sigmoidal curve fitting, calculating IC/EC50, and plotting the fitted curve

perlfun has asked for the wisdom of the Perl Monks concerning the following question:

Hi all,

I am searching for any existing perl modules to do a sigmoidal curve fitting, calculate IC/EC50, and plot the fitted curve. I don't seem to be able to find any good modules to do these.

Bio::SDRS is the only module I can find that will calculate EC50, but it's extremely slow, and it does not have method to draw the fitted curve. Could any of you please give me some suggestions regarding my problem above?

Thanks very much.

Comment on sigmoidal curve fitting, calculating IC/EC50, and plotting the fitted curve

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Re: sigmoidal curve fitting, calculating IC/EC50, and plotting the fitted curve by bitingduck (Deacon) on May 10, 2012 at 15:14 UTC
I've never done it in Perl, but did do it in C a few million years ago using algorithms from Numerical Recipes. A search on "Levenberg Marquardt perl" turns up this: Perl Data Language. It's not a totally canned tool for what you want, but you should be able to use Levmar to do what you want, at least fit-wise	[reply]
Re^2: sigmoidal curve fitting, calculating IC/EC50, and plotting the fitted curve by etj (Priest) on May 23, 2022 at 20:26 UTC
An updated URL for the latest release of PDL::Fit::Levmar: https://metacpan.org/dist/PDL-Fit-Levmar.	[reply]
Re: sigmoidal curve fitting, calculating IC/EC50, and plotting the fitted curve by zentara (Cardinal) on May 10, 2012 at 18:04 UTC
The PDL maillist has some very helpful people on it. Just ask. I'm not really a human, but I play one on earth. Old Perl Programmer Haiku ................... flash japh	[reply]
Re: sigmoidal curve fitting, calculating IC/EC50, and plotting the fitted curve by spx2 (Deacon) on May 14, 2012 at 09:16 UTC
Give an example of what you want to achieve. Some parameters and the result you expect to get. I see that maxima has least squares curve fitting , would that be a good method to fit the sigmoidal curve ? I wrote an interface to Maxima and you could use that to fit the curve you need. Oh btw, I just found found a java applet that does what you want here. Here is the .jar for it(here's a mirror for the jar just in case). Also here's a Java decompiler that worked for me. The next step is pretty obvious, just take all the Java source code and conver it to Perl. Not very hard, but it will take some time. Does this solve your problem ?	[reply]