Browsing Scholarly Works, Department of Mathematics by Author "Palmisano, Alida"

Now showing items 1-3 of 3

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations

Palmisano, Alida; Hoops, Stefan; Watson, Layne T.; Jones, Thomas C.; Tyson, John J.; Shaffer, Clifford A. (Biomed Central Ltd, 2015-12-24)

Background Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different parameterizations of the model to account for the ...
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

Palmisano, Alida; Hoops, Stefan; Watson, Layne T.; Jones, Thomas C, Jr.; Tyson, John J.; Shaffer, Clifford A. (Biomed Central Ltd, 2014-04-04)

Background Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more ...
A Stochastic Model Correctly Predicts Changes in Budding Yeast Cell Cycle Dynamics upon Periodic Expression of CLN2

Oguz, Cihan; Palmisano, Alida; Laomettachit, Teeraphan; Watson, Layne T.; Baumann, William T.; Tyson, John J. (PLOS, 2014-05-09)

In this study, we focus on a recent stochastic budding yeast cell cycle model. First, we estimate the model parameters using extensive data sets: phenotypes of 110 genetic strains, single cell statistics of wild type and ...