Revision as of 08:23, 30 May 2011

GFtbox Growth factor naming conventions

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)

_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].

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.

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).

@@ Line 44: / Line 44: @@
 {| border="0" cellpadding="1" cellspacing="1"
 |- valign="top"
-| width="200"| ''P'' || vector that specifies Polariser level at every node.
+| width="200"| '''''P''''' || vector that specifies '''Polariser level''' at every node.
 |- valign="top"
 | 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).