search

MyersResearchGroup / iBioSim

iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
http://www.async.ece.utah.edu/ibiosim
Apache License 2.0
53 stars 20 forks source link

BUG: Reaction-based abstraction does not speed up Monte Carlo simulation #161

Open buggsley opened 7 years ago

buggsley commented 7 years ago

The reb2sac gillespie simulator does not seem to speed up when reaction-based abstraction is applied. Example file is the phage lambda decision circuit in the Systems Biology tutorial. The SSA without abstraction took 13.61866835 seconds, but the one with reaction-based abstraction took 12.133898569 seconds. Note that the Total_CI assignment rule was disabled for the reaction-based abstraction.

buggsley commented 7 years ago

Also, the average of CI with abstraction settles at 7.5, whereas it settles at 20 on the screenshot of the Systems Biology tutorial.

buggsley commented 7 years ago

The problem with this one is that the event, rule, and constraints must be removed for the abstraction to take place completely. This should be updated in the tutorial to make this clear. Moving this to documentation.