Link to the University of Pittsburgh Homepage
Link to the University Library System Homepage Link to the Contact Us Form

RULEBENDER: INTEGRATED MODELING, SIMULATION, AND VISUALIZATION FOR RULE-BASED INTRACELLULAR BIOCHEMISTRY

Smith, Adam (2012) RULEBENDER: INTEGRATED MODELING, SIMULATION, AND VISUALIZATION FOR RULE-BASED INTRACELLULAR BIOCHEMISTRY. Master's Thesis, University of Pittsburgh. (Unpublished)

[img]
Preview
PDF
Primary Text

Download (1MB) | Preview

Abstract

Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less error prone, and to improve workflows. We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. We present the user requirements, visual paradigms, algorithms and design decisions behind RuleBender, with emphasis on visual global/local model exploration and integrated execution of simulations. The support of RBM creation, debugging, and interactive visualization expedites the RBM learning process and reduces model construction time; while built-in model simulation and results with multiple linked views streamline the execution and analysis of newly created models and generated networks. RuleBender has been adopted as both an educational and a research tool and is available as a free open source tool at http://www.rulebender.org. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community.


Share

Citation/Export:
Social Networking:
Share |

Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Smith, Adamams292@pitt.eduAMS292
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairMarai, G. Elisabetamarai@cs.pitt.eduMARAI
Committee MemberFaeder, James R.faeder@pitt.eduFAEDER
Committee MemberWang, Jingtaojingtaow@pitt.eduJINGTAOW
Date: 6 June 2012
Date Type: Publication
Defense Date: 28 March 2012
Approval Date: 6 June 2012
Submission Date: 18 April 2012
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 46
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Computer Science
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: BioInformatics, InfoVis, Information Visualization, Human Computer Interaction
Date Deposited: 06 Jun 2012 19:14
Last Modified: 19 Dec 2016 14:38
URI: http://d-scholarship.pitt.edu/id/eprint/11889

Metrics

Monthly Views for the past 3 years

Plum Analytics


Actions (login required)

View Item View Item