A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class org.simBio.bio.faber_rudy_2000.function.Diffusion
 
A - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.CrossBridgeForce
force of cross bridge and parallel elastic comp.
a - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.ICaPump
 
A - Variable in class org.simBio.bio.kuzumoto_et_al_2007.function.KoDependency_IK1
 
A - Variable in class org.simBio.bio.negroni_lascano_1996.CrossBridge
 
A - Variable in class org.simBio.bio.negroni_lascano_1996.exp.Model
 
a - Variable in class org.simBio.bio.oka_et_al_2006.function.kinetics.MultiStateModel
forward rate constant
a2 - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexIV
cytochrome a2+ (reduced) concentration
A2RCI - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.PKA
A2RCI concentration (mM)
A2RI - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.PKA
A2RI concentration (mM)
AbstractAfterProcess - Class in org.simBio.tools.remote.process
 
AbstractAfterProcess() - Constructor for class org.simBio.tools.remote.process.AbstractAfterProcess
 
AbstractAfterProcess(PrintWriter) - Constructor for class org.simBio.tools.remote.process.AbstractAfterProcess
 
AbstractAppender - Class in org.simBio.sim.analyzer.csv.result
append the parameters to CSV file at the end of calculation.
AbstractAppender() - Constructor for class org.simBio.sim.analyzer.csv.result.AbstractAppender
 
AbstractGraph - Class in org.simBio.sim.analyzer.graph
Provides a Graph framework. Constructs a framework in this class so that the Graph class which inherits from it can be implemented simply, without providing redrawing functions etc.
AbstractGraph() - Constructor for class org.simBio.sim.analyzer.graph.AbstractGraph
 
AbstractMeasure - Class in org.simBio.sim.analyzer.measure
Measuring.
AbstractMeasure() - Constructor for class org.simBio.sim.analyzer.measure.AbstractMeasure
 
AbstractPlot - Class in org.simBio.sim.analyzer.graph.plot
グラフ、描画対象(画面/プリンタ)毎の描画処理を行うための基底クラス.
AbstractPlot(AbstractGraph) - Constructor for class org.simBio.sim.analyzer.graph.plot.AbstractPlot
 
AbstractPlot - Class in org.simBio.sim.ps.view
jFreeChartのグラフで表示する。
AbstractPlot(String) - Constructor for class org.simBio.sim.ps.view.AbstractPlot
 
AC - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.CAMP
Adenylate cyclase concentration (mM)
aCa - Variable in class org.simBio.bio.takeuchi_et_al_2006.function.Electroneutrality
amount of intracellular Ca2+ [pEq]
accept(Visitor) - Method in class org.simBio.core.Component
use visitor pattern
visitorを受け容れ、訪問する。
accept(Visitor) - Method in class org.simBio.core.Composite
use visitor pattern
Visitorを受け容れ、訪問する。
ACh - Variable in class org.simBio.bio.himeno_et_al_2008.IKACh
 
ACh - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKACh
 
Acidity - Class in org.simBio.bio.matsuoka_et_al_2004.function
calculation of pH (acidity) of the optional solution.
Acidity() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.Acidity
 
aCl - Variable in class org.simBio.bio.takeuchi_et_al_2006.function.Electroneutrality
amount of intracellular Cl- [pEq]
Acoef - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction
coefficient of rate constant alpha (ms-1)
actionPerformed(ActionEvent) - Method in class org.simBio.tools.remote.RemoteGui
 
activation - Variable in class org.simBio.bio.himeno_et_al_2008.Ist
gate variable
activation - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.ICaT
open probability of activation gate
activation - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.Ist
gate variable
activation - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.ICaT
open probability of activation gate
activation - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Ist
 
ActivityFactor - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.Acidity
 
ACtot - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.CAMP
total adenylate cyclase concentration (mM)
add(Object) - Method in class org.simBio.core.ReactorList
IResetBeforeCalcをimplimentsしているクラスはリセットする必要があるReactorとして登録する。
add(Component, int) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar
 
add(Component) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar
 
addCalculationObserver(CalculationObserver) - Method in class org.simBio.core.Conductor
計算を開始・終了した時に、通知が行われる監視オブジェクトを追加します。
addCellEditorListener(CellEditorListener) - Method in class org.simBio.sim.gui.CheckedJTree.CheckedJTreeCellRenderer
 
addDoubles(double[]) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer
double 配列を書き出す.
addDydt(double) - Method in class org.simBio.core.Component
always throws UnsupportedOperationException, need to implement 'Node'
addDydt(double) - Method in class org.simBio.core.integrator.Concentration
 
addDydt(double) - Method in class org.simBio.core.integrator.Euler
 
addDydt(double) - Method in class org.simBio.core.integrator.RungeKutta
 
addDydt(double) - Method in interface org.simBio.core.Node
add parameter to the dydt
実数を受け取りdydtに足し合わせておく。
addEval(String, double) - Method in interface org.simBio.sim.ps.IReciever
Add evaluation name and value.
addKey(String, double) - Method in interface org.simBio.sim.ps.IReciever
Add changing parameter's name and value.
addLongs(long[]) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer
long 配列を書き出す.
addParamSpaceObservers(IParamSpaceObserver) - Method in class org.simBio.sim.ps.ParameterSpace
 
addValue(double) - Method in class org.simBio.core.Component
always throws UnsupportedOperationException, need to implement 'Node'
addValue(double) - Method in class org.simBio.core.integrator.Concentration
 
addValue(double) - Method in class org.simBio.core.integrator.Euler
log warn, this Method should not be used.
addValue(double) - Method in class org.simBio.core.integrator.RungeKutta
log warn, this Method should not be used.
addValue(double) - Method in interface org.simBio.core.Node
add value to the current value
実数を受け取り現在値に足し合わせる。
addValue(double) - Method in class org.simBio.core.Parameter
add value to the current value
実数を受け取り現在値に足し合わせる。
addValue(double, double[]) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues
現在時刻の計算結果を追加する.
AdenosineTotal - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationAMP
 
adjustDt() - Method in class org.simBio.core.VariableList
restrict maximum dy/Y and adjust time step
全てのVariableの最大のdy/yが閾値に合うように、time stepを決定する。 2004/11/12 dtが残り計算時間をオーバーしないように制限。 TODO 時々dt=0となってしまうことがある。
adjustDyOverY - Variable in class org.simBio.core.Conductor
for variable time step, empirical method
ADP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponinmit
 
ADP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.ICaPump
 
ADP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK
 
ADP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.IPMCA
 
ADP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.PLB
ADP concentration (mM)
ADP - Variable in class org.simBio.bio.matsuoka_et_al_2004.current.carrier.ICaPump
 
ADP - Variable in class org.simBio.bio.matsuoka_et_al_2004.current.carrier.INaK
 
ADP - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.buffer.Ca.TroponinNL_RK
 
ADP - Variable in class org.simBio.bio.sarai_et_al_2006.current.carrier.IPMCA
intracellular ADP concentration (mM)
ADPfcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
Mg free ADP concentration in cytosol (mM)
ADPfmito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
Mg free ADP concentration in mitohocndria (mM)
ADPfree - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
free ADP concentration in cytosol
ADPmg - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
Mg binding ADP concentration in cytosol
ADPtcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationAMP
 
ADPtcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
total ADP concentration in cytosol
ADPtcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
total ADP concentration in cytosol (mM)
ADPtmit - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
total ADP concentration in mitochondria
ADPtmito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase
total ADP concentration in mitochondrial matrix
ADPtotal - Variable in class org.simBio.bio.kuzumoto_et_al_2007.function.ConcentrationAMP
 
ADPtotal - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
total ADP concentration in cytosol
ADPtotal - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.CK
total ADP concentration in cytosol
AK - Class in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme
Adenylate Kinase (AK) System
AK() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
 
aK - Variable in class org.simBio.bio.takeuchi_et_al_2006.function.Electroneutrality
amount of intracellular K+ [pEq]
aLA - Variable in class org.simBio.bio.takeuchi_et_al_2006.function.Electroneutrality
amount of intracellular LA [pEq]
ALaCarte - Class in org.simBio.sim.analyzer.csv
Writes a numerical value of selected nodes to csv file.
ALaCarte() - Constructor for class org.simBio.sim.analyzer.csv.ALaCarte
 
ALaCarte - Class in org.simBio.sim.analyzer.csv.result
writes only chosen parameters, variables and nodes to csv file One has to write targets of desirable parameters in the xml file
特定のパラメータをCsvに書き込むクラス。 "target " + numberとして書き出したいNodeを設定して下さい。
ALaCarte() - Constructor for class org.simBio.sim.analyzer.csv.result.ALaCarte
 
alfa - Variable in class org.simBio.bio.function.Analytic2state
 
alfa - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IK1
rate constant
alfa - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.carrier.INaCa
 
alfa - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IK1
rate constant
alfa1 - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
alfa2 - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
alfa3 - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
alfa4 - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
alfa5 - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
This value is 9000 in Negroni and Lascano, 1996.
alpha - Variable in class org.simBio.bio.kurata_et_al_2005.molecule.CaBuffer_RK
association constant (/ms)
alpha - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.ODE
association constant (/ms)
alpha - Variable in class org.simBio.bio.oka_et_al_2006.function.kinetics.TwoStateModel
forward rate constant
AMP - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
AMP concentration in cytosol
AMP - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
AMP concentration in cytosol
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexI
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexIII
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexIV
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.SubstrateDehydrogenation
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.PhosphateCarrier
amplifying factor described in Kuzumoto et al, 2007.
Amp - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ProtonLeak
amplifying factor described in Kuzumoto et al, 2007.
amplitude - Variable in class org.simBio.bio.faber_rudy_2000.current.IK1
 
amplitude - Variable in class org.simBio.bio.faber_rudy_2000.function.Stimulus
 
amplitude - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_stim
amplitude of the stimulus current (microA_per_cm2)
amplitude - Variable in class org.simBio.bio.kuratomi_et_al_2003.current.carrier.Carrier
amplitude factor (A/F)
amplitude - Variable in class org.simBio.bio.kuzumoto_et_al_2007.function.KoDependency_IK1
amplitude factor
amplitude - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.Carrier
amplitude factor (A/F)
amplitude - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.pipette.CurrentClamp
amplitude of the stimulus current.
amplitude - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.KoDependency
amplitude factor
amplitude - Variable in class org.simBio.bio.sarai_et_al_2003.Ist
amplitude factor
amplitude - Variable in class org.simBio.bio.sarai_et_al_2006.current.cf.ICaL
amplitude factor
amplitude - Variable in class org.simBio.bio.takeuchi_et_al_2006.current.INaCa
amplitude factor [A/F]
amplitude - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.carrier.INaCa
 
amplitude - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.carrier.INaK
 
amplitude - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.pipette.CurrentClamp
amplitude of the stimulus current.
amplitude - Variable in class org.simBio.bio.terashima_et_al_2006.function.KoDependency
amplitude factor
amplitude - Variable in class org.simBio.bio.terashima_et_al_2006.function.KoDependency2
amplitude
Amplitude - Class in org.simBio.sim.analyzer.measure
get the difference between the maximum and minimum value of the target.
Amplitude() - Constructor for class org.simBio.sim.analyzer.measure.Amplitude
 
amplitude0 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK
control amplitude
amplitude0 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.IPMCA
 
amplitudecAMPf - Variable in class org.simBio.bio.himeno_et_al_2008.Iha
to modulate cAMP effect
AmplitudeInCycle - Class in org.simBio.sim.analyzer.measure
get the difference between the maximum and minimum value of the target in a cycle.
AmplitudeInCycle() - Constructor for class org.simBio.sim.analyzer.measure.AmplitudeInCycle
 
AmplitudeNaK - Class in org.simBio.bio.terashima_et_al_2006.function
Calculate volume-dependency of INaK amplitude.
AmplitudeNaK() - Constructor for class org.simBio.bio.terashima_et_al_2006.function.AmplitudeNaK
 
amplitudeNaK - Variable in class org.simBio.bio.terashima_et_al_2006.function.AmplitudeNaK
factor to define the maximum INaK [pA msec/pF]
amplitudePKAf - Variable in class org.simBio.bio.himeno_et_al_2008.ICaL
to modulate PKA effect
amplitudePKAf - Variable in class org.simBio.bio.himeno_et_al_2008.IKs
to modulate PKA effect
amplitudePKAf - Variable in class org.simBio.bio.himeno_et_al_2008.Ist
to modulate PKA effect
amplitudePKAf - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.ICaPump
to modulate PKA effect
amplitudePKAf - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK
to modulate PKA effect
amplitudePKAf - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.IPMCA
to modulate PKA effect
aNa - Variable in class org.simBio.bio.takeuchi_et_al_2006.function.Electroneutrality
amount of intracellular Na+ [pEq]
Analytic - Class in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca
instantaneous Ca buffer, using analytic equation as for Zeng et al, 1995 J.
Analytic() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.Analytic
 
Analytic2state - Class in org.simBio.bio.function
2 state gateの解析解を求めて現在の解に設定する。 「心臓のフィジオーム」p.
Analytic2state() - Constructor for class org.simBio.bio.function.Analytic2state
 
Analytic_RK - Class in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca
instantaneous Ca buffer using analytic equation as for Zeng et al, 1995.
Analytic_RK() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.Analytic_RK
 
analyze(double) - Method in class org.simBio.core.Analyzer
Please implements this Method to manipulate Nodes.
analyze(double) - Method in class org.simBio.sim.analyzer.csv.CsvMaker
Call MakeValueLine() to write current value.
analyze(double) - Method in class org.simBio.sim.analyzer.csv.result.ALaCarte
 
analyze(double) - Method in class org.simBio.sim.analyzer.graph.AbstractGraph
Default analyze operation. Called by Conductor on the Simulation thread.
analyze(double) - Method in class org.simBio.sim.analyzer.graph.Axis
Do nothing
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.AxisX
reset scaling factor if elapsed time is over the range.
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.AxisXFix
 
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.AxisY
do nothing
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.Graph
plot targets.
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.Graph4State
 
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.RateGraph
 
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.RateGraph_KA
 
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.RelationGraph
plot targets.
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.StepChart
plot targets.
analyze(double) - Method in class org.simBio.sim.analyzer.graph.simple.Viewer
do nothing
analyze(double) - Method in class org.simBio.sim.analyzer.graph.Viewer
Carries out a redrawing operation only when necessary.
analyze(double) - Method in class org.simBio.sim.analyzer.measure.AbstractMeasure
 
analyze(double) - Method in class org.simBio.sim.analyzer.measure.APD
 
analyze(double) - Method in class org.simBio.sim.analyzer.measure.Vmax
 
analyze(double) - Method in class org.simBio.sim.analyzer.StopWatch
 
analyze(double) - Method in class org.simBio.sim.analyzer.VisualizeAnalyzer
 
Analyzer - Class in org.simBio.core
Please inherit this Class to manipulate every Node.
Analyzer() - Constructor for class org.simBio.core.Analyzer
 
analyzeSub(double, double[], IPlot) - Method in class org.simBio.sim.analyzer.graph.AbstractGraph
Analyse operation for giving a description to a subclass.
analyzeSub(double, double[], IPlot) - Method in class org.simBio.sim.analyzer.graph.BasicGraph
Plot targets.
analyzeSub(double, double[], IPlot) - Method in class org.simBio.sim.analyzer.graph.Graph
Plots targets.
analyzeSub(double, double[], IPlot) - Method in class org.simBio.sim.analyzer.graph.RelationGraph
Plot targets.
Anoxia - Class in org.simBio.bio.matsuoka_et_al_2004.exp
Anoxia condition on ventricular cell model was occured to regulate the oxygen concentration.
Anoxia() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.exp.Anoxia
 
ANT - Class in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter
ADP/ATP carrier, ADP/ATP translocase, SLC25A4.
ANT() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
 
APA - Variable in class org.simBio.sim.analyzer.measure.APD
 
APA - Variable in class org.simBio.sim.analyzer.measure.APDforSA2
活動電位の大きさ (mV)
APD - Class in org.simBio.sim.analyzer.measure
Measuring Action Potential Duration.
APD() - Constructor for class org.simBio.sim.analyzer.measure.APD
 
APDforSA - Class in org.simBio.sim.analyzer.measure
ペースメーカモデルの活動電位持続時間を計測する。 閾値はmVで指定する。
APDforSA() - Constructor for class org.simBio.sim.analyzer.measure.APDforSA
 
APDforSA2 - Class in org.simBio.sim.analyzer.measure
ペースメーカモデルの活動電位持続時間を計測する。 閾値はAPAのパーセントで指定する。
APDforSA2() - Constructor for class org.simBio.sim.analyzer.measure.APDforSA2
 
ARCI - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.PKA
ARCI concentration (mM)
arel - Variable in class org.simBio.bio.tenTusscher_et_al_2004.flux.Release
 
ATP - Variable in class org.simBio.bio.himeno_et_al_2008.ICaL
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponin
 
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.ICaPump
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK
concentration of ATP[mM]
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.IPMCA
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.ICaL
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.ICFTR
concentration of intracellular ATP [mM]
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.CAMP
ATP concentration (mM)
ATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.PLB
ATP concentration (mM)
ATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.complex.ATPsynthesis
ATP concentration ([ATP]).
ATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.ICaPump
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK
concentration of ATP[mM]
ATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.ICaL
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
ATP - Variable in class org.simBio.bio.sarai_et_al_2006.current.carrier.IPMCA
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.sarai_et_al_2006.current.cf.ICaL
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.takeuchi_et_al_2006.current.ICaL
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.ICaL
intracellular ATP concentration (mM)
ATP - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.ICFTR
concentration of intracellular ATP [mM]
ATPconsumingRate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.ICaPump
consuming rate of ATP; (mM/min)
ATPconsumingRate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK
rate of ATP consumption
ATPconsumingRate - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
ATPconsumption - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.ICaPump
ATP consumed at the time t (mM)
ATPconsumption - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK
ATP consumption[mM]
ATPconsumption - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL
 
ATPfcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
Mg free ATP concentration in cytosol (mM)
ATPfmito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
Mg free ATP concentration in mitohocndria (mM)
ATPi - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKATP
concentration of intracellular ATP[mM]
ATPi - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKATP
concentration of intracellular ATP[mM]
ATPmg - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
Mg binding ATP concentration in cytosol
ATPonNCXvsPMCA - Class in org.simBio.bio.sarai_et_al_2006.figure
Make Figure 4 in Sarai et al.
ATPonNCXvsPMCA() - Constructor for class org.simBio.bio.sarai_et_al_2006.figure.ATPonNCXvsPMCA
 
ATPsynthase - Class in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain
Mitochondrial F1/F0 ATP Synthase.
ATPsynthase() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase
 
ATPsynthesis - Class in org.simBio.bio.matsuoka_et_al_2003.complex
The lumped model of ATP synthesis.
ATPsynthesis() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.complex.ATPsynthesis
 
ATPtcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationAMP
 
ATPtcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
total ATP concentration in cytosol
ATPtcell - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
total ATP concentration in cytosol (mM)
ATPtmit - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
total ATP concentration in mitochondria
ATPtmito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase
total ATP concentration in mitochondrial matrix
ATPtmito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT
total ATP concentration in mitohocndria (mM)
ATPtotal - Variable in class org.simBio.bio.kuzumoto_et_al_2007.function.ConcentrationAMP
 
ATPtotal - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.AK
total ATP concentration in cytosol
ATPtotal - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme.CK
total ATP concentration in cytosol
attributeDecl(String, String, String, String, String) - Method in class org.simBio.serialize.xml.LogSax2
Logs attribute details of elements when debugging.
AttributeString - Class in org.simBio.sim.analyzer.graph.plot
描画用にテキスト,フォント,色を組にして管理するクラス
AttributeString() - Constructor for class org.simBio.sim.analyzer.graph.plot.AttributeString
 
Average - Class in org.simBio.bio.kuzumoto_et_al_2007.function
 
Average() - Constructor for class org.simBio.bio.kuzumoto_et_al_2007.function.Average
 
Axis - Class in org.simBio.sim.analyzer.graph
Coordinate axis base class
Axis() - Constructor for class org.simBio.sim.analyzer.graph.Axis
 
Axis - Class in org.simBio.sim.analyzer.graph.simple
 
Axis() - Constructor for class org.simBio.sim.analyzer.graph.simple.Axis
 
axisX - Variable in class org.simBio.sim.analyzer.graph.AbstractGraph
coordinate axis object (horizontal direction)
AxisX - Class in org.simBio.sim.analyzer.graph
x axis
AxisX() - Constructor for class org.simBio.sim.analyzer.graph.AxisX
 
AxisX - Class in org.simBio.sim.analyzer.graph.simple
x axis
AxisX() - Constructor for class org.simBio.sim.analyzer.graph.simple.AxisX
 
axisX - Variable in class org.simBio.sim.analyzer.graph.simple.Graph
horizontal axis
AxisXFix - Class in org.simBio.sim.analyzer.graph
x axis (do not scroll) for RelationGraph.
AxisXFix() - Constructor for class org.simBio.sim.analyzer.graph.AxisXFix
 
AxisXFix - Class in org.simBio.sim.analyzer.graph.simple
 
AxisXFix() - Constructor for class org.simBio.sim.analyzer.graph.simple.AxisXFix
 
axisXFix - Variable in class org.simBio.sim.analyzer.graph.simple.RelationGraph
 
axisXFix - Variable in class org.simBio.sim.analyzer.graph.simple.RelationGraph_LP
 
AxisXLog - Class in org.simBio.sim.analyzer.graph
x axis by log scale.
AxisXLog() - Constructor for class org.simBio.sim.analyzer.graph.AxisXLog
 
axisY - Variable in class org.simBio.sim.analyzer.graph.AbstractGraph
coordinate axis object (vertical direction)
AxisY - Class in org.simBio.sim.analyzer.graph
y axis
AxisY() - Constructor for class org.simBio.sim.analyzer.graph.AxisY
 
AxisY - Class in org.simBio.sim.analyzer.graph.simple
y axis
AxisY() - Constructor for class org.simBio.sim.analyzer.graph.simple.AxisY
 
axisY - Variable in class org.simBio.sim.analyzer.graph.simple.Graph
vertical axis
axisY - Variable in class org.simBio.sim.analyzer.graph.simple.RelationGraph
 
axisY - Variable in class org.simBio.sim.analyzer.graph.simple.RelationGraph_LP
 
AxisYLog - Class in org.simBio.sim.analyzer.graph
y axis by log scale.
AxisYLog() - Constructor for class org.simBio.sim.analyzer.graph.AxisYLog
 

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