TY - THES A1 - Chodak, Jacek T1 - Spike - a tool for reproducible simulation experiments T1 - Spike - ein Werkzeug für reproduzierbare Simulationsexperimente N2 - 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. N2 - Die Reproduzierbarkeit von Simulationsexperimenten ist nach wie vor eine große Herausforderung und hat in den letzten Jahren viel Aufmerksamkeit bekommen. Eine Ursache für diese Situation sind schlechte Gewohnheiten der wissenschaftlichen Gemeinschaft. Aus irgendwelchen Gründen werden viele Ergebnisse ohne Daten und Quellcode veröffentlicht und es wird nur eine textliche Beschreibung des Simulationsaufbaus gegeben. Andere Ursachen sind: kein ordnungsgemäßer Simulationsaufbau, keine ordnungsgemäße Analyse der Ausgabedaten und Inkonsistenz der veröffentlichten Daten (was einen Vergleich der Ergebnisse unmöglich macht). Der Fortschritt der computergestützten Modellierung, die Datenmenge und die Komplexität der Modelle erfordern es, Experimente so zu gestalten, dass die Reproduzierbarkeit gewährleistet ist. Eine textliche Beschreibung liefert nicht alle Details. Ein Computercode ist zuverlässiger als eine Textbeschreibung. Es bedarf einer genauen Spezifikation einer Simulationskonfiguration, eines Modells usw. Durch die Bereitstellung von Computercode, Daten, Modellen und allen Parametern werden die Ergebnisse einer Simulation reproduzierbar. Das Hauptziel dieser Arbeit ist es, ein Werkzeug zu entwickeln, das die Reproduzierbarkeit und effiziente Durchführung von Simulationsexperimenten, die oft viele einzelne Simulationsläufe umfassen, gewährleistet. Das Werkzeug soll vielfältige Anwendungsszenarien unterstützen, wobei das typische Szenario die Simulation biochemischer Reaktionsnetzwerke ist, die als (farbige) Petri Netze dargestellt werden, die im stochastischen, kontinuierlichen oder hybriden Paradigma interpretiert werden. Das zu simulierende Modell kann in verschiedenen Formaten, einschließlich SBML, vorliegen. Das Ergebnis ist ein Kommandozeilenwerkzeug namens Spike, das in verschiedenen Anwendungsfällen eingesetzt werden kann, darunter Benchmarking, Simulation adaptiver Modelle und Parameteroptimierung. Es basiert auf einem für Menschen lesbaren Konfigurationsskript SPC und unterstützt die effiziente Spezifikation mehrerer Modellkonfigurationen sowie mehrerer Simulator-Konfigurationen in einer einzigen Konfigurationsdatei. KW - Petri nets KW - Parallel simulation KW - Parameter scanning KW - Reproducibility KW - Simulation of adaptive models KW - Petri Netze KW - Parallelsimulation KW - Parameterscannen KW - Reproduzierbarkeit KW - Simulation von adaptiven Modellen KW - Gefärbtes Petri-Netz KW - Simulation KW - Reproduzierbarkeit Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-58509 ER - TY - RPRT A1 - Schwarick, Martin A1 - Rohr, Christian A1 - Heiner, Monika T1 - MARCIE manual N2 - 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. T3 - Computer science reports / Institut für Informatik - 2016,02 KW - Petri nets KW - Model checking KW - Model Checking KW - Petri-Netz Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-40568 ER - TY - RPRT A1 - Sinha, Aman T1 - Comparison of stochastic simulation tools N2 - 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. T3 - Computer science reports / Institut für Informatik - 2014,01 KW - Benchmarks KW - Biochemical reaction networks KW - Evaluation protocol KW - SBML KW - Stochastic simulation KW - Stochastisches Modell KW - Petri-Netz Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-31460 ER - TY - RPRT A1 - Nolte, Jörg T1 - 12. GI/ITG Fachgespräch Sensornetze N2 - Drahtlose Sensornetze stellen eine vielversprechende Technologie zur Beobachtung und Beeinflussung von Vorgängen in der realen Welt dar. Autonome Sensorknoten nehmen dabei Parameter der Umwelt durch Sensoren wahr und können diese durch Aktoren beeinflussen. Viele solcher autonomen und ressourcenbeschränkten Knoten kooperieren dabei mittels drahtloser Kommunikation. Die Eigenschaften dieser Knoten und Netze implizieren eine Vielzahl von neuartigen Herausforderungen, die sich in einer regen Forschungsaktivität widerspiegeln. Ziel dieser Reihe von Fachgesprächen ist es, Wissenschaftlerinnen und Wissenschaftlern aus Hochschule und Industrie die Möglichkeit zu einem informellen Gedankenaustausch zu geben und die Kooperation in diesem multidisziplinären Forschungsbereich zu verstärken. T3 - Computer science reports / Institut für Informatik - 2013,03 KW - Drahtloses Sensorsystem Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-28986 ER - TY - RPRT A1 - Noack, Tino A1 - Schmitt, Ingo A1 - Saretz, Sascha T1 - OVA-based multi-class classification for data stream anomaly detection N2 - 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. T3 - Computer science reports / Institut für Informatik - 2013,01 KW - Informatik Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-28187 ER - TY - RPRT A1 - Schmitt, Ingo ED - Schmitt, Ingo T1 - Quantum-based construction of a probability measure N2 - 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. T3 - Computer science reports / Institut für Informatik - 2019, 1 KW - Quantum modelling KW - Probability measure KW - Wahrscheinlichkeitsmetrik KW - Mathematische Modellierung KW - Quanteninformatik Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-50760 ER - TY - RPRT A1 - Herajy, Mostafa A1 - Liu, Fei A1 - Rohr, Christian A1 - Heiner, Monika T1 - (Coloured) Hybrid Petri nets in Snoopy – user manual N2 - 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. T3 - Computer science reports / Institut für Informatik - 2017,01 KW - Petri net KW - Hierarchical graph KW - Gefärbtes Petri-Netz KW - Hybridsimulation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-41572 ER - TY - RPRT A1 - Lieske, Henry A1 - Noack, Daniel A1 - Schwalbe, Christoph A1 - Vogel, Elisabeth A1 - Hinze, Thomas T1 - Faszination Molekulares Rechnen: Studentische Beiträge vermitteln Erkenntnisse interdisziplinärer Forschung N2 - Molekulares Rechnen etabliert sich als interdisziplinär geprägtes Wissensgebiet mit hohem Anwendungspotential. Es beschäftigt sich mit Prinzipien biologischer Informationsverarbeitung. Moleküle bzw. molekulare Systeme übernehmen die Rolle eines Datenträgers, auf dem biochemische Prozesse oder physische Wechselwirkungen operieren. Facetten sind unter anderem DNA-Computing, chemisches Rechnen, Membrane Computing und ameisenbasiertes Computing. Vier studentische Beiträge stellen diese Forschungsrichtungen anhand eingängiger Beispiele anschaulich vor. N2 - Molecular Computing emerges as a highly interdisciplinary field of research with numerous applications. It is mainly focussed on principles of biological and biologically inspired information processing. Molecules or molecular systems act as data carrier operated by biochemical processes and physical interactions. There are various facets like DNA computing, chemical computing, membrane computing, and ant-based computing. Four contributions made by students illustrate these facets along with plausible examples. T3 - Computer science reports / Institut für Informatik - 2016,01 KW - Molekulares Rechnen KW - DNA Computing KW - Chemisches Rechnen KW - Membrane Computing KW - Ameisenbasiertes Computing KW - DNA computing KW - Chemical computing KW - Membrane computing KW - Molecular computing KW - Ant-based computing KW - Biocomputer KW - Molekulare Bioinformatik Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-40328 ER - TY - JOUR A1 - Kurth, Winfried A1 - Bachmann, Peter A1 - Heiner, Monika A1 - König, Hartmut A1 - Kraemer, Rolf A1 - Lewerentz, Claus A1 - Nolte, Jörg A1 - Thalheim, Bernhard A1 - Vierhaus, Heinrich Theodor A1 - Braunmühl, Burchard von A1 - Wagner, Gerd T1 - Jahresbericht 2003/2005 / Institut fuer Informatik, Informations- und Medientechnik T1 - Annual Report 2003/2005 / Department for Computer Science, Information and Media Technology N2 - Selbstdarstellung des Instituts für Informatik, Informations- und Medientechnik der BTU Cottbus und Berichte der Lehrstühle für die Jahre 2003, 2004 und 2005. N2 - Presentation of the Department for Computer Science, Information and Media Technology of the BTU Cottbus and reports of the chairs at the department for the years 2003, 2004 and 2005. T3 - Jahresbericht / Institut für Informatik, Informations- und Medientechnik - 2003/2005 KW - Cottbus / Technische Universität KW - Bericht KW - Informatik KW - Informations- und Medientechnik KW - BTU Cottbus KW - Computer Science KW - Information Technology KW - Media Technology KW - BTU Cottbus Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-3488 ER - TY - JOUR A1 - Thalheim, Bernhard A1 - Heiner, Monika A1 - Bachmann, Peter A1 - König, Hartmut A1 - Lewerentz, Claus A1 - Vierhaus, Heinrich Theodor A1 - Braunmühl, Burchard von T1 - Jahresbericht 2000/ Institut für Informatik T1 - Annual Report 2000 / Department for Computer Science N2 - Selbstdarstellung des Instituts für Informatik der BTU Cottbus und Berichte der Lehrstühle für das Jahr 2000. N2 - Presentation of the Department for Computer Science of the BTU Cottbus and reports of the chairs at the department for the year 2000. T3 - Jahresbericht / Institut für Informatik - 2000 KW - Cottbus / Technische Universität KW - Bericht KW - Informatik KW - BTU Cottbus KW - Computer Science KW - BTU Cottbus Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-3533 ER - TY - JOUR A1 - Thalheim, Bernhard A1 - Heiner, Monika A1 - Bachmann, Peter A1 - König, Hartmut A1 - Lewerentz, Claus A1 - Vierhaus, Heinrich Theodor A1 - Braunmühl, Burchard von T1 - Jahresbericht 1999 / Institut für Informatik T1 - Annual Report 1999 / Department for Computer Science N2 - Selbstdarstellung des Instituts für Informatik der BTU Cottbus und Berichte der Lehrstühle für das Jahr 1999. N2 - Presentation of the Department for Computer Science of the BTU Cottbus and reports of the chairs at the department for the year 1999. T3 - Jahresbericht / Institut für Informatik - 1999 KW - Cottbus / Technische Universität KW - Bericht KW - Informatik KW - BTU Cottbus KW - Computer Science KW - BTU Cottbus Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-3547 ER - TY - JOUR A1 - Thalheim, Bernhard A1 - Heiner, Monika A1 - Kurth, Winfried A1 - Bachmann, Peter A1 - König, Hartmut A1 - Lewerentz, Claus A1 - Vierhaus, Heinrich Theodor A1 - Braunmühl, Burchard von A1 - Nolte, Jörg T1 - Jahresbericht 2001/2002 / Institut für Informatik T1 - Annual Report 2001/2002 / Department for Computer Science N2 - Selbstdarstellung des Instituts für Informatik der BTU Cottbus und Berichte der Lehrstühle für die Jahre 2001 und 2002. N2 - Presentation of the Department for Computer Science of the BTU Cottbus and reports of the chairs at the department for the years 2001 and 2002. T3 - Jahresbericht / Institut für Informatik - 2001/2002 KW - Cottbus / Technische Universität KW - Bericht KW - Informatik KW - BTU Cottbus KW - Computer Science KW - BTU Cottbus Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-3527 ER - TY - JOUR A1 - Bachmann, Peter A1 - Thalheim, Bernhard A1 - Heiner, Monika A1 - Lux, Gregor A1 - König, Hartmut A1 - Lewerentz, Claus A1 - Vierhaus, Heinrich Theodor A1 - Braunmühl, Burchard von T1 - Jahresbericht 1998 / Institut für Informatik T1 - Annual Report 1998 / Department for Computer Science N2 - Selbstdarstellung des Instituts für Informatik der BTU Cottbus und Berichte der Lehrstühle für das Jahr 1998. N2 - Presentation of the Department for Computer Science of the BTU Cottbus and reports of the chairs at the department for the year 1998. T3 - Jahresbericht / Institut für Informatik - 1998 KW - Cottbus / Technische Universität KW - Bericht KW - Informatik KW - BTU Cottbus KW - Computer Science KW - BTU Cottbus Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-3559 ER - TY - JOUR A1 - Lewerentz, Claus A1 - Thalheim, Bernhard A1 - Heiner, Monika A1 - Lux, Gregor A1 - Bachmann, Peter A1 - König, Hartmut A1 - Vierhaus, Heinrich Theodor A1 - Braunmühl, Burchard von T1 - Jahresbericht 1997 / Institut für Informatik T1 - Annual Report 1997 / Department for Computer Science N2 - Selbstdarstellung des Instituts für Informatik der BTU Cottbus und Berichte der Lehrstühle für das Jahr 1997. N2 - Presentation of the Department for Computer Science of the BTU Cottbus and reports of the chairs at the department for the year 1997. T3 - Jahresbericht / Institut für Informatik - 1997 KW - Cottbus / Technische Universität KW - Bericht KW - Informatik KW - BTU Cottbus KW - Computer Science KW - BTU Cottbus Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-3563 ER - TY - RPRT A1 - Herajy, Mostafa A1 - Heiner, Monika T1 - Snoopy computational steering framework - user manual version 1.0 N2 - 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. T3 - Computer science reports / Institut für Informatik - 2013,02 KW - Datenstruktur KW - Zuverlässigkeit Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus-29034 ER - TY - RPRT A1 - Swapnil, Chiru T1 - Stochastic simulation efficiency N2 - 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]. T3 - Computer science reports / Institut für Informatik - 2014,02 KW - Petri Nets KW - SBML KW - Stochastic simulation KW - Biochemical reaction networks KW - Export KW - MathML KW - Stochastisches Modell KW - Petri-Netz KW - Export Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:co1-opus4-31479 ER -