Types of morphogens and factors: Difference between revisions
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{| border="0" cellpadding="1" cellspacing="1" | {| border="0" cellpadding="1" cellspacing="1" | ||
|- valign="top" | |- valign="top" | ||
| width="30"| _p || promotor: how much the expression of the factor is being promoted in the model | | width="30"| _p || vector representing promotor: how much the expression of the factor is being promoted in the model at every node (vertex) in the mesh. | ||
|- valign="top" | |- valign="top" | ||
| width="30"| _l || level of morphogen, i.e. *_p times *_a. This gets updated at the end of the interaction function and might change according to growth or mutation, see *_a. | | width="30"| _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. | ||
|- valign="top" | |- valign="top" | ||
| width="30"| _i || index into the main data structure morphogen field, m.morphogen. | | width="30"| _i || scalar index into the main data structure morphogen field, m.morphogen. | ||
|- valign="top" | |- valign="top" | ||
| width="30"| _a || 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]. | | width="30"| _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= | =Standard morphogens= | ||
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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'' || specify growth on the 'A' side parallel to the polariser and in the plane of the tissue | ||
|- 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'' || specify growth on the 'B' side parallel to the polariser and in the plane of the tissue | ||
|- 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'' || specify growth on the 'A' side perpendicular to the polariser and in the plane of the tissue | ||
|- 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'' || specify growth on the 'B' side perpendicular to the polariser and in the plane of the tissue | ||
|- valign="top" | |- valign="top" | ||
| width="200"| knor_p,knor_a,knor_l | | width="200"| ''knor_p, knor_a, knor_l'' || specify growth normal to the plane of the tissue (i.e. thickness) | ||
|} | |} | ||
==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'' || Polariser level. | ||
|- 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'' || 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'' || a number between 0 (no overall inhibition of growth, default) and 1 (fully inhibited) | ||
|} | |} | ||
Revision as of 08:03, 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 | specify growth on the 'A' side parallel to the polariser and in the plane of the tissue |
| kbpar_p, kbpar_a, kbpar_l | specify growth on the 'B' side parallel to the polariser and in the plane of the tissue |
| kaper_p, kaper_a, kaper_l | specify growth on the 'A' side perpendicular to the polariser and in the plane of the tissue |
| kbper_p, kbper_a, kbper_l | specify growth on the 'B' side perpendicular to the polariser and in the plane of the tissue |
| knor_p, knor_a, knor_l | specify growth normal to the plane of the tissue (i.e. thickness) |
Controlling growth
| P | Polariser level. |
| strainret_p, strainret_a, strainret_l | a number between 0 (no strain retention, default) and 1 (full strain retention). |
| arrest_p,arrest_a,arrest_l | a number between 0 (no overall inhibition of growth, default) and 1 (fully inhibited) |