documentation:course:module1
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| documentation:course:module1 [12:42 13.11.2017] – [Morpheus models] Fabian Rost | documentation:course:module1 [16:20 13.11.2017] (current) – [Delta-Notch] Fabian Rost | ||
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| * calculate steady state (do not calculate the stability, to complicated for biologists) | * calculate steady state (do not calculate the stability, to complicated for biologists) | ||
| * simulate in morpheus | * simulate in morpheus | ||
| + | * typical models for biochemistry/ | ||
| + | |||
| + | < | ||
| + | digraph { | ||
| + | size=" | ||
| + | |||
| + | node [shape = circle]; | ||
| + | a[label="", | ||
| + | ab[label="", | ||
| + | c[label="", | ||
| + | |||
| + | a -> ab[arrowhead=None]; | ||
| + | ab -> A; | ||
| + | A -> c | ||
| + | B -> ab[arrowhead=tee]; | ||
| + | |||
| + | {rank=same; a; ab; A; c}; | ||
| + | } | ||
| + | |||
| + | </ | ||
| + | |||
| + | \begin{align} | ||
| + | \dot A &= \frac{\theta^n}{\theta^n + B^n} - k A | ||
| + | \end{align} | ||
| ==== Delta-Notch ==== | ==== Delta-Notch ==== | ||
| Line 86: | Line 110: | ||
| * they could come up with something like: | * they could come up with something like: | ||
| \begin{align} | \begin{align} | ||
| - | \dot X_1 & | + | \dot A_1 &= \frac{\theta^n}{\theta^n + A_2^n} - A_1 \\ |
| - | \dot X_2 & | + | \dot A_2 &= \frac{\theta^n}{\theta^n + A_1^n} - A_2 |
| \end{align} | \end{align} | ||
| * this system is bistable for certain parameter ranges, if the students are advanced they might find this out themselves | * this system is bistable for certain parameter ranges, if the students are advanced they might find this out themselves | ||
| - | * bistable e.g. for $\theta=0.5$, | + | * bistable e.g. for $\theta=0.5$, |
| * if they have this system running in morpheus go spatial and let them simulate the system on a square and hexagonal grid | * if they have this system running in morpheus go spatial and let them simulate the system on a square and hexagonal grid | ||
| * then you could also move to shaped cpm cells or even moving cells | * then you could also move to shaped cpm cells or even moving cells | ||
| Line 108: | Line 132: | ||
| - | <code xml |h ExponentialGrowth.xml | + | <file xml ExponentialGrowth.xml> |
| <?xml version=' | <?xml version=' | ||
| Line 163: | Line 187: | ||
| </ | </ | ||
| + | </ | ||
| + | <file xml | LateralInhibition_2cell.xml> | ||
| + | |||
| + | <?xml version=' | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | <Lattice class=" | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | <Size symbol=" | ||
| + | </ | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <System solver=" | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | - k * A</ | ||
| + | </ | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | - k * A_neighbour</ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | <Logger time-step=" | ||
| + | < | ||
| + | <Symbol symbol-ref=" | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | <Plot time-step=" | ||
| + | <Style style=" | ||
| + | < | ||
| + | < | ||
| + | <Symbol symbol-ref=" | ||
| + | </ | ||
| + | < | ||
| + | <Symbol symbol-ref=" | ||
| + | <Symbol symbol-ref=" | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | |||
| + | |||
| + | </ | ||
| + | |||
| + | <file xml | LateralInhibition_space.xml> | ||
| + | |||
| + | <?xml version=' | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | <Lattice class=" | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | <Size symbol=" | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Input scaling=" | ||
| + | <Output symbol-ref=" | ||
| + | </ | ||
| + | <System solver=" | ||
| + | <DiffEqn symbol-ref=" | ||
| + | < | ||
| + | - X</ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | --> | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | < | ||
| + | <Cells value=" | ||
| + | </ | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| + | < | ||
| + | < | ||
| + | </ | ||
| + | </ | ||
| - | </code> | + | </file> |
documentation/course/module1.1510573338.txt.gz · Last modified: 12:42 13.11.2017 by Fabian Rost