Science Buddies: "Ask an Expert"

Do you guys no of any programs that would be useful in modeling the production of certain chemicals? I was thinking of using COPASI but I was wondering if other programs would be better suited...

COPASI seems to be the best program for modeling metabolic pathways one chemical reaction at a time. You are going to need the rates of each of your chemical reactions you enter into your model. Can you give me some more details on what kind of chemical reactions you are going to be looking at, and what kind of output you want?

-microkts

Thanks for responding,
I'm currently planning to model the production of free radicals over the mitochondria during oxidative phosphorylation to see if the concentration is great enough to override and possibly damage antioxidant defense systems. Either this or I might model the IGF-1 pathway. What program/ computer language would you suggest for the second one?

This project sounds really fascinating. Unfortunately I am only familiar with the language Perl, which I don't think will be helpful in this case. It looks like COPASI uses XML. I think you should be able to use COPASI for either of your proposed projects. The IGF-1 signaling pathways is really just a cascade of phosphorylation reactions. You should be able to use COPASI to model these chemical reactions the same way you would the chemical reactions in the mitochondria. If you need more help on the programming I would recommend posting those to the math and computer science part of the forum.

-microkts

I was wondering,
For my project I need to learn a computer programming language. One database on aging is run by Perl this is:http://genomics.senescence.info/software/index.html. Would you recommend using perl for a computing project such as this and is Perl hard to learn?

Thanks again.

Hi Scientia,

Perl is mainly based off of other computer languages. How much experience do you have with computer programming? It may be too difficult if you are new to programming. You will also have to be able to download the perl interpreter to run your scripts.

Here is a description of Perl from the website www.perl.org:

"Perl is a high-level programming language with an eclectic heritage written by Larry Wall and a cast of thousands.
Perl's process, file, and text manipulation facilities make it particularly well-suited for tasks involving quick prototyping, system utilities, software tools, system management tasks, database access, graphical programming, networking, and web programming.
Perl derives from the ubiquitous C programming language and to a lesser extent from sed, awk, the Unix shell, and many other tools and languages.
These strengths make it especially popular with web developers and system administrators, but mathematicians, geneticists, journalists, and managers also use Perl. Maybe you should, too."

This web page has a lot of really good resources to help you figure out if Perl is right for your project. The FAQ page (http://learn.perl.org/faq/perlfaq1.html#What-is-Perl-) has some subjects on whether or not to use Perl. And there learn tab has lots of great links to get you started if you decide to learn Perl.

You can always ask the computer science forum about your programming questions. We have lots of computer experts over there.

I hope this was helpful, and let me know if you have any more questions.
-microkts