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This project presents a SimBiology implementation of a physiologically-based pharmacokinetic (PBPK) model for trichloroethylene (TCE) and its metabolites. It is based on the article, “A human physiologically based pharmacokinetic model for trichloroethylene and its metabolites, trichloroacetic acid and free trichloroethanol” by Fisher et al. [1].
The human PBPK model for TCE and its metabolites presented here was developed by Fisher et al. [1] in order to assess human health risks associated with low level exposure to TCE. TCE is a commonly used solvent in the automotive and metal industries for vapor degreasing of metal parts. Exposure to TCE has been associated with toxic responses such as cancer formation and brain disorders in rodents and in humans [1]. In this PBPK model, TCE enters the systemic circulation through inhalation. Its disposition is described by a six-compartment model representing the liver, lung, kidney, fat, and slowly perfused and rapidly perfused tissues. In the liver, TCE is metabolized to trichloroacetic acid (TCA) and free trichloroethanol (TCOH-f) via P450-mediated metabolism where a fraction of TCOH-f is converted to TCA. For simplicity, a four-compartment submodel was used to describe the disposition of metabolites, TCA and TCOH-f, in the lung, liver, kidney, and body (muscle). Both metabolites are described to be excreted in the urine. TCOH-f is glucuronidated in the liver, forming glucuronide-bound TCOH (TCOH-b), and excreted in the urine via a saturable process whereas TCA is excreted by a first-order process by the kidney.
Reference: Fisher, J. W., Mahle, D., & Abbas, R. (1998). A human physiologically based pharmacokinetic model for trichloroethylene and its metabolites, trichloroacetic acid and free trichloroethanol. Toxicology and applied pharmacology, 152(2), 339-359.
Summary:
Dynamically accessing variable names can negatively impact the readability of your code and can cause it to run slower by preventing MATLAB from optimizing it as well as it could if you used alternate techniques. The most common alternative is to use simple and efficient indexing.
Explanation:
Sometimes beginners (and some self-taught professors) think it would be a good idea to dynamically create or access variable names, the variables are often named something like these:
- matrix1, matrix2, matrix3, matrix4, ...
- test_20kmh, test_50kmh, test_80kmh, ...
- nameA, nameB, nameC, nameD,...
Good reasons why dynamic variable names should be avoided:
- Slow
- Buggy
- Security Risk
- Difficult to Work With
- Obfuscated Code Intent
- Confuses Data with Code
- Code Helper Tools do not Work
- Magically Making Variables Appear in a Workspace is Risky
There are much better alternatives to accessing dynamic variable names:
- Indexing into Cell Array or ND-Array
- Non-scalar Structures (with Indexing)
- Dynamic Field-Names in a Structure
- load into a Structure, not into the Workspace
- save the Fields of a Scalar Structure
- Use a table or timetable Array
- Use more Efficient Ways to Pass Variables Between Workspaces
Note that avoiding eval (and assignin, etc.) is not some esoteric MATLAB restriction, it also applies to many other programming languages as well:
MATLAB Documentation:
If you are not interested in reading the answers below then at least read MATLAB's own documentation on this topic Alternatives to the eval Function, which states "A frequent use of the eval function is to create sets of variables such as A1, A2, ..., An, but this approach does not use the array processing power of MATLAB and is not recommended. The preferred method is to store related data in a single array." Data in a single array can be accessed very efficiently using indexing.
Note that all of these problems and disadvantages also apply to functions load (without an output variable), assignin, evalin, and evalc, and the MATLAB documentation explicitly recommends to "Avoid functions such as eval, evalc, evalin, and feval(fname)".
The official MATLAB blogs explain why eval should be avoided, the better alternatives to eval, and clearly recommend against magically creating variables. Using eval comes out at position number one on this list of Top 10 MATLAB Code Practices That Make Me Cry. Experienced MATLAB users recommend avoiding using eval for trivial code, and have written extensively on this topic.
Inspired by Chad Greene's " MATLAB jokes or puns " thread, and in celebration of 15 years of the MathWorks Community site, does anyone out there want to share their poetic creativity? Limericks, haiku, sonnets... Go!
And to start off, my (slightly off-topic) submission on Chad's thread:
There was an old math guy called Cleve
who, while teaching, a pipe-dream conceived:
of a language so clean
you can say what you mean!
From our suffering we've all been relieved.
The community is very helpful, yet I feel really powerless that I cannot find the appropriate way to code, nor find the problems with the codes I have written. I have read numerous books on MATLAB, mostly related with science and engineering applications. Any advice to improve would be greatly appreciated. Thanks.
Are there any good Matlab jokes? I don't mean why or any other Easter eggs, I mean good jokes involving Matlab. Actually, that bar may be a bit too high. Any jokes, good or bad, let's hear 'em.
Hello all,
Please explain good MATLAB programming practice methods. It will help to the guys who are new to programming like me.
Previously I used
for i=1:10
after following some suggestions from this answers pages I learnt to use
for i1=1:100
This is the good way to write programs.
Like this, as a professional programmer, please mention some good programming practice techniques.
It will useful to all!
Capital letters are obtained by capitalizing the LaTeX command for the lowercase version. Capital letters in grey are exceptions which have no LaTeX commands. For example, to produce a capital chi simply type X (this also applies for the lowercase omicron).
When two versions of the lowercase letter are available, a var prefix can be added to obtain the second version. For example, the two versions of epsilon are \epsilon and \varepsilon.
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The code used to generate the table:
greeks = ...
{'ALPHA' 'A' '\alpha'
'BETA' 'B' '\beta'
'GAMMA' '\Gamma' '\gamma'
'DELTA' '\Delta' '\delta'
'EPSILON' 'E' {'\epsilon','\varepsilon'}
'ZETA' 'Z' '\zeta'
'ETA' 'H' '\eta'
'THETA' '\Theta' {'\theta','\vartheta'}
'IOTA' 'I' '\iota'
'KAPPA' 'K' '\kappa'
'LAMBDA' '\Lambda' '\lambda'
'MU' 'M' '\mu'
'NU' 'N' '\nu'
'XI' '\Xi' '\xi'
'OMICRON' 'O' 'o'
'PI' '\Pi' {'\pi','\varpi'}
'RHO' 'P' {'\rho','\varrho'}
'SIGMA' '\Sigma' {'\sigma','\varsigma'}
'TAU' 'T' '\tau'
'UPSILON' '\Upsilon' '\upsilon'
'PHI' '\Phi' {'\phi','\varphi'}
'CHI' 'X' '\chi'
'PSI' '\Psi' '\psi'
'OMEGA' '\Omega' '\omega'};
h = figure('units','pixels','pos',[300,100,620,620],'Color','w');
axes('units','pixels','pos',[10,10,600,600],'Xcol','w','Ycol','w',...
'Xtick',[],'Ytick',[],'Xlim',[0 6],'Ylim',[0,4]);
% Loop by column and row
for r = 1:4
for c = 1:6
el = (r-1)*6 + c;
% Title
text(c-0.5,5-r,greeks{el,1},'Fonts',14,'FontN','FixedWidth',...
'Hor','center','Ver','cap')
% Color cap latter in grey or black
if strcmp(greeks{el,2}(1),'\')
clr = [0, 0, 0];
else
clr = [0.65, 0.65, 0.65];
end
% Cap letter
text(c-0.5,4.87-r,['$\rm{' greeks{el,2} '}$'],'Fonts',40,...
'Hor','center','Ver','cap','Interp','Latex','Color',clr)
% Lowercase letter/s (if two variants)
if iscell(greeks{el,3})
text(c-0.75,4.48-r,['$' greeks{el,3}{1} '$'],'Fonts',20,...
'Hor','center','Interp','Latex')
text(c-0.25,4.48-r,['$' greeks{el,3}{2} '$'],'Fonts',20,...
'Hor','center','Interp','Latex')
% Latex command
text(c-0.5,4.3-r,['\' greeks{el,3}{1}],'Fonts',12,'FontN','FixedWidth',...
'Hor','center','Ver','base')
else
text(c-0.5,4.48-r,['$' greeks{el,3} '$'],'Fonts',20,...
'Hor','center','Interp','Latex')
text(c-0.5,4.3-r,['\' greeks{el,3}],'Fonts',12,'FontN','FixedWidth',...
'Hor','center','Ver','base')
end
end
end
% Print to pdf
export_fig greeks.pdf
And here is the link to the pdf on scribd: http://www.scribd.com/doc/159011120/Greek-alphabet-in-latex
[INDEX]
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[MOTIVATION]
Why should we use markups in the body of our questions?
The answer is a question: which of the two versions is more likely to be understood in a glimpse and has more chances to be answered by our readers?
.
< Consider the following question >
I have a vector of weights W=[10,20,30,50,23434,1,2.4,2] and a matrix A=rand(100,8) and I would like to find the row-wise weighted sum of A. I am proceeding in the following way: B=zeros(size(A)); for c=1:numel(W) B(:,c)=A(:,c)*W(c); end B=sum(B,2); Somehow I get huge numbers can you please help?
.
< Now, consider its formatted version >
I have a vector of weights W = [10,20,30,50,23434,1,2.4,2] and a matrix A = rand(100,8) and I would like to find the row-wise weighted sum of A.
I am proceeding in the following way:
B = zeros(size(A));
for c = 1:numel(W)
B(:,c) = A(:,c)*W(c);
end
B = sum(B,2);
Somehow I get huge numbers can you please help?
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[AKNOWLEDGMENTS]
In alphabetical order by nickname, thanks for their suggestions to:
Walter Roberson
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[LOG]
- 06 Aug 2011, 13:17 BST - created and added boldface.gif
- 06 Aug 2011, 14:59 BST - added italic.gif
- 06 Aug 2011, 18:58 BST - added index section
- 07 Aug 2011, 00:03 BST - added code.gif and tutorial series section
- 07 Aug 2011, 01:50 BST - added monospaced.gif, numlist.gif, bullist.gif and hyperlink.gif
- 13 Aug 2011, 14:27 BST - added motivation section
- 18 Aug 2011, 01:44 BST - added aknowledgments section and link to wish-list
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[TUTORIAL Series]
Vote on Wish-list for MATLAB Answer sections my post if you think that a tutorial section on top of Answers could be useful.
Now, I am still a novice when it comes to programming. I believe MATLAB is definitely a great programming tool, one that I can play with, particularly, when I have free time.
I would love to hear from all answerers, what are the ways that can make one proficient in this field?
This topic is for unexpected or bizarre or humorous references to MATLAB. Specific citations would be appreciated.
Please post the easter eggs that you have found so far if they aren't already posted by someone else.
Let's try to make a good Matlab easter egg list because it seems that there isn't one.
What should be posted:
- Unexpected but intentional behaviour
- Special things that the programmers left for us to discover
- Extra code inside a function that can be used for other purposes
- Hidden pictures and audio clips
What shouldn't be posted:
- Repeated Easter Eggs, if someone already posted it please don't repeat
- Bugs in functions that cause trouble and might be fixed in later versions
- Matlab games that come with the program unless they aren't mentioned in the documentation (the games are in the other demos, try the xpbombs and fifteen, you can even see the code for both games)
What is the best way to learn MATLAB at home without a tutor?
