Category Archives: SBML

How do I change the simulation tolerances in Tellurium?

For very complicated and large models it may be necessary to adjust the simulator tolerances in order to get the correct simulation results. Sometimes the simulator will terminate a simulation because it was unable to proceed due to numerical errors. … Continue reading

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How to get the Stoichiometry Matrix using Tellurium

Here is a simple need, given a reaction model how do we get hold of the stoichiometry matrix? Consider the following simple model: import tellurium as te import roadrunner r = te.loada(“”” $Xo -> S1; k1*Xo; S1 -> S2; k2*S1; … Continue reading

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How to do a simple simulation using Telluirum

The most common requirement is the ability to carry out a simple time course simulation of a model. Consider the model:     Two reactions and three metabolites, S1, S2 and S3. We can describe this system using an Antimony … Continue reading

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How do I run a stochastic simulation using Tellurium/libRoadRunner?

In this post I will show you how to run a stochastic simulation using our Tellurium application. Tellurium is a set of libraries that can be used via Python. One of those libraries is libRoadRunner which is our very fast … Continue reading

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My First Mac OS Application

I finished my first Mac OS application. Two screenshots are shown below, I’ll be making it available download at the end of the week. This was a test application to see how easy it would be use write a portable … Continue reading

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File Format For JDesigner

I’m in the middle of redesigning JDesigner’s file format. I’ve been using SBML since its inception in 2000 and JDesigner uses SBML as its native format by using the annotation mechanism to store all the layout and rendering information plus … Continue reading

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New version of libRoadRunner Released 1.0.1

A new version of libroadrunner has just been released. Details are given below. Of particular interest to windows users is the availability of a new windows installer which installs everything you need to run libroadrunner, even if you haven’t got … Continue reading

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Announce: release of libRoadRunner 1.0.0

After a lot of work I am pleased to announce the first official release of libRoadRunner, 1.0.0. This represents a complete rewrite of the original C# RoadRunner developed by Frank Bergmann and Herbert Sauro. libRoadRunner is a high-performance cross-platform C/C++ library that supports … Continue reading

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Irreversible Bistability

Last week I was in need of an irreversible bistable switch to show my class. I remember seeing one in the well known review by Tyson et al, Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in … Continue reading

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Default Compartments in SBML

A reoccurring problem that I’ve had with SBML since day one is how to deal with a default compartment. Take for example a visual design tool such as JDesigner. At start up it creates an implicit compartment represented by the empty canvas. … Continue reading

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