A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems
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University of Cincinnati / OhioLINK
2011
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ndltd-OhioLink-oai-etd.ohiolink.edu-ucin12965943242021-08-03T06:14:34Z A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems Korukonda, Harika Computer Engineering Agent based modeling (ABM) is a type of computational modeling system which concentrates on interactions between the components of a model. It is thus based on a bottom-up paradigm. In systems biology, Agent based modeling is an emerging powerful tool. The main reason for its success lies in the fact that it can easily take into account the spatial dynamics and geometries of systems. Other modeling techniques fail to model the spatial interactions between the components. This research work aims at providing GenericSystem, an easy-to-use tool to simulate bio-molecular systems in MASON, a widely used ABM implementation. A basic GenericSystem is modeled in MASON. This system contains all the basic classes and functions that can best describe a typical bio-molecular system. All the classes and functions are based on usage of JAVA for programming. This tool is designed to be very easy to use and understand. It has well defined functions which can be readily customized and thus reduces the development time of the model. The model can be viewed by the rich GUI offered by MASON. Five systems, k bioluminescence in Vibrio fischeri bacteria, skin regulatory system, Phage Lambda system, epithelial cells growth cycle and Wnt signaling pathway have been successfully implemented using the GenericSystem tool. Various parameters for the systems have been changed and simulations run for various conditions. The simulations and previous work are compared and conlusions are drawn. Scope of future work has been provided. 2011-04-20 English text University of Cincinnati / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=ucin1296594324 http://rave.ohiolink.edu/etdc/view?acc_num=ucin1296594324 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws. |
| collection |
NDLTD |
| language |
English |
| sources |
NDLTD |
| topic |
Computer Engineering |
| spellingShingle |
Computer Engineering Korukonda, Harika A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems |
| author |
Korukonda, Harika |
| author_facet |
Korukonda, Harika |
| author_sort |
Korukonda, Harika |
| title |
A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems |
| title_short |
A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems |
| title_full |
A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems |
| title_fullStr |
A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems |
| title_full_unstemmed |
A Generic Agent Based Modeling Tool for Simulating Bio-Molecular Systems |
| title_sort |
generic agent based modeling tool for simulating bio-molecular systems |
| publisher |
University of Cincinnati / OhioLINK |
| publishDate |
2011 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1296594324 |
| work_keys_str_mv |
AT korukondaharika agenericagentbasedmodelingtoolforsimulatingbiomolecularsystems AT korukondaharika genericagentbasedmodelingtoolforsimulatingbiomolecularsystems |
| _version_ |
1719433309021274112 |