Small comments on papers - Revision history

Murray at 01:19, 21 September 2018

2018-09-21T01:19:18Z

← Older revision		Revision as of 01:19, 21 September 2018
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	* When typesetting subscripts and superscripts, if the subscript is an abbreviation or shorthand for a word (or words), then it should be typeset as text, not math. So <math>x_\text{d}</math> (where 'd' is for 'desired'), but <math>x_i</math> if <math>i</math> is an index variable.		* When typesetting subscripts and superscripts, if the subscript is an abbreviation or shorthand for a word (or words), then it should be typeset as text, not math. So <math>x_\text{d}</math> (where 'd' is for 'desired'), but <math>x_i</math> if <math>i</math> is an index variable.

	* Then defining abbreviations, don't capitalize the terms unless they would ordinarily be capitalized. So "simultaneous localization and mapping (SLAM) algorithms", not "Simultaneous Localization and Mapping (SLAM) algorithms".		* Then defining abbreviations, don't capitalize the terms unless they would ordinarily be capitalized. So "simultaneous localization and mapping (SLAM) algorithms", not "Simultaneous Localization and Mapping (SLAM) algorithms" and "hidden Markov model (HMM)".

Murray at 20:43, 20 September 2018

2018-09-20T20:43:09Z

← Older revision		Revision as of 20:43, 20 September 2018
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	=== Other suggestions ===		=== Other suggestions ===

	* You should update the abstract so that it works as a “standalone” ~~submission to q-bio~~. ~~For example, remove~~ “in this paper” ~~(since there won’t be a paper in the q-bio submission)~~. ~~You might also want~~ to ~~make it~~ a ~~bit longer, again since this part will go to q-bio without~~ the ~~benefit~~ of the ~~full~~ paper.		* You should update the abstract so that it works as a “standalone” description of the results of a paper. Remove terms like “in this paper” that aren't really useful. Keep the introductory comments to a minimum (once sentence should be enough) and focus instead on summarizing the contents of the paper.

	* I’m not a fan of the word “surprisingly” (or “interestingly”) in papers. Let the reader determine whether they are surprised. So perhaps change “surprisingly simple expression” to “simple expressions” (note also the plural).		* I’m not a fan of the word “surprisingly” (or “interestingly”) in papers. Let the reader determine whether they are surprised. So perhaps change “surprisingly simple expression” to “simple expressions” (note also the plural).
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	* "an holistic” → “a holistic” (at least in American English)		* "an holistic” → “a holistic” (at least in American English)

	* "well behaved” → “well-behaved”		* "well behaved” → “well-behaved” (more generally, multi-word phrases that are "converted" to an adjective are usually hyphenated. So "it was well behaved" and "well-behaved response".

	* I am not a fan of acronyms except when they are used in common speech. I think when you talk about sequestration feedback systems you say “sequestration feedback systems” and not “ess eff bee”. Assuming that is correct, “SFB” → “sequestration feedback systems” (globally).		* I am not a fan of acronyms except when they are used in common speech. I think when you talk about sequestration feedback systems you say “sequestration feedback systems” and not “ess eff bee”. Assuming that is correct, “SFB” → “sequestration feedback systems” (globally).

	* "Section 2.2 and section 2.3 uses” → "Section 2.2 and Section 2.3 use” ~~(two changes)~~		* "Section 2.2 and section 2.3 uses” → "Section 2.2 and Section 2.3 use”: the term "Section" should be capitalized and make sure that your verb agrees with the subject properly.

	* Figure 1 is about 2X too big. As a guide, the text in a figure should be roughly the same font size as in the caption.		* Figure 1 is about 2X too big. As a guide, the text in a figure should be roughly the same font size as in the caption.

	* I would change the title of Figure 1 to “A sequestration feedback architecture” (it is not the only one). Capitalization, font type (bold), and punctuation are up to you, but be consistent (you aren’t right now).

	* As a general note on the introduction: it would be good to say more here about previous work on feedback circuits, fundamental limits, and how this work relates. Right now, it seems like there is only 1 paper that has ever done work in this area. Remember that some of the people whose work you are not bothering to cite as relevant prior effort are likely reviewers of your (eventual) paper.		* As a general note on the introduction: it would be good to say more here about previous work on feedback circuits, fundamental limits, and how this work relates. Right now, it seems like there is only 1 paper that has ever done work in this area. Remember that some of the people whose work you are not bothering to cite as relevant prior effort are likely reviewers of your (eventual) paper.
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	* There appear to be several places where latex is putting extra space after a period. You can fix those by using “.\ “ when the period is not the end of a sentence (eg, in “et al.” or “eqs.”). Another approach, if you want to avoid a line break, is to use a tie (~): “.~(\ref{eqref})”.		* There appear to be several places where latex is putting extra space after a period. You can fix those by using “.\ “ when the period is not the end of a sentence (eg, in “et al.” or “eqs.”). Another approach, if you want to avoid a line break, is to use a tie (~): “.~(\ref{eqref})”.

	* I suggest eliminating the acronym “PD” unless (a) you say “pee dee” when speaking about this concept and (b) you are OK with confusing controls people who have already defined the concept of “pee dee” control.

	* There are several spots where you assume your reader knows more than he/she might. For example, you talk about the sensitivity function without giving a citation for people who might not know what you are talking about. Same for Bode’s integral theorem.		* There are several spots where you assume your reader knows more than he/she might. For example, you talk about the sensitivity function without giving a citation for people who might not know what you are talking about. Same for Bode’s integral theorem.
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	* The right way to get the symbol for a norm is $\\| x \\|$ not “\|\|”.		* The right way to get the symbol for a norm is $\\| x \\|$ not “\|\|”.

	* Some of the text in Figure 2 is too small (especially the legend in panel B). As a guide, the text in a figure should be roughly the same font size as in the caption. You can probably go 1 pt size smaller, but I wouldn’t go below that. Also, looks like you might be using png/jpg for the figure? Better to use PDF since it will use vector graphics => doesn’t get blurry when you zoom in.		* Some of the text in Figure X is too small (especially the legend in panel B). As a guide, the text in a figure should be roughly the same font size as in the caption. You can probably go 1 pt size smaller, but I wouldn’t go below that. Also, looks like you might be using png/jpg for the figure? Better to use PDF since it will use vector graphics => doesn’t get blurry when you zoom in.

	* At some point you might want to reference the paper by Victoria Hsiao and Emzo de los Santos on feedback regulation of protein concentration using a scaffold-based sequestration mechanism (it is pretty relevant).

	* In Figure 3, I wonder if you shouldn’t redraw things so that the range 0.01-7 nM doesn’t appears to be strictly greater than 1-5 nM (seems to me there is quite a bit of overlap there).

	* The right way to get “<<“ is to use \ll (and \gg for “>>”).		* The right way to get “<<“ is to use \ll (and \gg for “>>”).

	* Equation (9) is missing punctuation (good job on catching it most other places!).		* Equation (9) is missing punctuation (good job on catching it most other places!). As a general rule, punctuation inline and displayed equations as if they were text.

	* ~~I think you~~ should ~~rewrite Theorem 3.1 so that it stands on its own a bit more. In particular, remove the forward reference (which you somehow “recover”) to Theorem 6.3~~. ~~Also, first sentence appears to be some sort~~ of ~~explanation/motivation,~~ not ~~a formal part of the theorem~~. ~~I would start with something more like “We consider~~ the ~~sequestration feedback system modeled by equations~(X) and~(Y)…”~~.		* The body of a theorem or proposition should be italicized. The body of a remark should not be. For a definition, only italicize the defined term.

	* Punctuation in equations (10) and (11) is messed up.		* Expand “iff” to “if and only if” (unless you say “iffff” when you read it aloud). Similarly, write out "for all" and "for every" when it appears in body text. OK to use symbols ($\forall$ in an equation.

	* The “protein-dedgradation inequality” probably doesn’t need to be capitalized.

	* Expand “iff” to “if and only if” (unless you say “iffff” when you read it aloud).

	* I’m starting to get annoyed by references to supplementary information that seem relevant to me understanding the material. Is there a reason to relegate results to something that nobody is going to read? I would really only use SI (ess eye) for supporting information that is there to show some level of detail that would detract from the main flow of the paper.		* I’m starting to get annoyed by references to supplementary information that seem relevant to me understanding the material. Is there a reason to relegate results to something that nobody is going to read? I would really only use SI (ess eye) for supporting information that is there to show some level of detail that would detract from the main flow of the paper.

	* Last paragraph before Section 4.1: “illustrated” → “illustrate”

	* “Figure 7 A” → “Figure 7A”?

	* Figure 6 has text that is too big and too small.

	* Consider using a style that uses a smaller font for captions than for the main text. This makes it easier to separate these (I got confused on page 12, where it looked like the equations were part of the caption for a second).		* Consider using a style that uses a smaller font for captions than for the main text. This makes it easier to separate these (I got confused on page 12, where it looked like the equations were part of the caption for a second).

	* Figure 7 is blurry.

	* In the stochastic section, I seem to remember that you made the point in presenting the results that other authors had shown that noise stabilized an otherwise unstable (deterministic) model, but I don’t see that comment in the paper.

	* I skipped the supplemental information (figured it wasn’t important).

	* Check for consistent capitalization in the figure titles.		* Check for consistent capitalization in the figure titles.
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	* The terms “in vivo” and “in vitro” should be italicized		* The terms “in vivo” and “in vitro” should be italicized

	* For ~~reference [12]~~, you should give ~~the bioRxiv preprint number~~ or the ~~DOI~~.		* For references that are not available via a publisher, you should give a DOI (if available) or URL to the paper.

	* When typesetting subscripts and superscripts, if the subscript is an abbreviation or shorthand for a word (or words), then it should be typeset as text, not math. So <math>x_\text{d}</math> (where 'd' is for 'desired'), but <math>x_i</math> if <math>i</math> is an index variable.		* When typesetting subscripts and superscripts, if the subscript is an abbreviation or shorthand for a word (or words), then it should be typeset as text, not math. So <math>x_\text{d}</math> (where 'd' is for 'desired'), but <math>x_i</math> if <math>i</math> is an index variable.

			* Then defining abbreviations, don't capitalize the terms unless they would ordinarily be capitalized. So "simultaneous localization and mapping (SLAM) algorithms", not "Simultaneous Localization and Mapping (SLAM) algorithms".

Murray: /* Top Ten Most Common suggestions */

2018-09-12T14:25:15Z

Top Ten Most Common suggestions

← Older revision		Revision as of 14:25, 12 September 2018
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	# Don’t use contractions in formal writing		# Don’t use contractions in formal writing
	# Use display style (e.g. equation or displaymath) for typesetting mathematical expressions that are taller than the standard text		# Use display style (e.g. equation or displaymath) for typesetting mathematical expressions that are taller than the standard text
			# Definitions should be set in regular (non-italics) font with the defined term ''italicized''. Remarks and examples should be in normal (non-italics) font. Theorems are italicized.
	# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.		# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.

Murray: /* Other suggestions */

2017-12-22T20:04:37Z

Other suggestions

← Older revision		Revision as of 20:04, 22 December 2017
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	* For reference [12], you should give the bioRxiv preprint number or the DOI.		* For reference [12], you should give the bioRxiv preprint number or the DOI.

			* When typesetting subscripts and superscripts, if the subscript is an abbreviation or shorthand for a word (or words), then it should be typeset as text, not math. So <math>x_\text{d}</math> (where 'd' is for 'desired'), but <math>x_i</math> if <math>i</math> is an index variable.

Murray: /* Top Ten Most Common suggestions */

2017-12-22T20:02:02Z

Top Ten Most Common suggestions

← Older revision		Revision as of 20:02, 22 December 2017
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	# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.		# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.
	# Don’t use contractions in formal writing		# Don’t use contractions in formal writing
			# Use display style (e.g. equation or displaymath) for typesetting mathematical expressions that are taller than the standard text
	# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.		# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.

Murray: /* Top Ten Most Common suggestions */

2017-12-11T10:45:16Z

Top Ten Most Common suggestions

← Older revision		Revision as of 10:45, 11 December 2017
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	# All technical documents, even a draft paper, should have a title, authors, and “identifying information” (current date or “Submitted, 2017 Winter q-bio” or something similar).		# All technical documents, even a draft paper, should have a title, authors, and “identifying information” (current date or “Submitted, 2017 Winter q-bio” or something similar).
	# Get rid of acronyms unless you use the acronym when speaking about the term (eg, DNA is fine)		# Get rid of acronyms unless you use the acronym when speaking about the term (eg, DNA is fine)
			# Never use an equation number on its own; the equation number is an adjective, not a noun (so "(19)" should be "equation (19)" or "system (19)")
	# Punctuation equations as if they were part of the sentence		# Punctuation equations as if they were part of the sentence
	# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.		# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.

Murray: /* Top Ten Most Common suggestions */

2017-11-25T14:52:30Z

Top Ten Most Common suggestions

← Older revision		Revision as of 14:52, 25 November 2017
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	# Punctuation equations as if they were part of the sentence		# Punctuation equations as if they were part of the sentence
	# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.		# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.
			# Don’t use contractions in formal writing
	# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.		# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.

Murray: /* Other suggestions */

2017-11-25T14:52:10Z

Other suggestions

← Older revision		Revision as of 14:52, 25 November 2017
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	* For references: you should either put full names everywhere or use initials everywhere (I recommend the latter). Also, I strongly encourage the listing of references in alphabetical order, since that makes it easier to find a reference to a specific paper. In the end this differs by journal, so OK to leave this like you have it, if you prefer.		* For references: you should either put full names everywhere or use initials everywhere (I recommend the latter). Also, I strongly encourage the listing of references in alphabetical order, since that makes it easier to find a reference to a specific paper. In the end this differs by journal, so OK to leave this like you have it, if you prefer.

			* For citations, there should be a (non-breaking) space before the citation number [5]. In LaTeX, use the tie (~) to create a non-breaking space.

			* “e coli” should be “E. coli” (italicized)

			* The terms “in vivo” and “in vitro” should be italicized

			* For reference [12], you should give the bioRxiv preprint number or the DOI.

Murray: /* Top Ten Most Common suggestions */

2017-11-23T16:26:03Z

Top Ten Most Common suggestions

← Older revision		Revision as of 16:26, 23 November 2017
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	# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.		# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.
	# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.		# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.

			(more to come)

	=== Other suggestions ===		=== Other suggestions ===

Murray: /* Top Ten Most Common suggestions */

2017-11-23T16:25:52Z

Top Ten Most Common suggestions

← Older revision		Revision as of 16:25, 23 November 2017
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	=== Top Ten Most Common suggestions ===		=== Top Ten Most Common suggestions ===

	* Google "which versus that". If the word "which" doesn't have a comma before it, you probably got it wrong.		# Google "which versus that". If the word "which" doesn't have a comma before it, you probably got it wrong.
	* All technical documents, even a draft paper, should have a title, authors, and “identifying information” (current date or “Submitted, 2017 Winter q-bio” or something similar).		# All technical documents, even a draft paper, should have a title, authors, and “identifying information” (current date or “Submitted, 2017 Winter q-bio” or something similar).
	* Get rid of acronyms unless you use the acronym when speaking about the term (eg, DNA is fine)		# Get rid of acronyms unless you use the acronym when speaking about the term (eg, DNA is fine)
	* Punctuation equations as if they were part of the sentence		# Punctuation equations as if they were part of the sentence
	* Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.		# Typeset the math right: \|\|x\|\| << 1 is typeset in LaTeX as <tt>$\\| x \\| \ll 1$</tt>, which will come out as <math>\\| x \\| \ll 1</math> instead of <math>\|\|x\|\| << 1</math>.
	* Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.		# Read [https://doi.org/10.1137/1.9780898719550 Higham's book] on writing for the mathematical sciences.

	=== Other suggestions ===		=== Other suggestions ===