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Issue No.02 - April-June (2006 vol.3)
pp: 155-164
ABSTRACT
Converting a biochemical reaction network to a set of kinetic rate equations is tedious and error prone. We describe known interface paradigms for inputing models of intracellular regulatory networks: graphical layout (diagrams), wizards, scripting languages, and direct entry of chemical equations. We present the JigCell Model Builder, which allows users to define models as a set of reaction equations using a spreadsheet (an example of direct entry of equations) and outputs model definitions in the Systems Biology Markup Language, Level 2. We present the results of two usability studies. The spreadsheet paradigm demonstrated its effectiveness in reducing the number of errors made by modelers when compared to hand conversion of a wiring diagram to differential equations. A comparison of representatives of the four interface paradigms for a simple model of the cell cycle was conducted which measured time, mouse clicks, and keystrokes to enter the model, and the number of screens needed to view the contents of the model. All four paradigms had similar data entry times. The spreadsheet and scripting language approaches require significantly fewer screens to view the models than do the wizard or graphical layout approaches.
INDEX TERMS
Biochemical reaction networks, bioinformatics, modeling, user interface paradigms.
CITATION
Marc T. Vass, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson, "The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.3, no. 2, pp. 155-164, April-June 2006, doi:10.1109/TCBB.2006.27
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