(* Content-type: application/mathematica *) (*** Wolfram Notebook File ***) (* http://www.wolfram.com/nb *) (* CreatedBy='Mathematica 6.0' *) (*CacheID: 234*) (* Internal cache information: NotebookFileLineBreakTest NotebookFileLineBreakTest NotebookDataPosition[ 145, 7] NotebookDataLength[ 7930, 205] NotebookOptionsPosition[ 6386, 152] NotebookOutlinePosition[ 7572, 192] CellTagsIndexPosition[ 7529, 189] WindowFrame->Normal ContainsDynamic->False*) (* Beginning of Notebook Content *) Notebook[{ Cell[CellGroupData[{ Cell["Ex3: Math. Modelling in Biosciences 1", "Title", CellChangeTimes->{{3.415589585204612*^9, 3.415589598615617*^9}, { 3.415612138399819*^9, 3.415612142124673*^9}, {3.418375570847907*^9, 3.418375571000227*^9}, {3.42259016611127*^9, 3.422590166214294*^9}}], Cell["Summer 2008 ", "Subtitle", CellChangeTimes->{{3.41561211409342*^9, 3.415612134422485*^9}}], Cell["Due Friday 4 July (2.5 weeks)", "Subsubtitle", CellChangeTimes->{{3.415605888680184*^9, 3.41560590190364*^9}, { 3.418375565010216*^9, 3.41837556832417*^9}, {3.418444153818715*^9, 3.418444167633437*^9}, {3.418449387119722*^9, 3.41844938826529*^9}, { 3.422585087353535*^9, 3.422585093446563*^9}}, FontSize->22], Cell[TextData[{ "In this exercise, we use MATCONT to reproduce the bifurcation diagrams \ shown in \n\n", StyleBox["Sniffers, buzzers, toggles and blinkers: dynamics of regulatory \ and signaling pathways in the cell.", FontSlant->"Italic", FontColor->RGBColor[0.6, 0.4, 0.2]], StyleBox[" ", FontSlant->"Italic"], "John J. Tyson, Katherine C. Chen and Bela Novak. ", StyleBox["Current Opinion in Cell Biology", FontWeight->"Bold", FontSlant->"Italic", FontColor->RGBColor[0.5, 0, 0.5]], StyleBox[" 15:221-231 (2003)", FontColor->RGBColor[0.5, 0, 0.5]], "\n\nas was also discussed in Lecture 4.\n\nIt would be useful to look at:\n\ \n\t", StyleBox["run_BifAnalysis_ML.m\n\tMorrisLecarModel.m", FontColor->RGBColor[0.6, 0.4, 0.2]], "\n\t\nAlso useful would be information on the usage of MATCONT:\n\t\n\t", StyleBox["MATCONT_manual.pdf", FontColor->RGBColor[0.6, 0.4, 0.2]] }], "Text", CellChangeTimes->{{3.415605406565242*^9, 3.415605433891287*^9}, { 3.415605464231621*^9, 3.415605549469606*^9}, {3.415605580453104*^9, 3.415605694991905*^9}, {3.415605756477949*^9, 3.415605842835668*^9}, { 3.41560592575955*^9, 3.415605926779197*^9}, {3.415612161819669*^9, 3.415612164172899*^9}, {3.415612206830281*^9, 3.415612226928721*^9}, { 3.418375652291134*^9, 3.41837568525645*^9}, {3.422585117688557*^9, 3.422585195239557*^9}, {3.42258523979635*^9, 3.422585248559625*^9}, { 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