Re: [Help-mcsim] Fwd: questions about MCSim

[Frédéric BOIS]

Dear Cindy,

I actually love the [] syntax, it's one of my most brilliant ideas. That being 
said, it is also half-baked and imperfect. In particular you should be aware
of the fact that you will NOT be able to use the vector syntax in your input 
files... Some of my collaborators asked me when I will finish that, and I
had to explain to them that it was a large task. But to answer specifically 
your questions:
The first (sad) answer is no: you cannot dynamically change the size of an 
array defined in MCSim.
Alternatives may exist: 
- Can you work with a maximum length vector and use only part of it in various 
runs ? (that would assume a particular structure 
  for your system) You could combine that with conditional statements for the 
computation of  the derivatives (for example
  dt(Y[1-20]) = (n < 10 ? a*Y[i-1] - b*Y[i] : 0);
  That's somewhat wasteful, but not too much, because null derivative states 
take no time to integrate.
- If you really feel like programming, you can indeed change the code, it's 
free for all. But honestly, you would be stretching quite far the syntax
  and the code, and I don't even have an idea where you would start, because 
there is no connection between run time inputs (defined in input files)
  and the precompilation model definition files. You would have to define a 
mechanism to define dynamic allocation of space and on the fly ODE
  rewriting... sounds impractical to me. You may want to look at a way 
(scripting) to generate automatically the model files and a template input file,
  recompile the model on the fly and run it. That's would be a way (but slow). 
Actually, if you are in mood for programming, the best use of your time
  would be to change the mcsim/sim codes to allow the bracket syntax in input 
files...
- You may also want to look at the latest capability of the code: to use a 
collection of separate SBML files and a template transport model to generate
  automatically a global model (but still, that would be slow if you wanted to 
run 1000 different models...). I haven't explored everything it can be used 
  for, and probably never will , but it might be useful to you, depending on 
what you want to do exactly.

I hope this helps a bit. Feel free to mail me again if you need further 
clarifications.

Best regards. 

Frederic


>>> Zhenhong Li <> 14/04/2009 21:26 >>>

Hello,

I am a PhD student at Oregon Health & Science University. I am using MCSim to 
do my modeling work for hormone profiles in Fathead Minnows. The question I 
would like to ask is about "vectors". 

According to MCSim manual, vectors should be defined as 
<variable-name>'['<integer>']'. Can I define the <integer> as a variable? I 
mean, for example, I would like to use a 'n' to replace the <integer>; then in 
the first run, I define n=10 (the vector has a length of 10), and in the second 
run I define n=7 (the vector has a length of 7), as so on. Then, for different 
runs, the length of the vector varies.

I tried several times, it seems that the present program does not accept it. 
Would you please give me any suggestion? Can I modify the program a little bit 
to add this function in? and how? Thank you very much!

Best!

Cindy