G filter [10] assumptions. In the meantime, it can be viewed and used as a first order approximation, or as a temporary crutch. Computational details The computational environment R [11] was used with R packages of Bioconductor [12] to implement this study. Specifically, the package Biobase was used to manipulate microarray data as expression set (class eset) objects and SBMLR [13,14] was used to simulate a systems biology markup language (SBML) [15-17] representation of the9,ri – ri10,dTHF = ri – ri dt 1R,2R,4,6,7,10 1,2,5 dMangafodipir (trisodium) biological activity CHOTHF = ri – ri dt 5,8 6,7 dFGAR = r6 – r13 dtd(CH2THF) = ri – ri dt 1,2 1R,2R,3,8,9 dCHODHF = r11 – r12 dt dAICAR = r13 – r7 – r12 dtd(CH3THF) = r3 – r4 dt dHCHO = r2R – r2 dtThese equations restate the system configuration information of Figure 1A, i.e. they state that the rate at which a metabolite concentration increases equals the sum of the synthesis reaction fluxes (arrows into a node) minus the sum of the degradation reaction fluxes (arrows leaving a node). The ri in these equations are:r1 = VSHMT Serine / K SER THF / K THF 1 + THF / K THF 1 + Serine / K SER r1R = VSHMTR CH2THF / K CH2THF Glycine / K GLY 1 + CH2THF / K CH2THF 1 + Glycine / K GLYr2 = hp THF HCHOr2R = hl CH2THFr3 = VMTHFRNADPH / K NADPH 5 1 + NADPH / K NADPH xn DHF CH2THF /(K CH2THF [1 + MTX + DHF ]) + 1 n K3 1 K5 xn DHF CH2THF /(K CH2THF [1 + MTX + DHF ]) n K3 1 Kr4 = VMTR r5 = VFTSCH2THF / K CH2THF Homocysteine / K HCYS 1 + CH2THF / K CH2THF 1 + Homocysteine / K HCYSFormate / K formate THF / K THF ATP / K ATP 1 + THF / K THF 1 + ATP / K ATP 1 + Formate / K formate5 xn DHF CHODHF CHOTHF /(K CHOTHF [1 + MTX + DHF + CHODHF ]) n K6 K6 1 Kr6 = VGARTGAR / K GAR 5 1 + GAR / K GAR xn DHF CHODHF CHOTHF /(K CHOTHF [1 + MTX + DHF + CHODHF ]) + 1 n K6 K6 1 PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27597769 K6 AICAR / K AICAR 5 1 + AICAR / K AICAR xn DHF CHODHF CHOTHF /(K CHOTHF [1 + MTX + DHF + CHODHF ]) + 1 n K7 K7 1 K7 CH2THF / K CH2THF NADP / K NADP 1 + CH2THF / K CH2THF 1 + NADP / K NADP VTS dUMP CH2THF K dUMP K CH2THF5 xn DHF CHODHF CHOTHF /(K CHOTHF [1 + MTX + DHF + CHODHF ]) n K7 K7 1 Kr7 = VATICr8 = VMTHFDr9 =5 5 5 xn xn xn x1 dUMP CHODHF CHODHF DHF dUMP CH2THF DHF DHF 1+ + FH + 1 + MTX + DHF 1 + CHODHF + CHODHF MTX + 1 + MTX + DHF MTXn K n n K dUMP K CH2THF K9 K9 K9 K9 2 K 9 1 K dUMP 2 K9 2 K9 1 K9r10 = k(DHF T – DHF)5 xn DHF CHOTHF CHODHF /(K CHOTHF [1 + MTX + DHF + CHOTHF ]) n K7 K12 1 K7 5 xn DHF CHOTHF CHODHF /(K CHOTHF [1 + MTX + DHF + CHOTHF ]) + 1 n K7 K12 1 Kr11 = kFDS DHF AICAR / K AICAR 1 + AICAR / K AICARr12 = VATICGLN / K GLN FGAR / K FGAR r13 = VFA 1 + GLN / K GLN 1 + FGAR / K FGARwhere DHFT-DHF (total DHF minus free DHF) is the concentration of DHF bound to DHFR, xi is the concentration of i-glutamated MTX, and all folates are assumed to be penta-glutamated. Not shown are 10 additional differential equations for up to penta-glutamation of MTX either free or bound to DHFR. These 10 equations are irrelevant when MTX = 0 as in the microarray data analyses below; they were used here only to validate the current implementation of the model against its previously published responses, see Figure 2[1].Model limitations Since the model has only one compartment, the cytosol, it cannot handle changes in the mitochondrial enzymesPage 3 of(page number not for citation purposes)BMC Cancer 2005, 5:http://www.biomedcentral.com/1471-2407/5/0.0.CH2THF-20 0 10 20EMTXDHF0.0.-0.-0.0.0.0.HoursHoursHours0.CHOTHF0.CH3THF-20 0 10 200.THF.