Difference between revisions of "Types of morphogens and factors"

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{| border="0" cellpadding="1" cellspacing="1"
 
{| border="0" cellpadding="1" cellspacing="1"
 
|- valign="top"  
 
|- valign="top"  
| width="200"|'' kapar_p, kapar_a, kapar_l'' || specify growth on the 'A' side parallel to the polariser and in the plane of the tissue
+
| width="200"|'' kapar_p, kapar_a, kapar_l'' || vector that specifies growth on the 'A' side parallel to the polariser and in the plane of the tissue at every node.
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''kbpar_p, kbpar_a, kbpar_l'' || specify growth on the 'B' side parallel to the polariser and in the plane of the tissue
+
| width="200"| ''kbpar_p, kbpar_a, kbpar_l'' || vector that specifies growth on the 'B' side parallel to the polariser and in the plane of the tissue at every node.
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''kaper_p, kaper_a, kaper_l'' || specify growth on the 'A' side perpendicular to the polariser and in the plane of the tissue
+
| width="200"| ''kaper_p, kaper_a, kaper_l'' || vector that specifies growth on the 'A' side perpendicular to the polariser and in the plane of the tissue at every node.
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''kbper_p, kbper_a, kbper_l'' || specify growth on the 'B' side perpendicular to the polariser and in the plane of the tissue
+
| width="200"| ''kbper_p, kbper_a, kbper_l'' || vector that specifies growth on the 'B' side perpendicular to the polariser and in the plane of the tissue at every node.
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''knor_p, knor_a, knor_l'' || specify growth normal to the plane of the tissue (i.e. thickness)
+
| width="200"| ''knor_p, knor_a, knor_l'' || vector that specifies growth normal to the plane of the tissue (i.e. thickness) at every node.
 
|}
 
|}
 
==Controlling growth==
 
==Controlling growth==
 
{| border="0" cellpadding="1" cellspacing="1"
 
{| border="0" cellpadding="1" cellspacing="1"
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''P'' || Polariser level.  
+
| width="200"| ''P'' || vector that specifies Polariser level at every node.
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''strainret_p, strainret_a, strainret_l'' || a number between 0 (no strain retention, default) and 1 (full strain retention).  
+
| width="200"| ''strainret_p, strainret_a, strainret_l'' || vector that specifies strain retention at every node. It is a number between 0 (no strain retention, default) and 1 (full strain retention).  
 
|- valign="top"  
 
|- valign="top"  
| width="200"| ''arrest_p,arrest_a,arrest_l'' || a number between 0 (no overall inhibition of growth, default) and 1 (fully inhibited)
+
| width="200"| ''arrest_p,arrest_a,arrest_l'' || vector that specifies an overall inhibition of growth at every node of the mesh. It is a number between 0 (no overall inhibition of growth, default) and 1 (fully inhibited).
 
|}
 
|}

Revision as of 07:07, 30 May 2011

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GFtbox Growth factor naming conventions

Prefix

id_ identity factors (non-diffusible). Identity factors can be labelled as on the A or B side (ida_, idb_)
s_ signalling factors (diffuse not including polariser)
v_ visualising labels (e.g. theta, bend, kpar, other labels)
f_ finite element manipulation (e.g. seams, making holes)

Suffix

_p vector representing promotor: how much the expression of the factor is being promoted in the model at every node (vertex) in the mesh.
_l vector representing the level of morphogen, i.e. *_p times *_a at every node in the mesh. This gets updated at the end of the interaction function and might change according to growth or mutation, see *_a.
_i scalar index into the main data structure morphogen field, m.morphogen.
_a scalar specifying activity: by default it is 1 and if the factor is mutated or silenced then it is 0. However, it can be in the range [0,...,1].

Standard morphogens

Specifying growth

kapar_p, kapar_a, kapar_l vector that specifies growth on the 'A' side parallel to the polariser and in the plane of the tissue at every node.
kbpar_p, kbpar_a, kbpar_l vector that specifies growth on the 'B' side parallel to the polariser and in the plane of the tissue at every node.
kaper_p, kaper_a, kaper_l vector that specifies growth on the 'A' side perpendicular to the polariser and in the plane of the tissue at every node.
kbper_p, kbper_a, kbper_l vector that specifies growth on the 'B' side perpendicular to the polariser and in the plane of the tissue at every node.
knor_p, knor_a, knor_l vector that specifies growth normal to the plane of the tissue (i.e. thickness) at every node.

Controlling growth

P vector that specifies Polariser level at every node.
strainret_p, strainret_a, strainret_l vector that specifies strain retention at every node. It is a number between 0 (no strain retention, default) and 1 (full strain retention).
arrest_p,arrest_a,arrest_l vector that specifies an overall inhibition of growth at every node of the mesh. It is a number between 0 (no overall inhibition of growth, default) and 1 (fully inhibited).