Types of morphogens and factors: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
Line 29: | Line 29: | ||
{| border="0" cellpadding="1" cellspacing="1" | {| border="0" cellpadding="1" cellspacing="1" | ||
|- valign="top" | |- valign="top" | ||
| width="200"|'' kapar_p, kapar_a, kapar_l'' || | | 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'' || | | 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'' || | | 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'' || | | 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'' || | | 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 08:07, 30 May 2011
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). |