Experiment

class Experiment.Experiment(templatefile)

The class Experiments holds the data for a CC3D experiment as an xml object. This objects is created from a template xml file. Elements that are already present in the template can be changed or removed and new elements can be added. When the xml is written to file all unchanged content of the template, including commented xml, is written to the new file.

addStatistics(freq, basename)

Edit statistics save options

Parameters:

• freq – save frequency
• basename – basename for files (full path)

deletePlugin(name)

Delete plugin

Parameters:name – plugin name

deletePottsProperty(tagname)

Remove element from the Potts element

Parameters:tagname – name of element

deleteSteppable(type)

Delete steppable

Parameters:type – steppable type

setChemotaxis(celltype, towards, lam)

Set chemotaxis for cell type

Parameters:

• celltype – name of the cell type
• towards – cell type towards chemotaxis occurs
• lam – chemotactic strength

setContact(_type1, _type2, J)

Edit contact energy

Parameters:

• type1 – name of the first cell type
• type2 – name of the second cell type
• J – contact energy between type1 and type2

setDebugFrequencyInMeta(freq)

Set debug frequency

Parameters:frequency – frequency

setGenericPlugin(name, elements=[])

Set generic plugin. If the plugin is already in the template, it is updated. If not, the plugin is added to the model. This function does not support multi-level xml elements.

Parameters:

• name – plugin name
• elements – list of elements described by a dictionary: {‘name’:name,’value’:val,’attributes’:{}}

setGenericSteppable(type, freq=None, elements=[])

Set generic steppable. If the steppable is already in the template, it is updated. If not, the plugin is added to the model. This function does not support multi-level xml elements.

Parameters:

• type – steppable type
• freq – frequency
• elements – list of elements described by a dictionary with keys name, value and attributes

setMCS(mcs)

Set number of Monte Carlo steps

Parameters:mcs – number of MCS (note that mcs+1 appears in the xml)

setMotility(celltype, T)

Edit motility parameters per cell type

Parameters:

• celltype – name of the cell type
• T – motility

setMultiCore(threads=1, cores=1)

Set number of threads and cores for a simulation

Parameters:

• threads – number of threads per core
• cores – number of cores

setPottsProperty(tagname, attributes={}, value=None)

General function to set a parameter in the Potts element

Parameters:

• tagname – name of the element
• attributes – dictionary with attribute names as key and attribute values as values.
• value – element value

setSecretion(celltype, s, solver='FastDiffusionSolver2DFE')

Set secretion coefficient for specific cell type

Parameters:

• celltype – name of the cell type
• s – secretion coefficient
• solver – solver name

setSeed(seed)

Set simulation seed

Parameters:seed – random seed

setTemp(T)

Set temperature tag

Parameters:T – temperature

setVolume(celltype, vol, lam)

Set volume per cell type

Parameters:

• celltype – cell type name
• vol – target volume
• lam – lambda volume

write(filename)

Save xml to file

Parameters:filename – filename of new xml