@phdthesis{Chodak2021, author = {Chodak, Jacek}, title = {Spike - a tool for reproducible simulation experiments}, doi = {10.26127/BTUOpen-5850}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-58509}, school = {BTU Cottbus - Senftenberg}, year = {2021}, abstract = {Reproducibility of simulation experiments is still a significant challenge and has attracted considerable attention in recent years. One cause of this situation is bad habits of the scientific community. Many results are published without data or source code, and only a textual description of the simulation set-up is provided. Other causes are: no complete simulation set-up, no proper output data analysis and inconsistency of published data, which makes it impossible to compare results. The progress of computational modelling, amount of data and complexity of models requires designing experiments in such a way that ensures reproducibility. A textual description does not provide all the needed details. A computer code is more reliable than a textual description. It is the precise specification that describes a simulation configuration, model, etc. When computer code, data, models and all parameters are provided, the simulation results become reproducible. The main goal of this thesis is to develop a tool that ensures reproducibility and efficient execution of simulation experiments, often involving many individual simulation runs. The tool should support a wide range of application scenarios, where the typical scenario is simulation of biochemical reaction networks, which are represented as (coloured) Petri nets interpreted in the stochastic, continuous or hybrid paradigm. The model to be simulated can be given in various formats, including SBML. The result is a command line tool called Spike, which can be used for various scenarios, including benchmarking, simulation of adaptive models and parameter optimization. It builds on a human-readable configuration script SPC, supporting the efficient specification of multiple model configurations as well as multiple simulator configurations in a single configuration file.}, subject = {Petri nets; Parallel simulation; Parameter scanning; Reproducibility; Simulation of adaptive models; Petri Netze; Parallelsimulation; Parameterscannen; Reproduzierbarkeit; Simulation von adaptiven Modellen; Gef{\"a}rbtes Petri-Netz; Simulation; Reproduzierbarkeit}, language = {en} } @techreport{SchwarickRohrHeiner2016, author = {Schwarick, Martin and Rohr, Christian and Heiner, Monika}, title = {MARCIE manual}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-40568}, year = {2016}, abstract = {This manual gives an overview on MARCIE - Model Checking And Reachability analysis done effiCIEntly. MARCIE was originally developed as a symbolic model checker for stochastic Petri nets, building on its predecessor - IDDMC - Interval Decision Diagram based Model Checking - which has been previously developed for the qualitative analysis of bounded Place/Transition nets extended by special arcs. Over the last years the tool has been enriched to allow also quantitative analysis of extended stochastic Petri nets. We concentrate here on the user viewpoint. For a detailed introduction to the relevant formalisms, formal definitions and algorithms we refer to related literature.}, subject = {Petri nets; Model checking; Model Checking; Petri-Netz}, language = {en} } @techreport{Sinha2014, author = {Sinha, Aman}, title = {Comparison of stochastic simulation tools}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-31460}, year = {2014}, abstract = {This report compares some stochastic simulation tools for biochemical reaction networks. The stochastic simulation tools are selected on the basis of some selection criteria. Simulations are performed for the different stochastic simulation tools on different benchmark models. This report gives an overview of how the comparison is carried out for the chosen tools. The tools are compared on a common evaluation protocol. The evaluation protocol comprises a set of benchmark models along with the parameters which are provided as input to the tools. The benchmark models are represented as Petri nets and fed in SBML (System Biology Markup Language) to the different tools. Experiments are performed on each tool and the results are recorded. The tools are finally compared based on the comparison criteria.}, subject = {Benchmarks; Biochemical reaction networks; Evaluation protocol; SBML; Stochastic simulation; Stochastisches Modell; Petri-Netz}, language = {en} } @techreport{Nolte2013, author = {Nolte, J{\"o}rg}, title = {12. GI/ITG Fachgespr{\"a}ch Sensornetze}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-28986}, year = {2013}, abstract = {Drahtlose Sensornetze stellen eine vielversprechende Technologie zur Beobachtung und Beeinflussung von Vorg{\"a}ngen in der realen Welt dar. Autonome Sensorknoten nehmen dabei Parameter der Umwelt durch Sensoren wahr und k{\"o}nnen diese durch Aktoren beeinflussen. Viele solcher autonomen und ressourcenbeschr{\"a}nkten Knoten kooperieren dabei mittels drahtloser Kommunikation. Die Eigenschaften dieser Knoten und Netze implizieren eine Vielzahl von neuartigen Herausforderungen, die sich in einer regen Forschungsaktivit{\"a}t widerspiegeln. Ziel dieser Reihe von Fachgespr{\"a}chen ist es, Wissenschaftlerinnen und Wissenschaftlern aus Hochschule und Industrie die M{\"o}glichkeit zu einem informellen Gedankenaustausch zu geben und die Kooperation in diesem multidisziplin{\"a}ren Forschungsbereich zu verst{\"a}rken.}, subject = {Drahtloses Sensorsystem}, language = {en} } @techreport{NoackSchmittSaretz2013, author = {Noack, Tino and Schmitt, Ingo and Saretz, Sascha}, title = {OVA-based multi-class classification for data stream anomaly detection}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-28187}, year = {2013}, abstract = {Mobile cyber-physical systems (MCPSs), such as the International Space Station, are equipped with sensors which produce sensor data streams. Continuous changes like wear and tear influence the system states of a MCPS continually during runtime. Hence, monitoring is necessary to provide reliability and to avoid critical damage. Although, the monitoring process is limited by resource restrictions. Therefore, the focal point of the present paper is on time-efficient multi-class data stream anomaly detection. Our contribution is bifid. First, we use a one-versusall classification model to combine a set of heterogeneous one-class classifiers consecutively. Such a chain of one-class classifiers provides a very flexible structure while the administrative overhead is reasonably low. Second, based on the classifier chain, we introduce classifier pre-selection.}, subject = {Informatik}, language = {en} } @techreport{Schmitt2019, author = {Schmitt, Ingo}, title = {Quantum-based construction of a probability measure}, editor = {Schmitt, Ingo}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-50760}, year = {2019}, abstract = {From Gleason's theorem we know that in principle every probability measure can be expressed by Hermitian operators in a separable Hilbert space and the Born rule as part of a quantum mechanical system. However, that theorem is not constructive. For a given discrete and additive probability measure based on a σ-algebra we construct a quantum system with projectors expressing that probability measure.}, subject = {Quantum modelling; Probability measure; Wahrscheinlichkeitsmetrik; Mathematische Modellierung; Quanteninformatik}, language = {en} } @techreport{HerajyLiuRohretal.2017, author = {Herajy, Mostafa and Liu, Fei and Rohr, Christian and Heiner, Monika}, title = {(Coloured) Hybrid Petri nets in Snoopy - user manual}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-41572}, year = {2017}, abstract = {Hybrid simulation of biological processes becomes widely used to overcome the limitations of the pure stochastic or the complete deterministic simulation. In this manual, we present easy-to-follow steps for constructing and executing hybrid models via Snoopy [HHL+12]. Snoopy is a tool to design and animate or simulate hierarchical graphs, i.e., qualitative, stochastic, continuous, and hybrid Petri nets. This manual is concerned with hybrid Petri nets (HPN) [HH12] as well as their coloured counterpart (HPNC) [HLR14]. HPN combine the merits of stochastic and continuous Petri nets into one single class. Moreover, HPN in Snoopy supports state of the art hybrid simulation algorithms (e.g., [HH16]) to execute the constructed HPN models. Simulating a model using Snoopy's hybrid simulation involves first constructing the reaction network via HPN notations and afterwards executing such model.}, subject = {Petri net; Hierarchical graph; Gef{\"a}rbtes Petri-Netz; Hybridsimulation}, language = {en} } @techreport{LieskeNoackSchwalbeetal.2016, author = {Lieske, Henry and Noack, Daniel and Schwalbe, Christoph and Vogel, Elisabeth and Hinze, Thomas}, title = {Faszination Molekulares Rechnen: Studentische Beitr{\"a}ge vermitteln Erkenntnisse interdisziplin{\"a}rer Forschung}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-40328}, year = {2016}, abstract = {Molekulares Rechnen etabliert sich als interdisziplin{\"a}r gepr{\"a}gtes Wissensgebiet mit hohem Anwendungspotential. Es besch{\"a}ftigt sich mit Prinzipien biologischer Informationsverarbeitung. Molek{\"u}le bzw. molekulare Systeme {\"u}bernehmen die Rolle eines Datentr{\"a}gers, auf dem biochemische Prozesse oder physische Wechselwirkungen operieren. Facetten sind unter anderem DNA-Computing, chemisches Rechnen, Membrane Computing und ameisenbasiertes Computing. Vier studentische Beitr{\"a}ge stellen diese Forschungsrichtungen anhand eing{\"a}ngiger Beispiele anschaulich vor.}, subject = {Molekulares Rechnen; DNA Computing; Chemisches Rechnen; Membrane Computing; Ameisenbasiertes Computing; DNA computing; Chemical computing; Membrane computing; Molecular computing; Ant-based computing; Biocomputer; Molekulare Bioinformatik}, language = {de} } @misc{KurthBachmannHeineretal.2006, author = {Kurth, Winfried and Bachmann, Peter and Heiner, Monika and K{\"o}nig, Hartmut and Kraemer, Rolf and Lewerentz, Claus and Nolte, J{\"o}rg and Thalheim, Bernhard and Vierhaus, Heinrich Theodor and Braunm{\"u}hl, Burchard von and Wagner, Gerd}, title = {Jahresbericht 2003/2005 / Institut fuer Informatik, Informations- und Medientechnik}, organization = {Brandenburgische Technische Universit{\"a}t Cottbus / Institut f{\"u}r Informatik, Informations- und Medientechnik}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-3488}, year = {2006}, abstract = {Selbstdarstellung des Instituts f{\"u}r Informatik, Informations- und Medientechnik der BTU Cottbus und Berichte der Lehrst{\"u}hle f{\"u}r die Jahre 2003, 2004 und 2005.}, subject = {Cottbus / Technische Universit{\"a}t; Bericht; Informatik; Informations- und Medientechnik; BTU Cottbus; Computer Science; Information Technology; Media Technology; BTU Cottbus}, language = {de} } @misc{ThalheimHeinerBachmannetal.2001, author = {Thalheim, Bernhard and Heiner, Monika and Bachmann, Peter and K{\"o}nig, Hartmut and Lewerentz, Claus and Vierhaus, Heinrich Theodor and Braunm{\"u}hl, Burchard von}, title = {Jahresbericht 2000/ Institut f{\"u}r Informatik}, organization = {Brandenburgische Technische Universit{\"a}t Cottbus / Institut f{\"u}r Informatik}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-3533}, year = {2001}, abstract = {Selbstdarstellung des Instituts f{\"u}r Informatik der BTU Cottbus und Berichte der Lehrst{\"u}hle f{\"u}r das Jahr 2000.}, subject = {Cottbus / Technische Universit{\"a}t; Bericht; Informatik; BTU Cottbus; Computer Science; BTU Cottbus}, language = {de} } @misc{ThalheimHeinerBachmannetal.2000, author = {Thalheim, Bernhard and Heiner, Monika and Bachmann, Peter and K{\"o}nig, Hartmut and Lewerentz, Claus and Vierhaus, Heinrich Theodor and Braunm{\"u}hl, Burchard von}, title = {Jahresbericht 1999 / Institut f{\"u}r Informatik}, organization = {Brandenburgische Technische Universit{\"a}t Cottbus / Institut f{\"u}r Informatik}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-3547}, year = {2000}, abstract = {Selbstdarstellung des Instituts f{\"u}r Informatik der BTU Cottbus und Berichte der Lehrst{\"u}hle f{\"u}r das Jahr 1999.}, subject = {Cottbus / Technische Universit{\"a}t; Bericht; Informatik; BTU Cottbus; Computer Science; BTU Cottbus}, language = {de} } @misc{ThalheimHeinerKurthetal.2003, author = {Thalheim, Bernhard and Heiner, Monika and Kurth, Winfried and Bachmann, Peter and K{\"o}nig, Hartmut and Lewerentz, Claus and Vierhaus, Heinrich Theodor and Braunm{\"u}hl, Burchard von and Nolte, J{\"o}rg}, title = {Jahresbericht 2001/2002 / Institut f{\"u}r Informatik}, organization = {Brandenburgische Technische Universit{\"a}t Cottbus / Institut f{\"u}r Informatik}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-3527}, year = {2003}, abstract = {Selbstdarstellung des Instituts f{\"u}r Informatik der BTU Cottbus und Berichte der Lehrst{\"u}hle f{\"u}r die Jahre 2001 und 2002.}, subject = {Cottbus / Technische Universit{\"a}t; Bericht; Informatik; BTU Cottbus; Computer Science; BTU Cottbus}, language = {de} } @misc{BachmannThalheimHeineretal.1999, author = {Bachmann, Peter and Thalheim, Bernhard and Heiner, Monika and Lux, Gregor and K{\"o}nig, Hartmut and Lewerentz, Claus and Vierhaus, Heinrich Theodor and Braunm{\"u}hl, Burchard von}, title = {Jahresbericht 1998 / Institut f{\"u}r Informatik}, organization = {Brandenburgische Technische Universit{\"a}t Cottbus / Institut f{\"u}r Informatik}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-3559}, year = {1999}, abstract = {Selbstdarstellung des Instituts f{\"u}r Informatik der BTU Cottbus und Berichte der Lehrst{\"u}hle f{\"u}r das Jahr 1998.}, subject = {Cottbus / Technische Universit{\"a}t; Bericht; Informatik; BTU Cottbus; Computer Science; BTU Cottbus}, language = {de} } @misc{LewerentzThalheimHeineretal.1998, author = {Lewerentz, Claus and Thalheim, Bernhard and Heiner, Monika and Lux, Gregor and Bachmann, Peter and K{\"o}nig, Hartmut and Vierhaus, Heinrich Theodor and Braunm{\"u}hl, Burchard von}, title = {Jahresbericht 1997 / Institut f{\"u}r Informatik}, organization = {Brandenburgische Technische Universit{\"a}t Cottbus / Institut f{\"u}r Informatik}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-3563}, year = {1998}, abstract = {Selbstdarstellung des Instituts f{\"u}r Informatik der BTU Cottbus und Berichte der Lehrst{\"u}hle f{\"u}r das Jahr 1997.}, subject = {Cottbus / Technische Universit{\"a}t; Bericht; Informatik; BTU Cottbus; Computer Science; BTU Cottbus}, language = {de} } @techreport{HerajyHeiner2013, author = {Herajy, Mostafa and Heiner, Monika}, title = {Snoopy computational steering framework - user manual version 1.0}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus-29034}, year = {2013}, abstract = {In this manual we discuss the use of Snoopy's computational steering framework to simulate and interactively steer (stochastic, continuous, hybrid) Petri nets, e.g., biochemical network models. In a typical application scenario, a user constructs a model using a Petri net editing tool (e.g., Snoopy). Afterwards, the Petri net model is submitted to one of the running servers to quantitatively simulate it. Later, other users can adapt their steering GUIs to connect to this model. One of the connected users initialises the simulation while others could stop, pause, or restart it. When the simulator initially starts, it uses the current model settings to run the simulation. Later, other users can remotely join the running simulation and change on the fly parameters and the current marking.}, subject = {Datenstruktur; Zuverl{\"a}ssigkeit}, language = {en} } @techreport{Swapnil2014, author = {Swapnil, Chiru}, title = {Stochastic simulation efficiency}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:co1-opus4-31479}, year = {2014}, abstract = {The work described in this report can be broadly divided into two sections. The first section considers two export features. We describe how the export for stochastic Petri nets to SBML level 1 has been added to the Petri net modelling and simulation tool Snoopy. This task was accomplished by making appropriate changes to the existing export code to generate SBML level 2. Also we demonstrate in detail, how the direct export for coloured Petri nets to both levels (i.e. 1 and 2) of SBML was realised. The next section summarises the performed comparison of different stochastic simulation tools for biochemical reaction networks. We first compare BioNetGen and SSC with each other by performing simulations on non-coloured Petri nets. Then, we compare the remaining four tools, i.e. Cain, Marcie, Snoopy and Stochkit with each other by performing simulation on coloured Petri nets. This work builds on results by Aman Sinha [19].}, subject = {Petri Nets; SBML; Stochastic simulation; Biochemical reaction networks; Export; MathML; Stochastisches Modell; Petri-Netz; Export}, language = {en} }