Morpheus

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=== 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
      * dXi/dt = t/(t+aXj) - Xi + eta
      * Spatial patterning: checkerboard 

  * Assignment 1:
      * 


  * Introduce tau
      * Time to decision (tau) depends on noise amplitude
      * Tau is important in context of other timed processes (e.g. lateral stabilization) 
  * 
 

Paper:
  * de Back W, Zhou JX, Brusch L. 2012, On the role of lateral stabilization during early patterning in the pancreas. J R Soc Interface 10: 20120766. [[http://dx.doi.org/10.1098/rsif.2012.0766|link]] {{:course:pancreaspatterning_jrsocinterface2012.pdf|pdf}}
  * W. de Back, R. Zimm, L. Brusch 2013, Transdifferentiation of Pancreatic Cells by Loss of Contact-mediated Signaling. BMC Systems Biology 7:77. [[http://www.biomedcentral.com/1752-0509/7/77|link]]

Documents:
  * 

Morpheus models:

[[examples:miscellaneous#French Flag: Morphogen gradient|Link to Example page]]

<code xml |h MorpheusModel.xml |h>

<MorpheusModel version="1">
    <Description>
        <Title>Example-Model</Title>
    </Description>
    <Space>
        <Lattice class="linear">
            <Size value="100 0 0"/>
            <BoundaryConditions>
                <Condition boundary="x" type="periodic"/>
            </BoundaryConditions>
        </Lattice>
    </Space>
    <Time>
        <StartTime value="0"/>
        <StopTime value="100"/>
    </Time>
</MorpheusModel>

</code>