Hi there, I am a newbie to systems biology modeling. However, I am not new to Math. I am an engineer by training. I am currently evaluating Simbiology for my requirements for a research project. As I plow through the documentation related to systems biology modeling (mainly through SBML.org) I am confronted with a bewildering array of choices for modeling. However, I have narrowed it down to use either COPASI or Simbiology.
I have access to the full suite of MATLAB (including Simbiology) through the University. I am inclined to use Simbiology for my purposes. Here are my questions.
1) Do anyone of you perceive a big advantage to using one versus another? (Copasi vs Simbiology). With Simbiology, one of the advantages is of course the whole suite of MATLAB tools backing it up. But beyond that, are there any other perceived advantages?
2) My next question relates to Simbiology itself. As I go through literature, I have come across third party packages such as SBPOP package and the Potterswheel package for modeling. Are the packages COMPLEMENTARY to Simbiology package? Or do they have any additional benefits beyond what Simbiology can offer currently? Installation of those packages (Especially Potterswheel) does not seem straightforward and I am wondering if there is any advantage to adding them on.
3) I have been working with Simbiology examples as well. I am thoroughly confused about the need for a GUI based modeling setup versus using the .m file based approach. For example, I am working with the yeast example, and the code which is the MATLAB format seems quite comprehensive enough and easy to follow. Are there any outstanding reasons why I should use the GUI based approach to setup my model?
4) If I do create my model and analysis based on the GUI, is there a ready way to convert into MATLAB/Simbiology code?
5) I am not particularly impressed with the tutorials for setting up models currently available on the MATLAB help. Are there any resources for tutorials which will describe in detail the setup of a complex modeling scheme? I am looking for something beyond the 5 minute video introduction. I am particularly interested in using Simbiology for signaling pathway modeling and analysis. Are there any papers which use Simbiology and if so, would it be possible to have a look the code for the same? Any resources towards that end would be hugely useful!
These are probably newbie questions, but I would appreciate some ideas, resources and tips for me to move forward. Regards