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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
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BUG: problems with two biomodels #9

Open buggsley opened 7 years ago

buggsley commented 7 years ago

For two biomodels (13 and 70), simulation is incredibly slow. Details
of road runner on these examples is below. Can this be exploited to
improve our results.

Begin forwarded message:

From: "Frank T. Bergmann" fbergman@u.washington.edu Date: February 8, 2010 1:46:01 PM MST To: "'Chris J. Myers'" myers@ece.utah.edu Subject: RE: Question

We are using CVODE as available from here:

https://computation.llnl.gov/casc/sundials/description/ description.html

roadRunner can be controlled via web service ... and thus all values
can easily be changed ... currently roadRunner is using:

<section name = "integration" method ="CVODE" description = "CVODE Integrator"> <cap name = "BDFOrder" value = "5" hint = "Maximum order for BDF
Method" type = "int"/> <cap name = "AdamsOrder" value = "12" hint = "Maximum order for
Adams Method" type = "int"/> <cap name = "rtol" value = "1E-06" hint = "Relative Tolerance"
type = "double"/> <cap name = "atol" value = "1E-16" hint = "Absolute Tolerance"
type = "double"/> <cap name = "maxsteps" value = "10000" hint = "Maximum number of
internal steps" type = "int"/>

http://128.208.17.26/generate/edu_kgi_roadRunner.asmx/getCapabilities

however you are correct, CVODE uses adaptive step sizes, and
roadRunner only supplies the points closes to the requested output points.

best Frank

-----Original Message----- From: Chris J. Myers [mailto:myers@ece.utah.edu] Sent: Monday, February 08, 2010 12:40 PM To: Frank Bergmann Subject: Question

What ODE algorithm are you using in road runner? I assume that it is adaptive time step. What absolute and relative error are the
defaults for the web interface? Are there any other special parameters?

It seems that models 13 and 70 require a very small time step initially which bogs down my simulator. If I try to prevent the time step from getting too small, the results diverge. It is quite
strange.

Thanks,

Chris

buggsley commented 7 years ago

Should check these on the new Java simulator as well as reb2sac.