documentation:course:module6
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| documentation:course:module6 [11:51 11.01.2013] – Fabian Rost | documentation:course:module6 [10:06 17.11.2017] (current) – [Description] Fabian Rost | ||
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| ===== Aim ===== | ===== Aim ===== | ||
| - | * Main scientific goal | + | * this was planned as a one week project, students should develop a complex model |
| - | * Didactive aim | + | * teach them about biology: morphogenesis, |
| + | * teach them about mathematics: | ||
| ===== Description ===== | ===== Description ===== | ||
| - | * Step by step description | + | * good description |
| - | * Written such that other tutors can teach the same stuff | + | * it's been two days of teaching: |
| + | * first explain CPM and let them play with that a little (e.g. cell sorting) | ||
| + | * explain PDE system we are going to use | ||
| + | * I had to explain about phase plane analysis quite a bit | ||
| + | * then on day 3 start to couple PDE & CPM | ||
| + | * start with coupling in one direction only | ||
| + | * e.g. first give a fixed gradient and let CPM cells perform chemotaxis | ||
| + | * then formulate a PDE where a substance is only produced where CPM cells are | ||
| + | * then couple in both directions (implement | ||
| + | * perform clustering and slug movement experiment | ||
| ===== Paper ===== | ===== Paper ===== | ||
| Line 19: | Line 29: | ||
| * Stan Marée (2002), From pattern formation to morphogenesis: | * Stan Marée (2002), From pattern formation to morphogenesis: | ||
| * Alberto Quintero, Mirko Myllykoski, Anna Igolkina, Alexandra Rohde O’Sullivan Freltoft, Nitya Dixit, Fabian Rost (2012), Morphogenesis and Dynamics of Multicellular Systems, [[http:// | * Alberto Quintero, Mirko Myllykoski, Anna Igolkina, Alexandra Rohde O’Sullivan Freltoft, Nitya Dixit, Fabian Rost (2012), Morphogenesis and Dynamics of Multicellular Systems, [[http:// | ||
| + | |||
| ===== Morpheus models ===== | ===== Morpheus models ===== | ||
| + | <code xml |h ClusterFormation.xml |h> | ||
| + | <?xml version=' | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | <Lattice class=" | ||
| + | <Size symbol=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Target value=" | ||
| + | </ | ||
| + | < | ||
| + | <Layer symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Input symbol-ref=" | ||
| + | <Maximum symbol-ref=" | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | if(phase == 2 and phaseTime> | ||
| + | if(phase == 3 and max_c < 0.05, 1, | ||
| + | phase | ||
| + | ))) </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Target value=" | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | < | ||
| + | <Layer symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <CPM> | ||
| + | < | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | <PDE> | ||
| + | <Layer symbol=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <Layer symbol=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <System solver=" | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | if(c < 0.841, 0.0589, | ||
| + | 0.5))</ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | if(c < 0.841, -3*c+0.15, | ||
| + | 15*(c-1)))</ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <PDE symbol-ref=" | ||
| + | < | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | </ | ||
| + | </ | ||
| + | <Cells symbol-ref=" | ||
| + | <Cells symbol-ref=" | ||
| + | <PDE symbol-ref=" | ||
| + | < | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| - | [[examples: | ||
| - | <code xml |h MorpheusModel.xml |h> | + | * {{documentation: |
| + | * for the movie the system size was 500x500 with 4000 cells randomly placed, everything else was like in the example above | ||
| + | |||
| + | <code xml |h CrawlingSlug.xml |h> | ||
| + | |||
| + | <?xml version=' | ||
| < | < | ||
| < | < | ||
| - | < | + | < |
| </ | </ | ||
| < | < | ||
| - | <Lattice class=" | + | <Lattice class=" |
| - | <Size value=" | + | < |
| < | < | ||
| - | < | + | < |
| + | < | ||
| + | < | ||
| + | < | ||
| </ | </ | ||
| + | < | ||
| </ | </ | ||
| + | < | ||
| </ | </ | ||
| < | < | ||
| - | < | + | < |
| - | < | + | < |
| + | < | ||
| </ | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Target value=" | ||
| + | </ | ||
| + | < | ||
| + | <Layer symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Input symbol-ref=" | ||
| + | <Maximum symbol-ref=" | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | if(phase == 2 and phaseTime> | ||
| + | if(phase == 3 and max_c < 0.05, 1, | ||
| + | phase | ||
| + | ))) </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Target value=" | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | < | ||
| + | <Layer symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <CPM> | ||
| + | < | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | <Contact type1=" | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | <PDE> | ||
| + | <Layer symbol=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <Layer symbol=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <System solver=" | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | if(c < 0.841, -3*c+0.15, | ||
| + | 15*(c-1)))</ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | if(c < 0.841, 0.0589, | ||
| + | 0.5))</ | ||
| + | </ | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <PDE symbol-ref=" | ||
| + | < | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | </ | ||
| + | </ | ||
| + | <Cells symbol-ref=" | ||
| + | < | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | </ | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | <Cells symbol-ref=" | ||
| + | </ | ||
| + | <PDE symbol-ref=" | ||
| + | < | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | </ | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | <PDE symbol-ref=" | ||
| + | < | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | <Color value=" | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | <!-- | ||
| + | < | ||
| + | <Logger interval=" | ||
| + | < | ||
| + | <Format string=" | ||
| + | < | ||
| + | <PDE mapping=" | ||
| + | </ | ||
| + | <Plot interval=" | ||
| + | <X-axis column=" | ||
| + | <Y-axis columns=" | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| </ | </ | ||
| + | |||
| </ | </ | ||
| + | |||
| + | * {{documentation: | ||
documentation/course/module6.1357901500.txt.gz · Last modified: 11:51 11.01.2013 by Fabian Rost