Types of morphogens and factors
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 | promotor: how much the expression of the factor is being promoted in the model |
| _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. |
| _i | index into the main data structure morphogen field, m.morphogen. |
| _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]. |
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) |