https://imc.zih.tu-dresden.de/wiki/morpheus/ 2026-05-06T02:15:44+00:00 https://imc.zih.tu-dresden.de/wiki/morpheus/ https://imc.zih.tu-dresden.de/wiki/morpheus/lib/exe/fetch.php?media=favicon.ico text/html 2015-06-29T11:14:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:course&rev=1435569298 Course Material Modules * Module 0: Introduction * Module 1: Delta-Notch (ODE systems, ODEs on a grid) * Module 2: Morphogen Gradients (...) * Module 3: Activator-Inhibitor (reaction-diffusion) * Module 4: Vascular patterning (model comparison) * Module 5: Cell fate decisions (model assumptions) text/html 2012-12-14T14:36:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module0&rev=1355492167 Module 0: Introduction Author: Lutz Brusch Aim: * Define relation between experiment and theory, bottom-up versus top-down models * See model as tool, get to know a success story Description: * Discuss previous experiences by students with models text/html 2017-11-13T16:20:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module1&rev=1510586437 Module 1: Delta-Notch (ODE systems, ODEs on a grid) Author: Fabian Rost Aim * learn about ODE models (dynamics in morpheus, steady states analytically) * develop first models Description Basic ODEs * get to know what students know about ODEs and adjust the module to the pre-knowledge\begin{align} \dot A &= k_1 \\ \dot A &= k_2 A \\ \dot A &= - k_3 A \\ \dot A &= k_4 - k_5 A \end{align}\begin{align} \dot A &= \frac{\theta^n}{\theta^n + B^n} - k A \end{align}\begin{align} \dot A_1 … text/html 2012-12-14T12:49:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module2&rev=1355485771 Module 2: Morphogen gradients Author: Lutz Brusch Aim: * Adapt an established theoretical model to a fundamental developmental patterning process. * Thereby going through the typical modeling workflow seen in Module 1. Description: * Read abstract of Yu et al. text/html 2012-12-14T12:56:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module3&rev=1355486163 Module 3: Activator-Inhibitor Author: Lutz Brusch Aim: * Introduce self-organized pattern formation (Turing patterns) * Show the potential of qualitative/theoretical modeling Description: * Activator-Inhibitor models * Theoretical introduction on Turing patterns (1951) text/html 2012-12-21T15:52:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module4&rev=1356101539 Module 4: Vascular Patterning Author: * Walter de Back Aim: * Learn to distinguish between alternative hypothesis/mechanisms explaning the same phenomenon * When two different mechanisms can reproduce the same phenomenon, how can modeling help to distinguish between these mechanisms? text/html 2013-11-11T10:55:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module5&rev=1384163729 Module 5: Cell fate decisions (model assumptions) Author: Name Aim: * Learn to make implicit model assumptions explicit * Learn about effect of noise and motility on cell fate decisions Description: * Introduce Delta-Notch model and patterning text/html 2017-11-17T10:06:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module6&rev=1510909598 Module 6: Dictyostelium cluster formation & slug movement Author: Fabian Rost Aim * this was planned as a one week project, students should develop a complex model * teach them about biology: morphogenesis, cellular behavior, ... * teach them about mathematics: CPM, PDE, coupling text/html 2013-11-05T12:55:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module7&rev=1383652535 Module 7: Planar cell polarity Author: Lutz Brusch Aim * Main scientific goal * Didactive aim Description * Step by step description of module * Written such that other tutors can teach the same stuff Paper * Wolpert L (1969). “Positional information and the spatial pattern of cellular differentiation text/html 2015-06-30T10:15:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:module_cs&rev=1435652117 Tutorial Download tutorial (pdf) Model 1 Download CellSorting_MathBiol_SS15_1.xml Model 2 Download CellSorting_MathBiol_SS15_2.xml text/html 2013-01-11T11:36:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=documentation:course:template&rev=1357900570 Module #: Template Author: Name Aim * Main scientific goal * Didactive aim Description * Step by step description of module * Written such that other tutors can teach the same stuff Paper * Wolpert L (1969). “Positional information and the spatial pattern of cellular differentiation