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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.
Dear MATLAB community,
How can I help my close friend who's bad at math and programming learn MATLAB?
He's a final year chemical engineering student who struggles even to plot two functions on the same graph in his computational fluid dynamics class (there was no prereq for matlab skills).
In his first year, I saw him get dragged through the introductory engineering classes which was his first encounter with MATLAB. Students were taught a few rudimentary programming skills and then were expected to make a code for a 'simple' tic-tac-toe game. It took him hours of blank looks and tutoring to even understand the simplest of boolean operators. He was never able to write a working function without the supervision of a friend or tutor. Needless to say, he was permanently scarred by the experience and swore to avoid using it forever.
After 3 years of avoiding MATLAB, he realised how not knowing it hurt him during his final year project. He had to solve a system of pdes to model the performance of a reactor and practically speaking, MATLAB was the most suitable software at hand. He ended up having to get a friend to help him code the equations in while also having to oversimplify his model.
The weird thing is that: most students from his chemical engineering faculty were not expected or encouraged to use MATLAB, almost all of their prior assignments required no use of MATLAB except that infamous first year course, and most of his peers also avoided using MATLAB and resorted to Excel. It is my understanding that Excel cannot match MATLAB's efficiency and clarity when solving calculus problems so it was not uncommon to see extremely long Excel spreadsheets.
Anyway, my friend is, with the help of a friend's past year MATLAB codes, trying to finish up his computational fluid dynamics assignment that's due soon. He finishes university in 2 weeks time.
Even though he knows that not every engineer has to use MATLAB in the workplace, he somehow wishes he was able to learn MATLAB at his glacial pace. I find it such a pity that he was never able to keep up with the pace of learning that was expected which begs the question: are students who are too slow at learning programming better of in a different field of study?
If you've managed to read to the end of this, thank you so much. I just don't know how to help my friend and I'm hoping some of you might be able to suggest how I can help him be better at it. I believe he has potential but needs special help when it comes to MATLAB.
All helpful and constructive suggestions considered,
Thank You All
Hi there! This is kind of an unusual question, but here it goes. I am a big time Matlab enthusiast and I met some of your representatives at Formula Student Germany back in August. There was a booth were your product was showcased but most importantly there was Matlab merchandise such as stickers, rub-on-tattoos and pens with the mathworks logo being handed out. This merchandise is increadibly popular with me and my nerdy friends. But sadly I didnt bring much with me from the event. Is it possible to get ahold some of it? Is it for sale? Are you willing to sponsor some geeky engineering students?
I am new in MATLAB programming. I want to learn matlab . I want to know about is any matlab or simulink contest available. Please answer me. Thanks
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.
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.
Some of Matlab's toolbox functions are affected by magic strings or magic numbers, which are strings or numbers with a deeper meaning besides the normal value. Both are considered as bad programming patters, because they provoke confusions, when the magic keys appear with the normal meaning by accident. See http://en.wikipedia.org/wiki/Anti-pattern
Example 1:
clear('myVariable')
clear('variables')
While the 1st clears the variable myVariable, the later clears all variables. Here 'variables' has a meta-meaning. The problem appears, when 'variables' is an existing variable:
a = 1;
variables = 2;
clear('variables')
disp(a) % >> 1
Only variables is cleared, which cannot be understood directly when its definition is 1000 lines before.
Example 2:
uicontrol('String', 'default')
This creates a button with the empty string '' instead of the expected 'default', because this is the magic string to invoke the default value get(0, 'DefaultUIControlString'). The same concerns properties of other graphic objects also, e.g. the 'name' property of figure or the string of uimenu. There is a workaround which allows the user to display 'default': Simply use '\default'. Unfortunately this is doubled magic, because in consequence it is impossible to display the string '\default'. Obviously a bad idea.
Example 3:
Graphic handles are doubles (although gobject of the new R2013a seems, like this is subject to changes? [EDITED: Yes, it changed with HG2 in R2014a]). But then a handle can be confused with data:
a = axes; % e.g. 0.0048828125
plot(a, 2, '+')
But you cannot draw the point [0.0048828125, 2] by this way, because the 1st input is considered as handle of the parent. Here all possible values of handles are magic. Collisions are very unlikely, but there is no way to avoid them reliably - as long as handles have the type double.
Question:
Which functions are concerned by magic values? What are the pitfalls and workarounds?
How do I can delete my account?
I am wondering what others use for those little short-cuts or niceties in MATLAB. I have in mind something you wrote or something somebody else wrote or an underused MW function.
Here are my two favorites.
This is a simple script I use. Here is the entire contents of CLC.m (yes, it is capitalized):
clear all,close all,clc
Very simple, but I use it all the time. Here is another one I use so often that I forget not every machine has it (though every machine should, IMO):
Here is an underused MW function that I occasionally employ when working on someone else's machine. The usual response is, "Wait, what did you just do?"
home
What are some of yours?
As I'm becoming more and more familiar with MATLAB, I'm starting to fall in love with it. I was wondering what are the coolest things that you all know MATLAB can do? As for me so far, the auto-code generation into another language is the coolest thing.
It is not uncommon for students to be assigned questions which they are required to complete "without using any built-in functions". There is not a great deal that can be programmed in MATLAB without using any built-in functions, but a little can be done -- but what, exactly is possible?
What a "built-in function" is, exactly, is open to interpretation. In the below, I refer instead to "publicly visible routines". Keywords (see below) are not publicly visible routines (they are "statements" or components of statements.) Any documented operation or call that invokes a MATLAB-supplied .m or .p or mex file or built-in library to do its work is a publicly visible routines. If you can use documented methods override the normal meaning of a statement or expression in practice by supplying alternate code, then the code probably involves publicly visible routines. If the language design is such that you could use documented methods to override the normal meaning of a statement or expression in theory (such as the behavior of adding two double, the code for which is in practice bundled into an internal MATLAB library), then I would still consider that a call to a publicly visible routine.
A MATLAB-supplied routine that is not documented, which is used for internal MATLAB purposes, could perhaps be held not to be a publicly visible routine, but it certainly would still be a "built-in function".
I exclude from the list any routine which there is no direct way to access, and is only used for internal purposes, such as the memory allocation routines.
This is what I have come up with:
- the names defined as "keywords" do not in themselves involve function calls to publicly visible routines. These keywords currently include 'break', 'case', 'catch', 'classdef', 'continue', 'else', 'elseif', 'end', 'for', 'function', 'global', 'if', 'otherwise', 'parfor', 'persistent', 'return', 'spmd', 'switch', 'try', 'while'. There is no functional form of any of these: for example, one cannot use global(s) to declare the name contained in the variable "s" to be global. (However, you can define an "end" method; https://www.mathworks.com/help/matlab/matlab_oop/object-end-indexing.html )
- scalar numeric double precision real-valued constants are handled at parse time, including unary plus and unary minus in front of them
- scalar numeric double precision constants followed immediately by "i" or "j" create a complex-value constant at parse time, including unary plus and unary minus in front of them
- whether a complete complex constant with real and imaginary part is handled at parse time is unknown
- literal character vectors and string objects are handled at parse time
- in sufficiently new versions, int64() and uint64() around an integer constant is handled at parse time. This was a change from previous versions which handled it at run time (after the integer had been converted to double precision...)
- whether any other casts such as uint16() or logical() are now handled at parse time is unknown
- assignment of a compete variable (no indexing, no substructure references, etc.) to a plain variable (no indexing, no substructure references, etc.) does not involve any function calls to publicly visible routines (unless I have overlooked a case involving objects)
- "if" or "while" applied to a scalar logical constant or to a scalar logical variable does not involve any function calls to publicly visible routines. However, it is not known whether there is any method to construct a logical value without calling a MATLAB routine: "true" and "false" are MATLAB routines, not constants, and logical() of a numeric constant might be handled at run time
- "for" in which the range is named as a scalar constant or scalar variable do not involve any function calls to publicly visible routines; for example, "for K = 5"
- defining an anonymous function does not involve any function calls to publicly visible routines
I may have overlooked something due to shortage of chocolate in my bloodstream.
The language described above is not Turing complete, and is not "sufficiently powerful" for the purposes of the Church-Rosser Theorem of general-purpose computability. It is also not possible to do any arithmetic in it, as arithmetic must be reducible to the Peano Postulates, and those require at the very least the ability to compare a value for equality with 0, which in MATLAB would require a call to the MATLAB routine "eq".
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
We all know that MATLAB is probably the best software for engineering purposes, I think it's a little expensive unless you have it for free on your school or place you work, please share your opinion about MATLAB cost, including toolboxes, student versions... is it that expensive?
[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.
I think a lot about how to more effectively teach MATLAB, internally to new hires, but also through my blog.
How did you learn MATLAB, what knowledge of programming did you have coming into learning MATLAB? When did you learn it is important also as the resources available have expanded radically in the last 15 years.
Answers from new users who are just beginning down this path are of particular interest, as those are who we can help the most.
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?
Don't be shy, what was your matlab learning curve, how many years or months, what were the difficulties to begin with.
I think that the answers would be most valuable for new users, maybe you can also tell us the tricks that allowed you to master some parts or all matlab.
Now it's your turn...
Which Matlab related forums and newsgroups do you use beside MATLAB Answers? Which languages do they use? Which advantages and unique features do they have?
Do you think that these forums complement or compete against MathWorks and its communication platform?
Actually all answers are accepted.
O.k., admit it. Who has done this (or something that resulted in the same loss of info) before?
>> laster
??? Undefined function or variable 'laster'.
>> lasterr
ans =
Undefined function or variable 'laster'.
D'Oh! I need a ERRORBEFORELASTERR function.
What's one of your dumb MATLAB mistakes?
