Here are the possible errors and places that need clarification in
your bio book.
page 53, line 9, "Alternatively, one sample could be taken from the
start of an experiment monitoring a cells response to some stress
factor ....", "cells" should be "cell's".
page 68, the paragraph above Fig 2.11, "For example, this DBN
indicates both that cI's expression level influences cro's expression
level as well as that cI's expression level influences cro's
expression level". The two parts before and after "as well as" are the
same. Maybe you meant to say "cro's expression level influences cI's
expression level" after "as well as".
page 96, the paragraph right above Fig 3.8, line 7, "... the results
from Fig 3.4 (i.e., [CII] of about 18 and [CI] of about 8)". On Fig
3.4, [CII] never exceeds 17.5 and [CI] never exceeds 7.5.
page 110, the last two lines, "... the relative difference between
deterministic and stochastic trajectories decrease". "decrease" ->
"decreases".
page 142, the first step for operator identification, "O's initial
concentration must not be greater than a threshold". It is not quite
clear what this threshold is and who sets the threshold. Does the user
provide this threshold or does the tool somehow detect this threshold
automatically?
page 142, 3rd line from the bottom, "... (i.e., S2)". S2 here should
be S4 to match Fig 5.6(a).
page 147, Eq. 5.34. It is unclear to me what the summation on the
denominator includes. From the sample answer of Problem 5.3 (page 227
of the book), I noticed that there was always a term "1" appearing on
the bottom. My guess is that this term comes from the reference term
(i.e. s=0), because this is the only term that can produce a 1 from
the denominator's expression of Eq 5.34.
page 149, Fig 5.10. Maybe it is useful to add units to the vertical
axis to both subfigures.
page 159, last row of the table on the top (Problem 5.4). The protein
is RNAP_2. But it is RNAP that binds to O_2 on the table on the bottom
of page 158.
page 173, first line, "where m is the stoichiometry of s in the
corresponding reaction, ...". Here "s" does not appear in the
expression of q_k on the bottom of the previous page. Maybe it should
be "species" instead?
page 216 Fig 8.1. The caption refers to the wrong problem (Problem
1.1). It should be 1.3 instead.
page 234 Fig 8.11 (b). This figure does not match (a) or (c) because A
should repress Z, and B should repress Y.
Hi Chris,
Here are the possible errors and places that need clarification in your bio book.
page 53, line 9, "Alternatively, one sample could be taken from the start of an experiment monitoring a cells response to some stress factor ....", "cells" should be "cell's".
page 68, the paragraph above Fig 2.11, "For example, this DBN indicates both that cI's expression level influences cro's expression level as well as that cI's expression level influences cro's expression level". The two parts before and after "as well as" are the same. Maybe you meant to say "cro's expression level influences cI's expression level" after "as well as".
page 96, the paragraph right above Fig 3.8, line 7, "... the results from Fig 3.4 (i.e., [CII] of about 18 and [CI] of about 8)". On Fig 3.4, [CII] never exceeds 17.5 and [CI] never exceeds 7.5.
page 110, the last two lines, "... the relative difference between deterministic and stochastic trajectories decrease". "decrease" -> "decreases".
page 142, the first step for operator identification, "O's initial concentration must not be greater than a threshold". It is not quite clear what this threshold is and who sets the threshold. Does the user provide this threshold or does the tool somehow detect this threshold automatically?
page 142, 3rd line from the bottom, "... (i.e., S2)". S2 here should be S4 to match Fig 5.6(a).
page 147, Eq. 5.34. It is unclear to me what the summation on the denominator includes. From the sample answer of Problem 5.3 (page 227 of the book), I noticed that there was always a term "1" appearing on the bottom. My guess is that this term comes from the reference term (i.e. s=0), because this is the only term that can produce a 1 from the denominator's expression of Eq 5.34.
page 149, Fig 5.10. Maybe it is useful to add units to the vertical axis to both subfigures.
page 159, last row of the table on the top (Problem 5.4). The protein is RNAP_2. But it is RNAP that binds to O_2 on the table on the bottom of page 158.
page 173, first line, "where m is the stoichiometry of s in the corresponding reaction, ...". Here "s" does not appear in the expression of q_k on the bottom of the previous page. Maybe it should be "species" instead?
page 216 Fig 8.1. The caption refers to the wrong problem (Problem 1.1). It should be 1.3 instead.
page 234 Fig 8.11 (b). This figure does not match (a) or (c) because A should repress Z, and B should repress Y.
Zhen Zhang