Error Detection Support in a Cellular Modeling End-User Programming Environment
HCC '02 Proceedings of the IEEE 2002 Symposia on Human Centric Computing Languages and Environments (HCC'02)
Proceedings of the 35th conference on Winter simulation: driving innovation
The JigCell Model Builder and Run Manager
Bioinformatics
Challenges for modeling and simulation methods in systems biology
Proceedings of the 38th conference on Winter simulation
Converting macromolecular regulatory models from deterministic to stochastic formulation
Proceedings of the 2008 Spring simulation multiconference
Model Composition for Macromolecular Regulatory Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Multistate modeling and simulation forregulatory networks
Proceedings of the Winter Simulation Conference
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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.