VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology

Brinkrolf C, Ochel L, Hofestädt R (2021)
Biosystems: 104531.

Zeitschriftenaufsatz | E-Veröff. vor dem Druck | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Abstract / Bemerkung
Petri nets are a common method for modeling and simulation of systems biology application cases. Usually different Petri net concepts (e.g. discrete, hybrid, functional) are demanded depending on the purpose of the application cases. Modeling complex application cases requires a unification of those concepts, e.g. hybrid functional Petri nets (HFPN) and xHPN. Existing tools have certain limitations which motivated the extension of VANESA, an existing open-source editor for biological networks. The extension can be used to model, simulate, and visualize Petri nets based on the xHPN formalism. Moreover, it comprises additional functionality to support and help the user. Complex (kinetic) functions are syntactically analyzed and mathematically rendered. Based on syntax and given physical unit information, modeling errors are revealed. The numerical simulation is seamlessly integrated and executed in the background by the open-source simulation environment OpenModelica utilizing the Modelica library PNlib. Visualization of simulation results for places, transitions, and arcs are useful to investigate and understand the model and its dynamic behavior. The impact of single parameters can be revealed by comparing multiple simulation results. Simulation results, charts, and entire specification of the Petri net model as Latex file can be exported. All these features are shown in the demonstration case. The utilized Petri net formalism xHPN is fully specified and implemented in PNlib. This assures transparency, reliability, and comprehensible simulation results. Thus, the combination of VANESA and OpenModelica shape a unique open-source Petri net environment focusing on systems biology application cases. VANESA is available at: http://agbi.techfak.uni-bielefeld.de/vanesa. Copyright © 2021. Published by Elsevier B.V.
Erscheinungsjahr
2021
Zeitschriftentitel
Biosystems
Art.-Nr.
104531
eISSN
1872-8324
Page URI
https://pub.uni-bielefeld.de/record/2957504

Zitieren

Brinkrolf C, Ochel L, Hofestädt R. VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology. Biosystems. 2021: 104531.
Brinkrolf, C., Ochel, L., & Hofestädt, R. (2021). VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology. Biosystems, 104531. https://doi.org/10.1016/j.biosystems.2021.104531
Brinkrolf, C., Ochel, L., and Hofestädt, R. (2021). VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology. Biosystems:104531.
Brinkrolf, C., Ochel, L., & Hofestädt, R., 2021. VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology. Biosystems, : 104531.
C. Brinkrolf, L. Ochel, and R. Hofestädt, “VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology”, Biosystems, 2021, : 104531.
Brinkrolf, C., Ochel, L., Hofestädt, R.: VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology. Biosystems. : 104531 (2021).
Brinkrolf, Christoph, Ochel, Lennart, and Hofestädt, Ralf. “VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology”. Biosystems (2021): 104531.

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 34492317
PubMed | Europe PMC

Suchen in

Google Scholar