Paris/Sources

From 2007.igem.org

(Difference between revisions)
Line 74: Line 74:
g := set_gbfpos(g, (random(30)*|nord> + random(30)*|est>), {DAP = 6.0, DAPe=3.0, bactS}) ;;  
g := set_gbfpos(g, (random(30)*|nord> + random(30)*|est>), {DAP = 6.0, DAPe=3.0, bactS}) ;;  
evol[iter=1000,interlude=GBVexport((\v.("DAPe = "+(12 * v.DAPe )+if BactS(v) then ", bactS= 255" else  ", bactG = 255"fi )))](g) ;;
evol[iter=1000,interlude=GBVexport((\v.("DAPe = "+(12 * v.DAPe )+if BactS(v) then ", bactS= 255" else  ", bactG = 255"fi )))](g) ;;
 +
</pre></code>
 +
 +
 +
=Cell auto 2==
 +
 +
==Constant rate of differentiation==
 +
 +
<code><pre>
 +
record MecaBact = {x, y, vx, vy, fx, fy, radius}
 +
and record CellBact  = {dap:float, soma:bool}
 +
and record Bact = MecaBact + CellBact;;
 +
 +
 +
delaunay(2) D2 = (\e.(e.x, e.y)) ;;
 +
 +
fun noise(x) = x + 0.0005 - random(0.001) ;;
 +
// --- Mechanistic-------------------------------------------------------
 +
 +
DT    := 0.05;;
 +
K    := 1.0;;
 +
MU    := 1.8;;
 +
R0_Gm := 0.50;; //germinal cells minmal rayon
 +
R0_G  :=0.75;;
 +
R0_S  := 1.00;;
 +
 +
// interaction : the effect of the cells between each others
 +
fun interaction(ref, src) = (
 +
let X      = ref.x - src.x
 +
and Y      = ref.y - src.y in
 +
let dist  = sqrt(X*X+Y*Y) in
 +
let spring = 0.0-K*(dist-(ref.radius+src.radius))/dist in
 +
  {fx=X*spring - ref.vx*MU, fy = Y*spring - ref.vy*MU}
 +
) ;;
 +
 +
fun add_vect(u, v) = { fx = u.fx + v.fx, fy = u.fy + v.fy } ;;
 +
fun sum(x, u, acc) = add_vect(acc, interaction(x,u)) ;;
 +
 +
 +
trans Meca = {
 +
e => (
 +
  let f = neighborsfold(sum(e), {fx=0,fy=0}, e) in
 +
    e+{ x  = noise(e.x  + DT*e.vx),
 +
        y  = noise(e.y  + DT*e.vy),
 +
        vx = e.vx + DT*f.fx,
 +
        vy = e.vy + DT*f.fy,
 +
        fx = f.fx,
 +
        fy = f.fy
 +
      }
 +
)
 +
} ;;
 +
 +
 +
// --- grow -------------------------------------------------------
 +
 +
DIFF  := 1.0  ;;
 +
CONS  := 10.0  ;;
 +
DiffP := 0.00023  ;;
 +
DeathSP := 0.00001 ;;
 +
DivG := 0.00600 ;;
 +
DEPOT := 15.0 ;;
 +
CroitG :=0.004  ;;
 +
CroitS :=0.007;; 
 +
 +
 +
//cell division function
 +
fun divide(b) = (
 +
b+{dap= b.dap/2, radius=R0_Gm },
 +
b + {dap= b.dap/2,x=noise(b.x),y=noise(b.y), radius=R0_Gm}
 +
) ;;
 +
 +
 +
 +
trans Evol = {
 +
 +
x / x.soma => if (random(1.0) <= DeathSP) then <undef> else if ( ( x.radius < R0_S ) & ( random(1.0) < CroitS) ) then x + {radius = x.radius + (R0_S - R0_G)/4} else  x fi fi ; 
 +
 +
x => (
 +
  let dap_diff = neighborsfold((\y.\acc.( {dap=DT*DIFF*(y.dap-x.dap) + acc.dap, n=acc.n+1} )), {dap=0.0,n=0}, x) in
 +
  let dap' = if (x.dap + dap_diff.dap/dap_diff.n) - DT*CONS >= 0 then (x.dap + dap_diff.dap/dap_diff.n) - DT*CONS else 0 fi in
 +
 +
      if (random(1.0) <= DiffP)
 +
      then x + {dap=DEPOT,soma=true,radius=x.radius} //la nouvelle cellule S a la taille de la cellule G dont elle provient
 +
      else  if x.radius  >= R0_G then if  ( (random(1.0) <= DivG) & dap'> 1 )then divide(x + {dap=dap'}) else (x + {dap=dap'}) fi else  if random(1.0) < CroitG then x + {radius = x.radius + (R0_G - R0_Gm)/5 , dap=dap' } else x+{dap=dap'} fi fi fi
 +
)
 +
 +
} ;;
 +
 +
 +
 +
 +
// --- Visualisation ----------------------------------------------------
 +
 +
outname := "/tmp/sheet.imo" ;;
 +
outfile := (if (is_opened(outname)) then close(outname) else <undef> fi ; open(outname,1)) ;;
 +
 +
 +
 +
 +
fun show_cell(e) = (
 +
"\tTranslated { Translation <" + e.x + ", " + e.y + ", " + 0.0 + "> Geometry Sphere { Radius " + e.radius + " Slices 16 Stacks 16 " + "Color<" + if(e.soma) then 0 + ", " + 1.0 + ", " + 0 else if ((e.dap+0.4)*(0.5+R0_G/e.radius))< 1.0 then ((e.dap+0.4)*(0.5+R0_G/e.radius)) else  1.0  fi+ ", " + 0 + ", " + 0 fi + "> } }"
 +
) ;;
 +
 +
 +
 +
fun show[cpt=0](f, freq, c) = (
 +
cpt := 1 + cpt ;
 +
if (0 == cpt % freq)
 +
then (
 +
  stdout << cpt << "\n" ;
 +
  print_coll(f,
 +
              c,
 +
              show_cell,
 +
              "Scene a"+cpt+" {\n",
 +
              "\n",
 +
              "}\nReplace { Show a"+cpt+"}\n\n")
 +
) else <undef> fi ;
 +
c
 +
) ;;
 +
 +
// --- Etat initial ----------------------------------------------------
 +
 +
v0 := {vx=0, vy=0, vz=0, fx=0, fy=0, fz=0, dap=14.0,soma=false,radius=R0_Gm} ;;
 +
v1 :={vx=0, vy=0, vz=0, fx=0, fy=0, fz=0, dap=DEPOT,soma=true,radius=R0_S} ;;
 +
pre_init :=
 +
      v1+{x = 1.01,  y = 1.023, z = 0.101},
 +
      v1+{x = 0.07,  y = 1.0,  z = 0.095},
 +
      v1+{x = 1.0,  y = 0.01,  z = 0.098},
 +
      v1+{x = 0.52,  y = 0.53,  z = 0.1},
 +
      v1+{x = 0.01,  y = 0.02,  z = 0.099},
 +
      v0+{x = -0.4,  y = 0.02,  z = 0.099},
 +
      v0+{x = 1.4,  y = 0.02,  z = 0.099}
 +
;;
 +
 +
init := Meca[iter=1000](delaunayfy(D2:(), pre_init)) ;;
 +
 +
//show(outfile, 1, init);;
 +
//system("imoview "+outname);;
 +
 +
// --- Evolution -------------------------------------------------------
 +
 +
fun step(sys) = (
 +
Evol(Meca(sys))
 +
) ;;
 +
 +
step[iter=100000,interlude=show(outfile,10)](init) ;;
 +
 +
system("./imoview_black "+outname);;
 +
!quit ;;
</pre></code>
</pre></code>

Revision as of 13:55, 24 October 2007



Cell auto

!include "gbviewOutput.mgs" ;;

N := 30;;

gbf grille = <nord, est ; 30 * nord, 30 * est>
and record Bact = { DAP:float, DAPe:float }
and record BactG = Bact + { bactG }
and record BactS = Bact + { bactS} ;;

fun iota_v(v,n) = map((\x.v), iota(n,seq:())) ;;
fun new_grid(v) = iota_v(iota_v(v,N), N) following |nord>, |est> ;;

fun majBactG[DAPexport = 0.2, DAPimport = 0.2, DAPconso= 1, SupDiff = 2.4, InfDiff = 2.02 ](x) = 
 	if ( ( x.DAP > InfDiff ) & ( x.DAP < SupDiff ) & (random(1) < 0.8) ) then
		{DAP = x.DAP , DAPe = x.DAPe, bactS} else
		let dap = if x.DAP - DAPconso  > 0 then  x.DAP - DAPconso  else  0 fi
		 and dape= x.DAPe
		 in if 	dap > dape then 
                    x + {DAP = dap - DAPexport * dap, DAPe = dape + DAPexport * dap }
		   else x + {DAP = dap + DAPimport * dape, DAPe = dape - DAPimport * dape }
                  fi
        fi 
;;

fun majBactS[DAPexport = 0.2, DAPimport = 0.2, DAPprod=10](x) =  
		let dap =  x.DAP + DAPprod
		 and dape= x.DAPe
		 in if 	dap > dape then 
                    x + {DAP = dap - DAPexport * dap, DAPe = dape + DAPexport * dap }
		   else x + {DAP = dap + DAPimport * dape, DAPe = dape - DAPimport * dape }
                  fi

;;


trans evol[Delta_t=0.1,DAPeDiff=1, DAPeDegrad = 0.2] = {



  (* production of DAP *)
  x:BactS => ( 
	let d = neighborsfold(
      (\y.\acc.( DAPeDiff*Delta_t*(y.DAPe-x.DAPe) + acc)),
      x.DAPe,
      x)
    in majBactS( x + {DAPe = if ( d - DAPeDegrad * x.DAPe) > 0 then d - DAPeDegrad * x.DAPe else 0 fi } )
      );

  (* Diffirentiation and Consumption *)
 x:BactG => ( 
	let d = neighborsfold(
      (\y.\acc.( DAPeDiff*Delta_t*(y.DAPe-x.DAPe) + acc)),
      x.DAPe,
      x)
    in majBactG(x + {DAPe = if ( d - DAPeDegrad * x.DAPe) > 0 then  d - DAPeDegrad * x.DAPe else 0 fi } )
    

  )

} ;;





g := new_grid({DAP=6.0, DAPe=3.0, bactG}) ; 0 ;;
g := set_gbfpos(g, (random(30)*|nord> + random(30)*|est>), {DAP = 6.0, DAPe=3.0, bactS}) ;;
g := set_gbfpos(g, (random(30)*|nord> + random(30)*|est>), {DAP = 6.0, DAPe=3.0, bactS}) ;;
g := set_gbfpos(g, (random(30)*|nord> + random(30)*|est>), {DAP = 6.0, DAPe=3.0, bactS}) ;;
g := set_gbfpos(g, (random(30)*|nord> + random(30)*|est>), {DAP = 6.0, DAPe=3.0, bactS}) ;; 
evol[iter=1000,interlude=GBVexport((\v.("DAPe = "+(12 * v.DAPe )+if BactS(v) then ", bactS= 255" else  ", bactG = 255"fi )))](g) ;;


Cell auto 2=

Constant rate of differentiation

record MecaBact = {x, y, vx, vy, fx, fy, radius}
and record CellBact  = {dap:float, soma:bool}
and record Bact = MecaBact + CellBact;;


delaunay(2) D2 = (\e.(e.x, e.y)) ;;

fun noise(x) = x + 0.0005 - random(0.001) ;;
// --- Mechanistic-------------------------------------------------------

DT    := 0.05;;
K     := 1.0;;
MU    := 1.8;;
R0_Gm := 0.50;; //germinal cells minmal rayon 
R0_G  :=0.75;;
R0_S  := 1.00;;

// interaction : the effect of the cells between each others
fun interaction(ref, src) = (
 let X      = ref.x - src.x
 and Y      = ref.y - src.y in
 let dist   = sqrt(X*X+Y*Y) in
 let spring = 0.0-K*(dist-(ref.radius+src.radius))/dist in
   {fx=X*spring - ref.vx*MU, fy = Y*spring - ref.vy*MU}
) ;;

fun add_vect(u, v) = { fx = u.fx + v.fx, fy = u.fy + v.fy } ;;
fun sum(x, u, acc) = add_vect(acc, interaction(x,u)) ;;


trans Meca = {
 e => (
   let f = neighborsfold(sum(e), {fx=0,fy=0}, e) in
     e+{ x  = noise(e.x  + DT*e.vx),
         y  = noise(e.y  + DT*e.vy),
         vx = e.vx + DT*f.fx,
         vy = e.vy + DT*f.fy,
         fx = f.fx,
         fy = f.fy
       }
 )
} ;;


// --- grow -------------------------------------------------------

DIFF  := 1.0  ;;
CONS  := 10.0  ;;
DiffP := 0.00023  ;; 
DeathSP := 0.00001 ;;
DivG := 0.00600 ;;
DEPOT := 15.0 ;; 
CroitG :=0.004  ;; 
CroitS :=0.007;;  


//cell division function
fun divide(b) = (
 b+{dap= b.dap/2, radius=R0_Gm },
 b + {dap= b.dap/2,x=noise(b.x),y=noise(b.y), radius=R0_Gm}
) ;;



trans Evol = {

 x / x.soma => if (random(1.0) <= DeathSP) then <undef> else if ( ( x.radius < R0_S ) & ( random(1.0) < CroitS) ) then x + {radius = x.radius + (R0_S - R0_G)/4} else  x fi fi ;  

 x => (
   let dap_diff = neighborsfold((\y.\acc.( {dap=DT*DIFF*(y.dap-x.dap) + acc.dap, n=acc.n+1} )), {dap=0.0,n=0}, x) in
   let dap' = if (x.dap + dap_diff.dap/dap_diff.n) - DT*CONS >= 0 then (x.dap + dap_diff.dap/dap_diff.n) - DT*CONS else 0 fi in

       if (random(1.0) <= DiffP)
       then x + {dap=DEPOT,soma=true,radius=x.radius} //la nouvelle cellule S a la taille de la cellule G dont elle provient
       else  if x.radius  >= R0_G then if  ( (random(1.0) <= DivG) & dap'> 1 )then divide(x + {dap=dap'}) else (x + {dap=dap'}) fi else  if random(1.0) < CroitG then x + {radius = x.radius + (R0_G - R0_Gm)/5 , dap=dap' } else x+{dap=dap'} fi fi fi
 ) 

} ;;




// --- Visualisation ----------------------------------------------------

outname := "/tmp/sheet.imo" ;;
outfile := (if (is_opened(outname)) then close(outname) else <undef> fi ; open(outname,1)) ;;




fun show_cell(e) = (
 "\tTranslated { Translation <" + e.x + ", " + e.y + ", " + 0.0 + "> Geometry Sphere { Radius " + e.radius + " Slices 16 Stacks 16 " + "Color<" + if(e.soma) then 0 + ", " + 1.0 + ", " + 0 else if ((e.dap+0.4)*(0.5+R0_G/e.radius))< 1.0 then ((e.dap+0.4)*(0.5+R0_G/e.radius)) else  1.0  fi+ ", " + 0 + ", " + 0 fi + "> } }"
) ;;



fun show[cpt=0](f, freq, c) = (
 cpt := 1 + cpt ;
 if (0 == cpt % freq)
 then (
   stdout << cpt << "\n" ;
   print_coll(f,
              c,
              show_cell,
              "Scene a"+cpt+" {\n",
              "\n",
              "}\nReplace { Show a"+cpt+"}\n\n")
 ) else <undef> fi ;
 c
) ;;

// --- Etat initial ----------------------------------------------------

v0 := {vx=0, vy=0, vz=0, fx=0, fy=0, fz=0, dap=14.0,soma=false,radius=R0_Gm} ;;
v1 :={vx=0, vy=0, vz=0, fx=0, fy=0, fz=0, dap=DEPOT,soma=true,radius=R0_S} ;;
pre_init :=
       v1+{x = 1.01,  y = 1.023, z = 0.101},
       v1+{x = 0.07,  y = 1.0,   z = 0.095},
       v1+{x = 1.0,   y = 0.01,  z = 0.098},
       v1+{x = 0.52,  y = 0.53,  z = 0.1},
       v1+{x = 0.01,  y = 0.02,  z = 0.099},
       v0+{x = -0.4,  y = 0.02,  z = 0.099},
       v0+{x = 1.4,  y = 0.02,  z = 0.099}
;;

init := Meca[iter=1000](delaunayfy(D2:(), pre_init)) ;;

//show(outfile, 1, init);;
//system("imoview "+outname);;

// --- Evolution -------------------------------------------------------

fun step(sys) = (
 Evol(Meca(sys))
) ;;

step[iter=100000,interlude=show(outfile,10)](init) ;;

system("./imoview_black "+outname);;
!quit ;;
Retrieved from "http://2007.igem.org/wiki/index.php/Paris/Sources"