software Code The following are snippets of code that cover a wide range of specific research applications. There are tools for kinetic model-building, regression, image analysis, neural networks, and web applications. Some are well-documented, others not. cell2csv.m Convert cell array to CSV cell2sbm.m Convert 2-row cell array to SBmodel cleantc.m Clean up time-course data csv2cell.m Convert CSV to cell array ff2narx.m Convert feedforward network to NARX model findsynergy.m Calculate synergy ratio for data set gencomb.m Generate all combinations of n variables with d states getexpt.m Extract experimental data from Flex-station experiment issteadySB.m Determine whether or not SBmodel states are at rest lle.m Calculate local linear embedding (Roweis and Saul, 2000) maxdiss.m Calculate maximally dissimilar vectors mltc2narx.m Convert multilayer time-course NN to NARX model newmltc.m Create new multilayer time-course NN model newtc.m Create new time-course NN model Models The following are SBML models that were developed as part of my doctoral work. plt1.xml Human platelet v1.0 plt2.xml Human platelet v2.0