "This exercise demonstrates that these formalisms,"

All> Changed, also changed everything else below. Additioanlly, there are some comments as well.

Section 1:

"It is a chemical reaction involving small molecules, so is different from biological" -> "It is a chemical reaction involving small molecules, so it is different from biological"

The two paragraphs "Process calculi, originally designed" and "Another way to model biochemical reactions" obviously belong together, why not make them one paragraph?

"The presented here CCB ... of atoms reactions between them ...": bad grammar, rephrase

"neuronal processes" -?-> "neural processes"

"modelcan": missing space

"from single molecules, to cells, to multicellular aggregations." -> "from single molecules, to cells, and to multicellular aggregations."

"been used to describe different systems" -?-> "been used to describe different chemical systems" (would be more precise this way)

A&K> Fixed

"briefly discuss software support for the formalisms." -> "briefly discuss software support for the three formalisms."

Section 2:

Consider cutting "The" from the title, i.e., make it \section{Autoprotolysis of Water}

"and since it has some interesting aspects to represent." -> "and has some interesting aspects to be represented."

"more than one bonds" -> "more than one bond"

Section 3.1:

"details can be fond" -> "details can be found"

Section 3.2:

"used in Bonding Calculus" -> "used in the Bonding Calculus", similar corrections multiple places, in general do this in the text (but not the title): whenever you write "Bonding Calculus" you should have "the" in front (as you do in some places but not all).

SK> I tried to find them all, sorry if I missed any.

"Just like in BNGL": what is BNGL? Put a reference.

> BNGL is mentioned in Related Work, and we have provided the reference once more for clarity.

"in bonding calculus" -> "in the Bonding Calculus"

"model the creation and breaking of the covalent bonds" -> "model the creation and breaking of covalent bonds"

The one-liner paragraph "The operational semantics of the Bonding Calculus..." and "The rules (CREATE1) and (CREATE2)..." should be merged into a single paragraph.

Section 3.3:

"a RPN" -> "an RPN" multiple places in the paper (it's a phonetic rule, and since you when you read it aloud "RPN" starts with a wovel sound, it's "an", similar to e.g. "an FFT" and so on).

A&K> Actually we do not mean RPN as an initialism but as an abbreviation to be read as "reversing Petri nets" (in the same way as PN is pronounced as "Petri net" or H as "hydrogen"). We have clarified this when the abbreviation is introduced.

"we need to introduce some notations." -> "we need to introduce some notation."

"Note that in the sequel": what sequel, what do you mean here? Rewrite.

A&K> We have fixed this.

Section 4:

"which can be used successfully to model" -> "which can be used to model"

"atoms and reactions such as, for example, involving" -> "atoms and reactions, for example involving"

The paragraph "In CCB, we can actually distinguish" directly continues the text from the previous paragraph, continue merging the two paragraphs to increase readability.

The sentence "Reversing Petri Nets are Petri net structures" is too long, I can't read it. Rewrite.

A&K> Fixed

"where where" -> "where"

"The other criterion": what was the first criterion? Rephrase/clarify.

"for this type of reactions" -> "for this type of reaction"