BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL0403954746?filename=MODEL0403954746.mprimaryOK200Ricardo del RosarioNon-curatedordinary differential equation modelL2V1https://www.ebi.ac.uk/biomodels/MODEL040395474617708428falseBioModelsSBMLModelsNutsch2005 phototaxis noncyc repellent dark2007MODEL0403954746R C H del Rosario, W F Staudinger, S Streif, F Pfeiffer, E Mendoza, D OesterheltR C H del Rosario17708428, A recent phototaxis model of Halobacterium salinarum composed of the signalling pathway and the switch complex of the motor explained all considered experimental data on spontaneous switching and response time to repellent or attractant light stimuli. However, the model which considers symmetric processes in the clockwise and counter-clockwise rotations of the motor cannot explain the behaviour of a CheY(D10K,Yl00W) mutant which always moves forward and does not respond to light. We show that the introduction of asymmetry in the motor switch model can explain this behaviour. Sensitivity analysis allowed us to choose parameters for which the model is sensitive and whose values we then change in either direction to obtain an asymmetric model. We also demonstrate numerically that at low concentrations of CheYP, the symmetric and asymmetric models behave similarly, but at high concentrations, differences in the clockwise and counter-clockwise modes become apparent. Thus, those experimental data that could previously be explained only by ad hoc assumptions are now obtained 'naturally' from the revised model.. 4, 1. Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. rcdelros@biochem.mpg.dercdelros@biochem.mpg.deDepartment of Membrane Biochemistry, Max Planck Inst of BiochemistryA recent phototaxis model of Halobacterium salinarum composed of the signalling pathway and the switch complex of the motor explained all considered experimental data on spontaneous switching and response time to repellent or attractant light stimuli. However, the model which considers symmetric processes in the clockwise and counter-clockwise rotations of the motor cannot explain the behaviour of a CheY(D10K,Yl00W) mutant which always moves forward and does not respond to light. We show that the introduction of asymmetry in the motor switch model can explain this behaviour. Sensitivity analysis allowed us to choose parameters for which the model is sensitive and whose values we then change in either direction to obtain an asymmetric model. We also demonstrate numerically that at low concentrations of CheYP, the symmetric and asymmetric models behave similarly, but at high concentrations, differences in the clockwise and counter-clockwise modes become apparent. Thus, those experimental data that could previously be explained only by ad hoc assumptions are now obtained 'naturally' from the revised model.Modelling the CheY(D10K,Yl00W) Halobacterium salinarum mutant: sensitivity analysis allows choice of parameter to be modified in the phototaxis model.del Rosario R C H RC, Staudinger W F WF, Streif S S, Pfeiffer F F, Mendoza E E, Oesterhelt D DHac-1/Dark, dark/dapaf-1/hac-1, hac-1, Dapaf-1/HAC-1, D-Apaf-1, taxis in response to light, DmelCG6829, dApaf-1, dapaf-1, anon-53Fa, arc, l(2)SH0173, Photokineses, Dark/Dapaf-1/HAC1, apaf1, dapaf, hac1, Photokinesis, dark, dark/hac-1/dapaf-1., Apaf-1, ark, dApaf-1/DARK/HAC-1, T1, dapaf-1S, Dark/Hac-1/dApaf1, APAF1, apaf-1, Hac1, phototactic behavior, dapaf-1L, Dark/Hac-1/dApaf-1, DARK, Hac-1, Apaf1, dApaf1, Dark, phototactic behaviour, dArk, Dapaf-1, ARK, Dark/Apaf-I, CG6829, dAPAF-1Previously, experimental, asymmetry, determination, Effects, Visible Light, Motor(s), model, composed of, My pet moves normally, Long Term, Ly113, protrusion, Motor, phototactic behavior, sensitive, responsivity, Acquisition, Switch, Low, Effect, Models, asymmetric, sensitivity, Obtained, Bacterium halobium, signal transduction by protein phosphorylation, motor, Modification, reactivity, Modeling System, me75, methods, Selection, Longterm, Halobacterium halobium, experimental section, Direction, Counter Device, Clockwise, composition, Former, Photokinesis, Long-Term, Visible, Elected, Selected, D17Mit170, T1, Did, allergic reaction, signalling pathway, TNFSF14, Pick, Acquire, Flavobacterium (subgen. Halobacterium) halobium, Halobacterium piscisalsi, Switch Device, signal transduction by cis-phosphorylation, Sensitivity, Long-Term Effect, TR2, Choose, Delta, Select, Model, Forward, Switch/Relay, Long-Term Effects, Bacillus halobius ruber, single-organism behavior, Choice, FORMER, Adapted, Revised, Spontaneous, Radiation, anatomical protrusion, cou, taxis in response to light, Halobacterium salinarium, Difference, UNQ391/PRO726, signal transduction by conformational transition, Longterm Effect, Counter, Light, compositionality, Tl3, CD258, Tl2, signal transduction by trans-phosphorylation, signaling cascade, Lr, LIGHT, Pet Moves Normally, Flavobacterium (subgen. Halobacterium) salinarium, Do, Long Term Effects, chemical analysis, Obtain, Revision, Halobacterium cutirubrum, Mutant, signalling cascade, Does, Pseudomonas salinaria, Halobacter salinaria, Chose, Stimuli, Visible Radiations, Radiations, Adapt, Modified, Visible Radiation, Serratia salinaria, Motor Device, HVEML, Model System, HVEM-L, content, symmetric, Chosen, Photoradiation, attractant, Specificity, Photokineses, Changed, Picked, Longterm Effects, LTg, Revise., experimental procedures, Serratia cutirubrum, Stimulus, Photoradiations, signaling pathway, Specificity and Sensitivity, spine, Change, Election, structure, Bra, assay, response, moves, phototactic behaviour, Previousextent, Hac-1/Dark, GrpL, GRPL, Public Sectors, dmMOF, dei, del, F5E6_13, DmelCG6829, fond, AUTSX5, organ of sensory system, ADP-ribosylation factor binding, Ral GTPase binding, 1/s, Visible Light, NOVH, CycEI, Apaf-1, F5E6.13, CCN3, QM, prevention, Long Term, DmelCG9648, Ccne, dMOF, Apaf1, GTP-Rho binding, Public Enterprise, prevention and control, ARK, Effect, asymmetric, DmelCG8432, fs(1)M104, Arp, 2210417O06Rik, increased, reference sample, hac-1, Biology, dMax, C2, Public Domains, arc, sensory organ, DmelCG9750, ark, T1, Ran protein binding, IBP-9, preventive measures, TNFSF14, indolepyruvate oxidoreductase activity, Grf40, dApaf1, CP-22, NOVh, Long-Term Effects, REP, GRBLG, preventive therapy, Radiation, Rab escort protein, D-Apaf-1, completeness, UNQ391/PRO726, anon-53Fa, CG9648, Longterm Effect, l(2)SH0173, Light, AthREP, Cyc E, br37, rep, bHLHd7, GrbX, bHLHd6, bHLHd9, bHLHd8, organ of sensory organ system, bHLHd5, bHLHd4, LIGHT, one turn per second, BG:DS07108.3, DEL cells, Public Domain, 3-(indol-3-yl)pyruvate synthase (ferredoxin) activity, Ras interactor activity, dmax, Domains, P38, NOV, GRAP-2, l(2)05206, END, PlexA1, CG6829, Domain, anon-WO0142479.1, dark/hac-1/dapaf-1, Visible Radiations, CoA-indole-acetylating), Visible Radiation, Plxn1, HVEML, GADS, CG9750, symmetric, Mona, nov, organ of sense organ system, hac1, Ran-binding protein, mKIAA4053, fs(1)Y[b], dapaf-1S, MOF, Mof, apaf-1, dapaf-1L, Sector, l35Dd, CG8432, hyaline, GTP-Ral binding, C130088N23Rik, Tip48, sense organ system organ, PLXN1, Ras GTPase binding, phototactic behaviour, DXS648E, accessory, V19, Sectors, Rab interactor activity, cycline, Dapaf-1/HAC-1, YB, asymmetry, Effects, DmcyclinE, number, stalk, cycE, GRAP2, ARP87C, Copyrights, Actr87C, presence, supernumerary, l(2)br37, DmelCG9252, CYCLE, Ly113, cdi7, Dark/Hac-1/dApaf1, DmelCG5441, Hac1, DmelCG3025, phototactic behavior, Dark/Hac-1/dApaf-1, cyclinE, Gads, Yb, gdl, Cdi7, CDI7, bHLHc10, Enterprises, CG2706, MAX, CYCE, Longterm, DmelCG3938, Reptin, CyclE, Delilah, dapaf-1, REPT, 3938, dapaf, Visible, dark, TSPAN, Photokinesis, Long-Term, IGFBP9, DmcycE, Public Enterprises, culm, 3-(indol-3-yl)pyruvate:ferredoxin oxidoreductase (decarboxylating, GRB2L, l(2)k05007, Kiaa4053, dm-cycE, max, GRID, DARK, CG6174, L10, CP22, sensillum, Long-Term Effect, TR2, grid, Sor, dArk, Enterprise, Dapaf-1, Rab GTPase binding, HHT1, Controlled, delilah, Sinnesorgan, dark/dapaf-1/hac-1, Controlling, Edg, taxis in response to light, axis, CG9252, dApaf-1, 2900070H08Rik, DmelCG2706, CG3025, DXS648, CG5441, apaf1, drep, ARF binding, CD258, Tip48/Reptin, arp1, presence., AI875693, sensory system organ, count in organism, APAF1, Rab escort protein activity, l(2)k02514, DmCycE, Hac-1, IGFBP-9, Public, Systems, Long Term Effects, Rept, CyeE, Dark, dRep, Ran GTPase binding, sensor, Dark/Apaf-I, Data Base, DmelCG6174, Radiations, dReptin, Arp87c, l(3)06945, l(2)k02602, HVEM-L, ARP1, prophylaxis, sensory organ system organ, increased number, l(2)35Dd, Photoradiation, attractant, Dark/Dapaf-1/HAC1, Photokineses, Rho GTPase binding, dApaf-1/DARK/HAC-1, LTg, Longterm Effects, Arp87C, D-CycE, present in greater numbers in organism, Photoradiations, Rac GTPase binding, clear, Dei, control, DEL, Arp-1, IOR, AA960152, EG:95B7.8, 2600013D04Rik, ORW1, CG3938, dAPAF-1, SCNVAL, Choice, Adapted, Programming Parameter, determination, Halobacterium salinarium, phototactic behavior, Flavobacterium (subgen. Halobacterium) salinarium, sensitive, Population Parameter, chemical analysis, Input Parameter, Data Change Date, Halobacterium cutirubrum, Mutant, Pseudomonas salinaria, sensitivity, Halobacter salinaria, Chose, Bacterium halobium, Adapt, Modification, Modified, Argument, taxis in response to light., Serratia salinaria, Selection, PARM, Halobacterium halobium, Chosen, Specificity, Photokineses, parameter, Changed, Photokinesis, Picked, Elected, Selected, allergic reaction, Modified-release Mechanism of Action, Serratia cutirubrum, Pick, Flavobacterium (subgen. Halobacterium) halobium, Specificity and Sensitivity, Halobacterium piscisalsi, Change, Election, Population Measure, Sensitivity, assay, Choose, phototactic behaviour, Select, Parameter, Parameter Value, Bacillus halobius ruberfalseNutsch2005_phototaxis_noncyc_repellent_dark A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control, Nutsch et al, Biophys. J. 2005 ( 16192281 ) and del Rosario et al, IET Syst. Biol. 2007 ( 17708428 ). This is the non-cyclic model for spontaneous simulations used in creating Figure 5C of del Rosario 2007. The value plotted in the figure is ks*A_43(t)/max(ks*A_43(t)), where ks is a model parameter. In the figure, the asymmetric model with 10% and 50% increase in parameter R_cw are compared with data for spontaneous, repellent and attractant stimuli. There are 5 SBML models provided: spontaneous simulations (all light parameters Iuv, Ibl and Ior are zero) repellent dark (sensor via SRII but with Ibl = 0) repellent light (sensor via SRII) attractant dark (sensor via SRI but with Iuv=Ior=0) attractant light (sensor via SRI) The 5 SBML files are "symmetric" models since the parameters in the clockwise and counter-clockwise directions are equal. For the asymmetric simulations in Figure 5c, parameter R_cw must be increased 10% and 50%. We provide the following Matlab code to plot figure 5c using the Systems Biology Toolbox: ---- begining of Matlab code myodeoptions = odeset('AbsTol', 1e-10, 'RelTol', 1e-8); dark1 = linspace(0, 2, 1000); lighton = linspace(2, 2+0.02, 100); dark2 = linspace(2+0.02, 60, 1000); %for spontaneous, no need to separate since all dark tspan = [dark1,lighton(2:end),dark2(2:end)]; sbmodspont = SBmodel('Nutsch2005_phototaxis_noncyc_spont.xml'); sbmodrepdark = SBmodel('Nutsch2005_phototaxis_noncyc_rep_dark.xml'); sbmodreplight = SBmodel('Nutsch2005_phototaxis_noncyc_rep_light.xml'); sbmodattdark = SBmodel('Nutsch2005_phototaxis_noncyc_att_dark.xml'); sbmodattlight = SBmodel('Nutsch2005_phototaxis_noncyc_att_light.xml'); R_cw_nominal = SBparameters(sbmodspont, 'R_cw'); R_cw_10inc = R_cw_nominal + 0.1*R_cw_nominal; R_cw_50inc = R_cw_nominal + 0.5*R_cw_nominal; sbmodspont10 = SBparameters(sbmodspont, 'R_cw', R_cw_10inc); sbmodspont50 = SBparameters(sbmodspont, 'R_cw', R_cw_50inc); clear sbmodspont sbmodrepdark10 = SBparameters(sbmodrepdark, 'R_cw', R_cw_10inc); sbmodreplight10 = SBparameters(sbmodreplight, 'R_cw', R_cw_10inc); sbmodrepdark50 = SBparameters(sbmodrepdark, 'R_cw', R_cw_50inc); sbmodreplight50 = SBparameters(sbmodreplight, 'R_cw', R_cw_50inc); clear sbmodrepdark sbmodreplight sbmodattdark10 = SBparameters(sbmodattdark, 'R_cw', R_cw_10inc); sbmodattlight10 = SBparameters(sbmodattlight, 'R_cw', R_cw_10inc); sbmodattdark50 = SBparameters(sbmodattdark, 'R_cw', R_cw_50inc); sbmodattlight50 = SBparameters(sbmodattlight, 'R_cw', R_cw_50inc); clear sbmodattdark sbmodattlight %Asymmetric Spontaneous Simulations, 10% increase in parameter R_cw sboutput_spont_Rcw10 = SBsimulate(sbmodspont10, 'ode15s', tspan, [], myodeoptions); %Asymmetric Spontaneous Simulations, 50% increase in parameter R_cw sboutput_spont_Rcw50 = SBsimulate(sbmodspont50, 'ode15s', tspan, [], myodeoptions); %Asymmetric Repellent Simulations, 10% increase in parameter R_cw sboutput_rep_dark1_Rcw10 = SBsimulate(sbmodrepdark10, 'ode15s', dark1, [], myodeoptions); initcondafterdark1 = sboutput_rep_dark1_Rcw10.statevalues(end,:); sboutput_rep_light_Rcw10 = SBsimulate(sbmodreplight10, 'ode15s', lighton, initcondafterdark1, myodeoptions); initcondafterlight = sboutput_rep_light_Rcw10.statevalues(end,:); sboutput_rep_dark2_Rcw10 = SBsimulate(sbmodrepdark10, 'ode15s', dark2, initcondafterlight, myodeoptions); %Asymmetric Repellent Simulations, 50% increase in parmaeter R_cw sboutput_rep_dark1_Rcw50 = SBsimulate(sbmodrepdark50, 'ode15s', dark1, [], myodeoptions); initcondafterdark1 = sboutput_rep_dark1_Rcw50.statevalues(end,:); sboutput_rep_light_Rcw50 = SBsimulate(sbmodreplight50, 'ode15s', lighton, initcondafterdark1, myodeoptions); initcondafterlight = sboutput_rep_light_Rcw50.statevalues(end,:); sboutput_rep_dark2_Rcw50 = SBsimulate(sbmodrepdark50, 'ode15s', dark2, initcondafterlight, myodeoptions); %Asymmetric Attractant Simulations, 10% increase in parameter R_cw sboutput_att_dark1_Rcw10 = SBsimulate(sbmodattdark10, 'ode15s', dark1, [], myodeoptions); initcondafterdark1 = sboutput_att_dark1_Rcw10.statevalues(end,:); sboutput_att_light_Rcw10 = SBsimulate(sbmodattlight10, 'ode15s', lighton, initcondafterdark1, myodeoptions); initcondafterlight = sboutput_att_light_Rcw10.statevalues(end,:); sboutput_att_dark2_Rcw10 = SBsimulate(sbmodattdark10, 'ode15s', dark2, initcondafterlight, myodeoptions); %Asymmetric Attractant Simulations, 50% increase in parameter R_cw sboutput_att_dark1_Rcw50 = SBsimulate(sbmodattdark50, 'ode15s', dark1, [], myodeoptions); initcondafterdark1 = sboutput_att_dark1_Rcw50.statevalues(end,:); sboutput_att_light_Rcw50 = SBsimulate(sbmodattlight50, 'ode15s', lighton, initcondafterdark1, myodeoptions); initcondafterlight = sboutput_att_light_Rcw50.statevalues(end,:); sboutput_att_dark2_Rcw50 = SBsimulate(sbmodattdark50, 'ode15s', dark2, initcondafterlight, myodeoptions); A44cwindex = stateindexSB(sbmodspont10, 'A_cw43'); A44ccwindex = stateindexSB(sbmodspont10, 'A_ccw43'); ks_cw = SBparameters(sbmodspont10, 'ks_cw'); ks_cc = SBparameters(sbmodspont10, 'ks_cc'); yfig5cspontRcw10 = (sboutput_spont_Rcw10.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw10.statevalues(:, A44ccwindex)*ks_cc) / ... max(sboutput_spont_Rcw10.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw10.statevalues(:, A44ccwindex)*ks_cc); yfig5cspontRcw50 = (sboutput_spont_Rcw50.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw50.statevalues(:, A44ccwindex)*ks_cc) / ... max(sboutput_spont_Rcw50.statevalues(:, A44cwindex)*ks_cw + sboutput_spont_Rcw50.statevalues(:, A44ccwindex)*ks_cc); A44cwindex = stateindexSB(sbmodrepdark10, 'A_cw43'); A44ccwindex = stateindexSB(sbmodrepdark10, 'A_ccw43'); ks_cw = SBparameters(sbmodrepdark10, 'ks_cw'); ks_cc = SBparameters(sbmodrepdark10, 'ks_cc'); tfig5crepRcw10 = [sboutput_rep_dark1_Rcw10.time(:)', sboutput_rep_light_Rcw10.time(:)', sboutput_rep_dark2_Rcw10.time(:)']; A44cwrepRcw10 = [sboutput_rep_dark1_Rcw10.statevalues(:, A44cwindex); sboutput_rep_light_Rcw10.statevalues(:, A44cwindex); sboutput_rep_dark2_Rcw10.statevalues(:, A44cwindex)]; A44ccwrepRcw10 = [sboutput_rep_dark1_Rcw10.statevalues(:, A44ccwindex); sboutput_rep_light_Rcw10.statevalues(:, A44ccwindex); sboutput_rep_dark2_Rcw10.statevalues(:, A44ccwindex)]; yfig5crepRcw10 = (A44cwrepRcw10*ks_cw + A44ccwrepRcw10*ks_cc) / ... max(A44cwrepRcw10*ks_cw + A44ccwrepRcw10*ks_cc); tfig5crepRcw50 = [sboutput_rep_dark1_Rcw50.time(:)', sboutput_rep_light_Rcw50.time(:)', sboutput_rep_dark2_Rcw50.time(:)']; A44cwrepRcw50 = [sboutput_rep_dark1_Rcw50.statevalues(:, A44cwindex); sboutput_rep_light_Rcw50.statevalues(:, A44cwindex); sboutput_rep_dark2_Rcw50.statevalues(:, A44cwindex)]; A44ccwrepRcw50 = [sboutput_rep_dark1_Rcw50.statevalues(:, A44ccwindex); sboutput_rep_light_Rcw50.statevalues(:, A44ccwindex); sboutput_rep_dark2_Rcw50.statevalues(:, A44ccwindex)]; yfig5crepRcw50 = (A44cwrepRcw50*ks_cw + A44ccwrepRcw50*ks_cc) / ... max(A44cwrepRcw50*ks_cw + A44ccwrepRcw50*ks_cc); A44cwindex = stateindexSB(sbmodattdark10, 'A_cw43'); A44ccwindex = stateindexSB(sbmodattdark10, 'A_ccw43'); ks_cw = SBparameters(sbmodattdark10, 'ks_cw'); ks_cc = SBparameters(sbmodattdark10, 'ks_cc'); tfig5cattRcw10 = [sboutput_att_dark1_Rcw10.time(:)', sboutput_att_light_Rcw10.time(:)', sboutput_att_dark2_Rcw10.time(:)']; A44cwattRcw10 = [sboutput_att_dark1_Rcw10.statevalues(:, A44cwindex); sboutput_att_light_Rcw10.statevalues(:, A44cwindex); sboutput_att_dark2_Rcw10.statevalues(:, A44cwindex)]; A44ccwattRcw10 = [sboutput_att_dark1_Rcw10.statevalues(:, A44ccwindex); sboutput_att_light_Rcw10.statevalues(:, A44ccwindex); sboutput_att_dark2_Rcw10.statevalues(:, A44ccwindex)]; yfig5cattRcw10 = (A44cwattRcw10*ks_cw + A44ccwattRcw10*ks_cc) / ... max(A44cwattRcw10*ks_cw + A44ccwattRcw10*ks_cc); tfig5cattRcw50 = [sboutput_att_dark1_Rcw50.time(:)', sboutput_att_light_Rcw50.time(:)', sboutput_att_dark2_Rcw50.time(:)']; A44cwattRcw50 = [sboutput_att_dark1_Rcw50.statevalues(:, A44cwindex); sboutput_att_light_Rcw50.statevalues(:, A44cwindex); sboutput_att_dark2_Rcw50.statevalues(:, A44cwindex)]; A44ccwattRcw50 = [sboutput_att_dark1_Rcw50.statevalues(:, A44ccwindex); sboutput_att_light_Rcw50.statevalues(:, A44ccwindex); sboutput_att_dark2_Rcw50.statevalues(:, A44ccwindex)]; yfig5cattRcw50 = (A44cwattRcw50*ks_cw + A44ccwattRcw50*ks_cc) / ... max(A44cwattRcw50*ks_cw + A44ccwattRcw50*ks_cc); figure plot(tfig5crepRcw10, yfig5crepRcw10, 'y', 'linewidth', 2) hold on plot(tfig5crepRcw50, yfig5crepRcw50, 'k') legend('R_{cw} increased 10%', 'R_{cw} increased 50%') plot(sboutput_spont_Rcw10.time, yfig5cspontRcw10, 'y', 'linewidth', 2) plot(sboutput_spont_Rcw50.time, yfig5cspontRcw50, 'k') plot(tfig5cattRcw10, yfig5cattRcw10, 'y', 'linewidth', 2) plot(tfig5cattRcw50, yfig5cattRcw50, 'k') grid on myaxis = axis; axis([0 60 0 1.2]) text(1, 1.1, 'repellent'); text(10, 1.1, 'spontaneous'); text(25, 1.1, 'attractant') xlabel('time, s'); ylabel('reversals per time interval (1/s)') ---- end of Matlab code This model originates from BioModels Database: A Database of Annotated Published Models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. 2012-01-202005-01-012008-03-17MODEL040395474617708428MODEL0403954746GO:00423312242