Terminology clarification: what exactly are the difference between chemotaxis on a "type-by-type" basis and "cell-by-cell" basis?

3 months ago by
The python codes are introduced for chemotaxis on a cell-by-cell basis at http://pythonscriptingmanual.readthedocs.io/en/latest/chemotaxis_on_a_cell-by-cell_basis.html

Say without the "break" instruction at the end of the first loop, what would be the significance difference occur in the simulation between chemotaxis on a "type-by-type" basis and one on a "cell-by-cell" basis?

Or what would the python codes for chemotaxis on a type-by-type basis might look like compared to ones for cell-by-cell?

Thank you,
Community: CompuCell3D

1 Answer

3 months ago by
Can't seem to access the page you have the link to but this is what the answer is based on what I understood from the question - a type-by-type chemotaxis property will allow you to specify chemotaxis properties for the entire group of cells belonging to a particular type. Something like {for all cells of type A -> add some chemotaxis properties}. In this case all cells of type A will possess the same chemotaxis attribute.

You can also specify properties at the level of an individual cell. For example if you have a particular cell of type A with id i that you want to add chemotaxis properties to and not to the rest you can assign attributes on a cell-by-cell basis {cell_i = some_cell_with_id_i -> add chemotaxis to cell_i}
I am sorry, here is the active link:


Thank you for sharing your thought.  if you take a look at the python codes, I am just wondering, if the "break" instruction is being removed, the "for" loop will eventually go through all the cells and assign the chemotaxis properties to each. Then what might possibly be the difference between doing this loop through all cells than assign the chemotaxis property to the whole type using the chemotaxis plugin in XML?
written 3 months ago by Yen Nguyen Edalgo  
Right. If you remove the break statement all cells of type Macrophage will be assigned the same property and effectively will be the same as defining the property in XML. The idea here was to demonstrate that it is possible to define chemotaxis for a single cell;in this case the first cell from the list of Macrophages and so the break statement came in handy. But it could be any cell (eg a cell with id 100, the last cell from the macrophage list) and the chemotaxis property can be added separately. 
cell = self.attemptFetchingCellById(100)
cd = self.chemotaxisPlugin.addChemotaxisData(cell, "ATTR")
cd.assignChemotactTowardsVectorTypes([self.MEDIUM, self.BACTERIUM])​

written 3 months ago by priyomadhyapok  
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