Abstract
In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.
Highlights
Modeling biological systems is necessary to understand and predict behavior
Some of the features, such as export of simulation results are implemented in Cell Illustrator and Snoopy, while some features are implemented in only one of the tools
The new features implemented in VANESA significantly facilitated modeling the aerobic metabolism of C. reinhardtii
Summary
Modeling biological systems is necessary to understand and predict behavior. Depending on available information about the system of interest, different modeling approaches can be selected, e.g. static versus dynamic, discrete versus continuous or deterministic versus probabilistic. With advances in high throughput measurement techniques in systems biology, an increasing amount of large-scale biological data will be produced These quantitative data sets enable the construction of (partially) quantitative models which can be realized using HFPN formalism. The extended hybrid Petri net formalism (xHPN) [6] unifies different Petri net concepts, such as HPN, HFPN, and stochastic Petri nets [7], among others It offers hybrid modeling using discrete, continuous, and stochastic transitions as well as discrete and continuous places and standard arcs, inhibitory arcs, and test arcs. VANESA [12] is a software for modeling, simulating and analyzing biological networks. We describe important changes of VANESA, and compare them with the implementations of Cell Illustrator 4.0 (latest scientific publication) and Snoopy 1.21
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