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Welcome to the website for DiStefano III, J: Dynamic Systems Biology Modeling and Simulation.
Companion Lecture Slides for Courses Taught from
Dynamic Systems Biology Modeling and Simulation (DSBMS)
JJ DiStefano III Academic Press/Elsevier 2015
A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course.
Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content.
The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: joed@cs.ucla.edu
Errata & Addendum for the first printing of Dynamic Systems Biology Modeling and Simulation
Author: Joseph DiStefano III, Academic Press (December 2013)
The following corrections and additions are for inclusion in the first print version of the textbook. The electronic textbook includes these corrections and additions within the text. The list appears large, but most of the entries are additions of useful Tables of Contents (TOC) for the six Appendices, in two places. Most corrections are minor.
IMPORTANT
The December 2013 print version is no longer available for sale. These errata and addenda are corrected and included in the currently available and updated version of the textbook – in both printed and electronic versions – Updated Version JANUARY 2015.
Page  Location 
Correction 

v 
Under Dr. Yate’s comments – second line 
The line should read, “In that chapter you generously acknowledge some of us who tried to accomplish this earlier…” 

xii 
Chapter 14 title 
Biocontrol System Modeling, Simulation & Analysis 

xii 
Chapter 15 title 
DataDriven Modeling & Alternative Hypothesis Testing 

xiii 
Chapter 16 title 
Experiment Design & Optimization 

xiii 
Chapter 17 title 
Model Reduction & Network Inference in Dynamic Systems Biology 

xiii 
Added TOC to Appendix A entries in main TOC 
Appendix A – A SHORT COURSE IN LAPLACE TRANSFORM REPRESENTATIONS & ODE SOLUTIONS


xiii 
Added TOC to Appendix B entries in main TOC 
Appendix B –LINEAR ALGEBRA FOR BIOSYSTEM MODELING


xiii 
Added TOC to Appendix C entries in main TOC 
Appendix C – INPUTOUTPUT & STATE VARIABLE BIOSYSTEM MODELING: GOING DEEPER


xiii 
Added TOC to Appendix D entries in main TOC 
Appendix D – CONTROLLABILITY, OBSERVABILITY & REACHABILITY


xiii 
Added TOC to Appendix E entries in main TOC 
Appendix E – DECOMPOSITION, EQUIVALENCE, MINIMAL & CANONICAL STATE VARIABLE MODELS


xiii 
Added TOC to Appendix F entries in main TOC 
Appendix F – MORE ON SIMULATION ALGORITHMS & MODEL INFORMATION CRITERIA


xvii 
Fourth line of item numbered 2. 
Add footnote on word “logo.” Footnote should read: Biomodeling/Theory+Data Images (The Logo: parent and children) are reproduced above and in the chapters and back cover of this book with permission by the author Joseph DiStefano III. It is a Trademark ™ and service mark of the author, Copyright © 2012. 

2 & 3 
Humpty Dumpty 
Cartoon design by Allegra DiStefano. Quote attributed to Schnell et al. 2007. Also, the 1 in HumptyDumpty quote on bottom of page 3 should not be italicized. 

30 
Fig. 1.9 
Add to end of Figure legend: Biomodeling/Theory+Data Image (The Logo) is reproduced here and in other chapters and back cover of this book with permission by the author Joseph DiStefano III. It is a Trademark (TM) and service mark of the author, Copyright © 2012. 

41 
Quotes 
Both quotes should be centered. 

61 
Example 2.21 
Typo: In Example 2.21, last equation should have dv/da replaced by dv/dt 

82 
E2.3 
Exercise 2.3 should begin with "Transform the equation in Exercise E2.1…." 

119 
Numbered bullets 
Numbered bullets should be black, not red. 

141 
E3.8 
In the 6th line, the last equation should read: k1*=2k1 (lower case k) 

149 
Just above Example 4.2 
Inline equation for VBLOOD should be inverted: . 

158 
Table 4.1 
The title of Table 4.1 should be in boldface. 

178 
Last paragraph 
“If this assumption... “ should not be indented. 

239 
Bullet 2. 
“ks” inside the matrix brackets also should be caps, i.e. cap K11, K21 and K22 

245 
Remark following Eq. (5.41) 
The “u” in u(t)should be boldface, reading as u(t). 

265 
Volume & Temperature Effects 
Add another space between “V is” and 

273 
3rd paragraph 
The “Km” in last sentence of the third paragraph should be italic Km 

274 
Eq. 6.40 
Equation number (6.40) should be black, not red. 

279 
Eq. 6.46 
Equation number (6.46) should be black, not red. 

279 
Eq. 6.46 
At the end of the top equation, the minus sign should have a space after it, to separate it from the s. 

291 
1st paragraph 
Fifth line from the top, the cursive “s” should be a noncursive, italicized “s” 

300 
Under Eq. 6.90 
The following phrase should be bolded as well as italicized to read: “the modern QSSA is simply: tC << tS.” 

323 
Eqs. 7.25 & 7.26 
(7.25) should have and Eq. 7.26 third row should be: 0 1 1 1 0 0. 

333 
Just above Eq. 7.30 
The space between x1 and x2 should be smaller (they multiply). 

355 
Line 13 
“larger (volumetric) plasma...” should read “smaller (volumetric) plasma...”. 

355 
Line 16 
Inline equation: Fp = FB / (1 – Hct) should read: Fp = FB(1 – Hct) (i.e. no slash, multiplication, not division) 

363 
2nd remark 
The last words of the last line should read “ from Blood or Plasma is cAFCardiac.” The “X” “times” symbol is extraneous in this product of cA and FCardiac . 

369 
Fig. 8.8 
The figure legend should read as follows (i.e. with more matching caps): “Whole body PBTK model structure. Left: PBTK model with rate constants (kij day1) shown on arrows. Right: Same model structure, but with wholebody Mn distribution (% of total) and Mn compartment interchange rates as mass fluxes (μg Mn/day) shown on arrows. The olfactory submodel nodes: OLFACTORY EPITHELIUM 1 (EP1), OLFACTORY EPITHELIUM 2 (EP2) and OLFACTORY BULB (BULB) (boxed in); brain compartments: OLFACTORY submodel components + STRIATUM, CEREBELLUM and brainresto/olfactory tract and tubercle (BRESTO/OTT) (boxed in). Whole body components (nodes) include (lumped) CENTRAL + LUNG1 + BLOOD, LUNG2, (lumped) Restofbody (RESTO), and (lumped) PANCREAS/TESTES/KIDNEY (PTK), and LIVER, (gray). EP2 and LUNG2 were needed to accommodate best 2exponential fits to epithelium and lung data in preliminary analyses. Exogenous inputs are u1 into EPI and u2 into CENTRAL + LUNG1 + BLOOD. Measurements are from 8 of the 11 compartments, as shown.” 

371 
Eq. 8.19 
The lambda symbols should be closer to the parentheses. 

380 
9 lines from bottom 
AUCP should be AUCp 

387 
Last paragraph 
In the second to last line, “complete dissolution” should read “incomplete dissolution.” 

388 
Relative bioavailability (RB) paragraph 
There should be a comma after “same route” to read as follows: Relative bioavailability (RB)of two different preparations (1 and 2) of the same drug, introduced via the same route, is defined as: 

388 
Bioequivalence paragraph 
In the third line, BE should be italicized. 

391 
Fig. 8.17 legend 
PR1 and PR2 should read “PR1” and “PR2” (matching the figure) respectively. 

391 
Eq. (8.46) 
The Qs in (8.46) should both be lowercase. 

396 
Example 8.11 
There should be spaces between each of the three equation lines. 

428 
Last sentence 
The sentence beginning on the last line and continuing onto the next page, first two lines, should be fully deleted, i.e. delete the entire sentence starting with, “A mode, however, has a “shape” (eigenvector) as well as a “frequency” (eigenvalue) component, so it is represented more completely as a twodimensional function … each with its own ... and eigenvector vj.” 

429 
1st paragraph 
Shorten to: “ A most important feature of linear modes is that they are a minimal set of invariants of the dynamical system and, for any set of ICs or input(s), the modes accurately capture essential system dynamics. Importantly, λj can be complex as well as real.” 

431 
E9.2 a) 
[xeye]T should be corrected to read [xe ye]T (space out). 

432 
E9.9 
Another space should be added after ODEs: 

437 
2nd paragraph 
In the last line, Kuo et al. should be corrected to Meshkat et al. 

437 
Fig. 10.1 
In the figure legend, “y” should be in green, like in the figure. 

442 
3rd paragraph 
4th line from the bottom, Kuo should be replaced with Meshkat. 

444 
Transfer Functions & SI 
There should be no comma before (10.7) in last line. 

451 
First equation list 
All equations should be aligned. 

454 
Eq. 10.60 
Another space should be added before tє[t0, T] 

456 
Eq. 10.68 
The third equation line from the bottom should be centered. 

457 
Eq. 10.7010.75 
There should be more line space separating each of these equations. 

460 
Line between Eq. 10.90 and 10.91 
Add another space between kjj, and j=2, .... 

462 
Above Fig 10.7 
Delete the 2 or 3 extra spaces after the first “<” symbol, in all rows. 

463 
Top of the page 
Ditto. i.e. delete the 2 or 3 extra spaces after the first “<” symbol, in all rows. 

465 
Eq. 10.100 
Add more spaces after the comma, before t ≥ 0. 

470 
Fig 10.10 caption 
Change “constrained” to “unconstrained” 

471 
Fig 10.11 caption 
Change “unconstrained” to “constrained” 

478 
5th line from the bottom 
Delete “a,b” in first reference and replace “Kuo” with “Meshkat” in second reference. 

486 
Kuo, C., Meshkat, N., ... reference 
Reverse order of first two authors. 

494 
Example 11.3 
Add more line space between the two equation lines. 

497 
1st sentence 
x(t,p) should read x(t, p) 

506 
Example 11.7 
RMS should be italicized in both places. 

512 
Fig. 11.7 caption 
Figure legend should be deleted. 

514 
Fig. 11.9 caption 
Figure legend should be deleted. 

515 
Fig. 11.10 caption 
Figure legend should be deleted. 

515 
Fig. 11.11 caption 
Figure legend should be deleted. 

531 
Eqs. 12.13 & 12.14 
Add a space between pj and fj. 

534 
Eq. 12.26 
Delete space between W and E in the middle of the equation. 

534 
Eq. 12.29 
Add a space between z1(t2) and z2(t2) 

535 
Just above Eq. 12.32 
Add a space between pP and a b c. 

544 
Just below Eq. 12.46 
Subscript j should be italicized. 

547 
Example 12.5 
p1 p2 p3 column headers should be moved slightly down. 

549 
First Remark 
The parentheses in the Hessian matrix approximation equation should be larger, the same size as the contents. 

549 
Just below Eq. 12.52 
Paragraph should be left justified. 

549 
Example 12.6 
CORR should be italicized. 

550 
Eq. 12.53 
This equation should all be colored dark green. 

552 
Blue header COV(p) 
(p) should be italicized. 

557 
Von Neumann Quote 
Should be centered. 

592 
E13.5 
“50 units” should be replaced with “100%” 

594 
Kuo, C., Meshkat, N., ... reference 
Reverse order of first two authors. 

604 
Table 14.1 
4th equation should be indented like the next 4. 

617 
2nd line 
Insert square brackets in front of  a and after the root sign, before the / 

626 
Last paragraph 
Second and third lines, delete “presence of”. 

627 
Line 11 
Delete comma after “consolidation” 

669 
Kuo, C., Meshkat, N., ... reference 
Reverse order of first two authors 

679 
Table 16.1 
Hij and SI (within column headers) should be italicized. Also, insert line separators between numbered equations. 

682 
Identifiability Analysis for Each Hij 
Hij should be italicized. 

683 
Table 16.2 
Table should read as attached file, including colors (and numbered 16.2, not 0.1).


687 
Cutset Analysis Solution paragraph 
Each red superscript B should be italicized. 

687 
Footnote 
Replace “Kuo” with “Meshkat.” 

689 
2nd paragraph 
Italicized “dependent parameters” and “independent parameters” should be just boldface, no italicized. 

690 
Blue section header 
kji should be italicized. 

694 
Blue section header 
F should be italicized. 

697 
Footnote 11 
“Web site” should be one word. 

700 
Last paragraph 
Kuo should be replaced with Meshkat. 

704 
Kuo, C., Meshkat, N., reference 
Reverse order of first two authors 

710 
Eq. 17.5 
Subscripts should all be aligned. 

714 
Just above Example 17.3 
“web site” should be one word. 

720 
Blue section header 
Add “(MPSA)” to end of the header. 

725 
Under title 
Add TOC.


730 
Example A.12 
e2t in the first step of the solution should be et. 

732 
Example A.15 
Last line of example (at top), comma should be close to the 0, not next to t ≤ 1 

736 
Eq. A.25 
Shorten space between first two parts of the equation. Its a product. 

740 
Under title 
Add TOC.


759 
Under title 
Add TOC. Appendix C – INPUTOUTPUT & STATE VARIABLE BIOSYSTEM MODELING: GOING DEEPER


779 
Eq. C.78 
Under the matrices, change “= cΓ11” to “=cγ11” (upper to lower case gamma) 

784 
SISO Models – first sentence 
Change “y = cTu” to “y = cTx” 

787 
Under title 
Add TOC.


787 
1st line under Controllability 
Change “iff” to “(iff)” 

804 
2nd paragraph 
First letter of the last line of the second paragraph – change “N” to “N”. 

809 
Under title 
Add TOC.


811 
In Other Words 
Bold italic “In Other Words:” 

833 
Under title 
Add TOC.




