20.500.12556/RUL-96525 Pregled orodij za agentno modeliranje bioloških sistemov in njihova uporaba na modelu večceličnega biološkega oscilatorja Overview of the agent-based tools for the modelling of biological systems and their application to the analysis of multi-cellular biological oscillator V magistrski nalogi smo opravili pregled orodij za agentno modeliranje bioloških sistemov. Agentno modeliranje je osredotočeno na modeliranje opazovanega sistema z avtonomnimi entitetami imenovanimi agenti. Tovrstno modeliranje nam omogoča predstavitev biološkega sistema na različnih nivojih abstrakcije. V pregled smo vključili splošno orodje za agentno modeliranje in orodja, ki so specializirana na modeliranje celice kot agent. Orodja smo primerjali in pregledali z vidika načina opisa agentove dinamike, modelirnega programskega jezika, simuliranega virtualnega okolja in z vidika implementiranih celičnih lastnosti, procesov ter dinamike, kot je na primer celična rast in celično gibanje. Podrobneje smo opisali okolja NetLogo, BSim, Gro in CellModeller. Pri vsakem smo opisali interaktivno okolje, modelirni jezik in arhitekturo oziroma implementacijo orodja. Uporabo izbranih orodij smo demonstrirali na vzorčnem primeru večceličnega modela biološkega oscilatorja. V zaključku smo podali predlog ogrodja orodja za agentno modeliranje bioloških sistemov, ki bi uporabnikom še dodatno olajšal postavitev tovrstnih modelov. In this thesis, we overview computational tools for agent-based modelling of biological systems. Agent-based modelling focuses on the modelling of observed system with individual components called agents. This type of modelling offers a representation of a biological system at multiple levels of abstraction. We overview general-purpose agent-based framework and agent-based tools, which use cells as the primary agents. We compare and examine available tools from different perspectives. We examine how agent dynamics can be modelled, and properties of modelling languages, simulated environments, and built-in complex cellular traits (e.g. growth and movement) are checked. Afterwards, we examine NetLogo, BSim, Gro, and CellModeller framework. For each tool we provide description of their interactive environment, properties of modelling language, and their design and implementation principles. In the last part, we perform analysis of the above mentioned tools on the case study of a multi-cellular biological oscillator model. We conclude with the agent-based framework proposition, which would simplify the process of implementation of multi-agent biological models. agentno modeliranje večcelično modeliranje simulacija biološki sistemi skupinsko vedenje oscilator agent-based modelling multicellular modelling simulation biological systems emergent behaviour oscillator true false false Slovenski jezik Angleški jezik Magistrsko delo/naloga 2017-10-04 10:19:41 2017-10-04 10:19:45 2022-08-12 11:31:30 0000-00-00 00:00:00 2017 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 1970-01-01 19304 Gazvoda_Silvo_-_Pregled_orodij_za_agentno_modeliranje_bioloskih_sistemov_in_njihova_uporaba_na_m.pdf Gazvoda_Silvo_-_Pregled_orodij_za_agentno_modeliranje_bioloskih_sistemov_in_njihova_uporaba_na_m.pdf 1 E92C7319E27068CE5D8D03F6542777B0 c31b096aa473a4b2e5b5b7800952fb50faa0714dea3bcf1bd0631429f83724e2 f02a9170-a1b3-11eb-a523-00155dcfd717 20.500.12556/rul/6f9109ce-99b2-47a3-aad6-1a97abeb7abc https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=105235 Fakulteta za računalništvo in informatiko 0 0 0