Simbiology webinar

 

 

This week I attended the mathworks webinar on Simbiology.  I had seen this software used by researchers at Imperial Collage and was interested to see what it could do in comparison with Copasi.  The webinar was delivered using Webex and was well presented with a mixture of slides to structure the talk, and live matlab interaction.

Simbiology is an extension to matlab and provides a point and click style interface for building models of interactions, performing simulations, and outputting graphical data.

Simbiology can import data from a number of databases, such as Kegg, and can import entire pathways into a graphical tool, similar to JDesigner.

Reactions are inputted using a similar interface to Copasi, which includes species, reactions, and compartments, as well as the facility to code custom rate laws.

Simulations can be run using deterministic, stochastic, and hybrid integrators.  Simbiology can also perform parameter estimation using experimental data to fit the model behavior.

Overall, Copasi appears to incorporate a larger number of parameter estimation algorithms, and this remains the major strength of it over the likes of Simbiology.  Simbiology however integrates with the command line of matlab, enabling users to drop into the code at any time and write/edit their own functions.  Simbiology can interface with many different databases to pull down model parameter data from virtually anywhere, and provides a much more flexible tool for modeling than Copasi.  The user is also presented with the opportunity of coding additional functions and tools from Matlab, which is not possible in Copasi without editing the applications source code, in C.

Simbiology can perform sensitivity analysis, but appears to lack metabolic control analysis (although the two are synonymous, so I don’t suppose this really matters).  Simbiology is also unable to analyse steady states, and expand around them to find multiple steady states and bifurcation points.  Bifurcation analysis is apparently being worked on for future versions, but no further information was available on the development of this.  I was surprised that once again XPPAUT appears to retain it’s unique ability to do this from a GUI, and remains the best software for this kind of analysis.

For the price difference, Copasi contains a significant proportion of functions of simbiology, and is certainly sufficient for systems biologists, with the language bindings to access it from the command line. Coupled with XPPAUT, these tools provide more features than simbiology.

Simbiology is going to continue to develop however, and the flexibility of matlab, together with the awesome amount of code available at the matlab file exchange provides a much more flexible toolkit for the hardcore modeler.  Simbiology could also potentially output graphs using matlab plotting functions, which would enable surface plots, and matlabs extensive graphics functions, which is lacking from Copasi.  Statistical analysis could also be done alongside the simulations as well, which would require additional software if using other open source applications.  For the freelancer or poor academic however, the open source tools still give mathworks a run for their money, for now.  If you have a matlab + simbiology license already however, it’s a comprehensive tool set that is accessible to biologists, and builds a matlab coding skill alongside modeling the biology.