Petri-Netz-basierte Simulation biologischer Prozesse mit OpenModelica

Ochel L. Petri-Netz-basierte Simulation biologischer Prozesse mit OpenModelica. Bielefeld: Universität Bielefeld; 2017

Symbolic Initialization of Over-determined Higher-index Models

Abstract The quantity of initial equations required in an objectoriented model can only be determined at system level. Since Modelica models are generally designed by components, it is difficult to calculate the amount of initial equations needed at system level, especially when changes are applied to the model, e.g. by adding or removing components. Therefore, it is more convenient to define initial equations at component level. Due to component connections, algebraic dependencies between states may be introduced, which eventually lead to the removal of states when symbolic index reduction algorithms are applied. In this process, the corresponding initial equations are not automatically removed, which results in an over-determined initial system. This paper describes an algorithm that detects such redundant equations and determines if they are consistent or not. Consistent redundant initial equations can thus be removed automatically, and inconsistent ones can be reported to the modeler. A prototype of the algorithm is implemented in OpenModelica, tested on several representative cases, and compared to previously presented concepts

The OpenModelica integrated environment for modeling, simulation, and model-based development

OpenModelica is a unique large-scale integrated open-source Modelica- and FMI-based modeling, simulation, optimization, model-based analysis and development environment. Moreover, the OpenModelica environment provides a number of facilities such as debugging; optimization; visualization and 3D animation; web-based model editing and simulation; scripting from Modelica, Python, Julia, and Matlab; efficient simulation and co-simulation of FMI-based models; compilation for embedded systems; Modelica- UML integration; requirement verification; and generation of parallel code for multi-core architectures. The environment is based on the equation-based object-oriented Modelica language and currently uses the MetaModelica extended version of Modelica for its model compiler implementation. This overview paper gives an up-to-date description of the capabilities of the system, short overviews of used open source symbolic and numeric algorithms with pointers to published literature, tool integration aspects, some lessons learned, and the main vision behind its development.Fil: Fritzson, Peter. Linköping University; SueciaFil: Pop, Adrian. Linköping University; SueciaFil: Abdelhak, Karim. Fachhochschule Bielefeld; AlemaniaFil: Asghar, Adeel. Linköping University; SueciaFil: Bachmann, Bernhard. Fachhochschule Bielefeld; AlemaniaFil: Braun, Willi. Fachhochschule Bielefeld; AlemaniaFil: Bouskela, Daniel. Electricité de France; FranciaFil: Braun, Robert. Linköping University; SueciaFil: Buffoni, Lena. Linköping University; SueciaFil: Casella, Francesco. Politecnico di Milano; ItaliaFil: Castro, Rodrigo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Investigación en Ciencias de la Computación. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Investigación en Ciencias de la Computación; ArgentinaFil: Franke, Rüdiger. Abb Group; AlemaniaFil: Fritzson, Dag. Linköping University; SueciaFil: Gebremedhin, Mahder. Linköping University; SueciaFil: Heuermann, Andreas. Linköping University; SueciaFil: Lie, Bernt. University of South-Eastern Norway; NoruegaFil: Mengist, Alachew. Linköping University; SueciaFil: Mikelsons, Lars. Linköping University; SueciaFil: Moudgalya, Kannan. Indian Institute Of Technology Bombay; IndiaFil: Ochel, Lennart. Linköping University; SueciaFil: Palanisamy, Arunkumar. Linköping University; SueciaFil: Ruge, Vitalij. Fachhochschule Bielefeld; AlemaniaFil: Schamai, Wladimir. Danfoss Power Solutions GmbH & Co; AlemaniaFil: Sjolund, Martin. Linköping University; SueciaFil: Thiele, Bernhard. Linköping University; SueciaFil: Tinnerholm, John. Linköping University; SueciaFil: Ostlund, Per. Linköping University; Sueci

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

Brinkrolf C, Ochel L, Hofestädt R. VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology. Biosystems. 2021: 104531.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

Rural cycling in focus

Even though cycling is slowly starting to get recognised as the sustainable mode of transport it is, this is mostly limited to short trips in urban areas. However, also in rural environments the bicycle has potential to replace the car for many trips. Best practice and research findings from urban areas cannot necessarily be directly applied to the rural environment, as preconditions can differ substantially. Speeds are higher, most interactions are longitudinal, the road is often shared, and the trip purposes and road users are likely to have different characteristics. This is also reflected in the differences in crash typology for rural and urban environments. This project aimed at further describing conflicts on rural roads between motorists and active travellers in a Swedish context by analysing crash statistics. The development of a logger that provides measurements of overtaking and oncoming passes in detail and can in the future then be used to quantify the context for situations that do not result in a (documented) collision. This way, collisions can be put into perspective for example in relation to the context (road type, speed limit, average annual daily traffic, etc.). Objective and reliable measurements of longitudinal interactions between motorists and active road users – namely overtaking and oncoming passes – are one important ingredient to assessing the current situation and the effectiveness of potential countermeasures. The measurement devices used in research so far are usually custom-built and the data reduction process is often not fully transparent. Within this project, we built an expandable device for logging the lateral distance to overtaking and oncoming vehicles and the approach speed of overtaking vehicles. The process to extract the passing occasions and the correct overtaking distance is made available as open source

Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA

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

Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA

Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics. 2018;15(3): 20180018.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