Category Archives: SBML

New version of libRoadRunner Released 1.0.1

A new version of libRoaduner has just been released. Details are given below. Of particular interest to windows users is the availability of a new windows installer which installer 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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New Release of SBW 2.8.3

This is to announce the release of a new version of SBW (Systems Biology Workbench). To those who are not familiar with it, SBW is a collection of collaborating tools for carrying out simulations of biochemical networks. Download here The … Continue reading

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Modeling Course at Indiana University

Not that kind of modeling, but the kind that involves building computational models of biochemical networks and multicellular systems. James Glazier, the Director of the Biocomplexity Institute at Indiana University is the lead organizer behind a series of workshops that … Continue reading

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Standards in Synthetic Biology: Part 1

Standards What are standards and why should we bother developing them? I suspect to many people including my fellow scientists and perhaps even some engineers, that standards are nether a rewarding nor worthwhile endeavor. Standards however are the invisible hand … Continue reading

Posted in General Science Interest, Molecular Biology, Pathways, SBML, Synthetic Biology | 2 Comments

SBML Parts Decomposition Tool

Biochemical Pathway Component Finder Ever wanted to extract a particular enzyme or reaction from a computational model? Perhaps not, but those of you who have, there is now a tool available to do that very task. Maxwell Neal from University … Continue reading

Posted in Enzyme Kinetics, General Science Interest, Modeling, Pathways, SBML | Leave a comment