Newbie questions in Simbiology

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

Answer 1

[Ingrid Tigges]

I am not sure how much I can help you with your first two questions, but let me help you with the other three. There is no need to use the SimBiology Desktop, if you do not want to. The desktop is just a place where you can find examples. You can use the examples also from the command line. The examples all have a name with the ending .sbproj. If you want to load one of them from the command line simply use the following kind of syntax

    sbioexample=sbioloadproject('Goldbeter_Mitotic_Oscillator_with_reactions.sbproj')

If I understand you correctly you are used to programming in MATLAB. Most things you can do programmatically in SimBiology you can also do via the Desktop and vice versa. Not everyone who would like to do modelling is familiar with programming and for these kind of users the Desktop is really helpful. Even if you are good in programming you might want to use the Desktop in order to get a nice diagram showing the pathway you were modelling. In order to export a model from the SimBiology Desktop to the command line simply click on the right triangle next to the navigation panel and select Export to Workspace.

It might be also good to keep in mind that "A project saves related models, tasks, and data in a project file with an .sbproj extension." (see Documentation about .sbproj files)

Have you been on this webpage SimBiology project page ? There you can find a link to (free) Webinars, of which some are longer than 45 min and much more.

On this page MathWorks Support you can find links to useful resources that can help you, among them a page to contact Technical Support. Please do not hesitate to contact Technical Support if you need help, have enhancement requests etc..

I hope this helps.

Ingrid