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="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] || specify growth normal to the plane of the tissue (i.e. thickness)
+
| 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 07:03, 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 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)