(************** Content-type: application/mathematica ************** CreatedBy='SBW JDesigner Export This notebook can be used with any Mathematica-compatible application, such as Mathematica, MathReader or Publicon. The data for the notebook starts with the line containing stars above. synopsis: xdot = Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF (time, x) x0 = Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF can be used with odeN functions as follows: x0 = untitled; [t,x] = ode23s(@Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF, [0 100], Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF); plot (x); where 100 is the end time When Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF is used without any arguments it returns a vector of the initial concentrations of the 22 floating species. Otherwise Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF should be called with two arguments: time and x. time is the current time. x is the vector of the concentrations of the 22 floating species. When these parameters are supplied Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF returns a vector of the rates of change of the concentrations of the 22 floating species. the following table shows the mapping between the vector index of a floating species and the species name. index Name x[1][t] := n x[2][t] := na x[3][t] := nan x[4][t] := mf x[5][t] := f x[6][t] := bp x[7][t] := bn x[8][t] := a x[9][t] := k x[10][t] := b x[11][t] := max x[12][t] := rasa x[13][t] := erka x[14][t] := xa x[15][t] := mdusp x[16][t] := dusp x[17][t] := rast x[18][t] := erkt x[19][t] := xt x[20][t] := d x[21][t] := kt x[22][t] := fgf ########## Distributed Biodata and Biomodel Resource Annotations ######################## In this file Ontology Term URN Ontology Term Synonyms DBBR: Rasi urn:miriam:interpro:IPR001806 Small GTPase superfamily DBBR: D urn:miriam:interpro:IPR003351 Dishevelled protein DBBR: N urn:miriam:interpro:IPR008297 Notch DBBR: ERKa urn:miriam:interpro:IPR008349 ERK1/2 MAP kinase DBBR: Bp urn:miriam:interpro:IPR013284 Beta-catenin DBBR: Fgf urn:miriam:interpro:IPR017338 Fibroblast growth factor, 15/19/21 DBBR: MF urn:miriam:interpro:IPR017374 Fringe DBBR: Bp urn:miriam:kegg.compound:C00562 Phosphoprotein DBBR: urn:miriam:kegg.pathway:ko04330 Notch signaling pathway DBBR: Rasa urn:miriam:obo.chebi:CHEBI%3A15996 GTP Guanosine 5'-triphosphate DBBR: Rasi urn:miriam:obo.chebi:CHEBI%3A17552 GDP Guanosine 5'-diphosphate, Guanosine diphosphate DBBR: urn:miriam:obo.chebi:CHEBI%3A33699 messenger RNA DBBR: urn:miriam:obo.go:GO%3A0001756 somitogenesis formation of mesodermal clusters DBBR: cytosol urn:miriam:obo.go:GO%3A0005829 cytosol DBBR: urn:miriam:obo.go:GO%3A0006402 mRNA catabolic process mRNA breakdown, mRNA catabolism, mRNA degradation DBBR: urn:miriam:obo.go:GO%3A0006412 translation protein biosynthesis, protein formation DBBR: urn:miriam:obo.go:GO%3A0006468 protein phosphorylation protein amino acid phosphorylation DBBR: urn:miriam:reactome:REACT_11045.1 Pathway: Signaling by Wnt (Homo sapiens) DBBR: urn:miriam:reactome:REACT_11065.1 Pathway: Beta-catenin phosphorylation cascade (Homo sapiens) DBBR: urn:miriam:reactome:REACT_1482.4 Pathway: ERK activation (Homo sapiens) DBBR: urn:miriam:reactome:REACT_299.2 Pathway: Signaling by Notch (Homo sapiens) DBBR: urn:miriam:reactome:REACT_9470.2 Pathway: Signaling by FGFR (Homo sapiens) DBBR: urn:miriam:taxonomy:32524 Amniota amniotes DBBR: D urn:miriam:uniprot:O14640 DVL1 Segment polarity protein dishevelled homolog DVL-1 Dishevelled-1, DSH homolog 1 DBBR: Bp urn:miriam:uniprot:P35222 Catenin beta-1 Beta-catenin, CTNNB1, CTNNB DBBR: N urn:miriam:uniprot:P46531 Notch 1 Neurogenic locus notch homolog protein 1, hN1, Translocation-associated notch protein TAN-1, Notch1, Tan1 DBBR: K urn:miriam:uniprot:P49841 GSK-3 beta Glycogen synthase kinase-3 beta, GSK3B DBBR: MDusp urn:miriam:uniprot:Q16828 DUSP6 Dual specificity protein phosphatase 6, Dual specificity protein phosphatase PYST1, Mitogen-activated protein kinase phosphatase 3, MKP3, PYST1 DBBR: MF urn:miriam:uniprot:Q8NES3 LFNG Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe, O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase DBBR: A urn:miriam:uniprot:Q9Y2T1 AXIN2 Axin-2, Axin-like protein, Axil, Axis inhibition protein 2, Conductin *) initdata = { x'[1][0.] == 0.5, (* n *) x'[2][0.] == 0.2, (* na *) x'[3][0.] == 0, (* nan *) x'[4][0.] == 0.1, (* mf *) x'[5][0.] == 0.001, (* f *) x'[6][0.] == 0.1, (* bp *) x'[7][0.] == 0.001, (* bn *) x'[8][0.] == 0.1, (* a *) x'[9][0.] == 3, (* k *) x'[10][0.] == 0.1, (* b *) x'[11][0.] == 0.1, (* max *) x'[12][0.] == 0.5, (* rasa *) x'[13][0.] == 0.2, (* erka *) x'[14][0.] == 0.1, (* xa *) x'[15][0.] == 0.1, (* mdusp *) x'[16][0.] == 0.1, (* dusp *) x'[17][0.] == 2, (* rast *) x'[18][0.] == 2, (* erkt *) x'[19][0.] == 2, (* xt *) x'[20][0.] == 2, (* d *) x'[21][0.] == 3, (* kt *) x'[22][0.] == 1, (* fgf *) } vsFK = vsF * (KIG1 / (KIG1 + K)); AK = Kt - K; Rasi = Rast - Rasa; ERKi = ERKt - ERKa; Xi = Xt - Xa; Array[p, 77]; p[1] = 0.5; (* __src__*) p[2] = 0.5; (* __waste__*) p[3] = 1.8; (* a1*) p[4] = 0.5; (* ak*) p[5] = 0.1; (* d1*) p[6] = 0.3; (* epsilon*) p[7] = 0.5; (* erki*) p[8] = 0.3; (* eta*) p[9] = 2; (* j*) p[10] = 0.28; (* k1*) p[11] = 0.03; (* k2*) p[12] = 0.05; (* ka*) p[13] = 0.7; (* kab*) p[14] = 0.05; (* kaerk*) p[15] = 0.5; (* kafgf*) p[16] = 0.5; (* kamdusp*) p[17] = 0.103; (* karas*) p[18] = 0.05; (* kax*) p[19] = 0.05; (* kaxa*) p[20] = 3.45; (* kc*) p[21] = 1.35; (* kcdusp*) p[22] = 0; (* kd1*) p[23] = 7.062; (* kd2*) p[24] = 0.63; (* kdax*) p[25] = 0.5; (* kddusp*) p[26] = 0.05; (* kderk*) p[27] = 0.37; (* kdf*) p[28] = 0.5; (* kdmdusp*) p[29] = 0.768; (* kdmf*) p[30] = 1.4; (* kdn*) p[31] = 0.001; (* kdna*) p[32] = 0.001; (* kdnan*) p[33] = 0.1; (* kdras*) p[34] = 0.05; (* kdx*) p[35] = 0.5; (* kid*) p[36] = 0.5; (* kif*) p[37] = 2.5; (* kig1*) p[38] = 0.48; (* kmd*) p[39] = 0.02; (* ksax*) p[40] = 0.5; (* ksdusp*) p[41] = 0.3; (* ksf*) p[42] = 0.1; (* kt1*) p[43] = 0.1; (* kt2*) p[44] = 0.7; (* kt3*) p[45] = 1.5; (* kt4*) p[46] = 2; (* m*) p[47] = 2; (* n*) p[48] = 2; (* p*) p[49] = 2; (* q*) p[50] = 2; (* r*) p[51] = 0.5; (* rasi*) p[52] = 1.5; (* theta*) p[53] = 0.06; (* v0*) p[54] = 0.6; (* vdax*) p[55] = 2; (* vddusp*) p[56] = 0.39; (* vdf*) p[57] = 2.82; (* vdn*) p[58] = 0.01; (* vdna*) p[59] = 0.1; (* vdnan*) p[60] = 3.3; (* vmaerk*) p[61] = 4.968; (* vmaras*) p[62] = 1.6; (* vmax*) p[63] = 1.64; (* vmb*) p[64] = 0.8; (* vmd*) p[65] = 0.5; (* vmdmdusp*) p[66] = 0.41; (* vmdras*) p[67] = 0.5; (* vmdx*) p[68] = 1.92; (* vmf*) p[69] = 5.08; (* vmk*) p[70] = 1; (* vmp*) p[71] = 0.9; (* vmsmdusp*) p[72] = 0.5; (* vmxa*) p[73] = 0.087; (* vsb*) p[74] = 3; (* vsf*) p[75] = 0; (* vsfk*) p[76] = 0.23; (* vsn*) p[77] = 0.5; (* xi*) Array[rates, 33]; rates[1] := cytosol*p[5]*p[75]; rates[2] := p[5]*cytosol*p[56]*x[0][t]/(p[29]+x[0][t]); rates[3] := p[5]*cytosol*p[19]*x[0][t]*Power(p[35],p[8])/(Power(p[35],p[8])+Power(x[4][t],p[8])); rates[4] := p[5]*cytosol*p[57]*x[1][t]/(p[30]+x[1][t]); rates[5] := p[5]*cytosol*(p[41]*x[1][t]-p[42]*x[2][t]); rates[6] := p[5]*cytosol*p[58]*x[2][t]/(p[31]+x[2][t]); rates[7] := p[5]*cytosol*p[74]*Power(x[2][t],p[47])/(Power(p[11],p[47])+Power(x[2][t],p[47])); rates[8] := p[5]*cytosol*p[67]*x[3][t]/(p[28]+x[3][t]); rates[9] := p[5]*cytosol*p[40]*x[3][t]; rates[10] := p[5]*cytosol*p[55]*x[4][t]/(p[26]+x[4][t]); rates[11] := p[51]*cytosol*(p[4]*p[3]-p[2]*x[7][t]*x[8][t]); rates[12] := p[51]*cytosol*p[72]; rates[13] := p[51]*cytosol*p[21]*x[9][t]; rates[14] := p[51]*cytosol*p[68]*p[34]/(p[34]+x[19][t])*x[9][t]/(p[9]+x[9][t])*p[3]/x[20][t]; rates[15] := p[51]*cytosol*p[69]*x[5][t]/(p[10]+x[5][t]); rates[16] := p[51]*cytosol*(p[44]*x[6][t]-p[43]*x[9][t]); rates[17] := p[51]*cytosol*p[22]*x[5][t]; rates[18] := p[51]*cytosol*p[52]; rates[19] := p[51]*cytosol*(p[62]*Power(x[6][t],x[0][t])/(Power(p[12],x[0][t])+Power(x[6][t],x[0][t]))); rates[20] := p[51]*cytosol*(p[71]*Power(x[13][t],p[45])/(Power(p[18],p[45])+Power(x[13][t],p[45]))); rates[21] := p[51]*cytosol*p[63]*x[10][t]/(p[37]+x[10][t]); rates[22] := p[51]*cytosol*p[38]*x[10][t]; rates[23] := p[51]*cytosol*p[53]*x[7][t]/(p[23]+x[7][t]); rates[24] := p[7]*cytosol*p[60]*Power(x[21][t],p[49])/(Power(p[14],p[49])+Power(x[21][t],p[49]))*p[50]/(p[16]+p[50]); rates[25] := p[7]*cytosol*p[65]*x[11][t]/(p[32]+x[11][t]); rates[26] := p[7]*cytosol*p[59]*x[11][t]/x[16][t]*p[6]/(p[13]+p[6]); rates[27] := p[7]*cytosol*p[20]*x[15][t]*x[12][t]/(p[25]+x[12][t]); rates[28] := p[7]*cytosol*p[61]*x[12][t]/x[17][t]*p[76]/(p[17]+p[76]); rates[29] := p[7]*cytosol*p[66]*x[13][t]/(p[33]+x[13][t]); rates[30] := p[7]*cytosol*p[70]*Power(x[13][t],p[48])/(Power(p[15],p[48])+Power(x[13][t],p[48])); rates[31] := p[7]*cytosol*p[64]*x[14][t]/(p[27]+x[14][t]); rates[32] := p[7]*cytosol*p[39]*x[14][t]; rates[33] := p[7]*cytosol*p[54]*x[15][t]/(p[24]+x[15][t]); x'[1][t] == { + rates[1] - rates[2] - rates[3]}/.rates; x'[2][t] == { + rates[3] - rates[4] - rates[5]}/.rates; x'[3][t] == { + rates[5] - rates[6]}/.rates; x'[4][t] == { + rates[7] - rates[8]}/.rates; x'[5][t] == { + rates[9] - rates[10]}/.rates; x'[6][t] == { + rates[14] - rates[15] - rates[17]}/.rates; x'[7][t] == { - rates[16]}/.rates; x'[8][t] == { + rates[11] + rates[22] - rates[23]}/.rates; x'[9][t] == { + rates[11]}/.rates; x'[10][t] == { + rates[12] - rates[13] - rates[14] + rates[15] + rates[16]}/.rates; x'[11][t] == { + rates[18] + rates[19] + rates[20] - rates[21]}/.rates; x'[12][t] == { + rates[24] - rates[25]}/.rates; x'[13][t] == { + rates[26] - rates[27]}/.rates; x'[14][t] == { + rates[28] - rates[29]}/.rates; x'[15][t] == { + rates[30] - rates[31]}/.rates; x'[16][t] == { + rates[32] - rates[33]}/.rates; x'[17][t] == { }/.rates; x'[18][t] == { }/.rates; x'[19][t] == { }/.rates; x'[20][t] == { }/.rates; x'[21][t] == { }/.rates; x'[22][t] == { }/.rates; sol = NDSolve[Evaluate[Join[Table[x'[i][t], {i,22}], Table[x'[i][0], {i, 22}]]/.p, Table[x[i], {i, 22}], {t, 0, tmax}]]; Plot[Evaluate[Table[x[i][t], {i, 22}]/.sol], {t, 0, tmax}];