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

M

m - Variable in class org.simBio.bio.faber_rudy_2000.current.INa

m - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_Na

gate variable (dimensionless)

m - Variable in class org.simBio.bio.noble_et_al_1998.Model

m - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.INa

main(String[]) - Static method in class org.simBio.Composer

最初の引数にmodelの基礎となるxmlを指定します。 2番目の引数に結果のmodel xmlの名前を指定しても良いです。 指定しない場合、composed.xmlが作成されます。 以下のように記述すると、external.xml及びpage.xmlの内容に置き換えます。 以下のように記述すると、2から10まで9個複製をし、 xpathで指定されているnodeの値に含まれる #numberをnumberに、#previousをnumber-1の値に変更します。

main(String[]) - Static method in class org.simBio.Entry

TODO parse Options.

main(String[]) - Static method in class org.simBio.JSEntry

main(String[]) - Static method in class org.simBio.ResultGenerator

main(String[]) - Static method in class org.simBio.Run

Main entry.

main(String[]) - Static method in class org.simBio.RunGUI

Create GUI

main(String[]) - Static method in class org.simBio.sim.js.Retriever

main(String[]) - Static method in class org.simBio.sim.js.Stop

TODO add feature to list up active servers and workers.

main(String[]) - Static method in class org.simBio.sim.js.Worker

main(String[]) - Static method in class org.simBio.sim.ps.serialize.TocReader

main(String[]) - Static method in class org.simBio.tools.remote.CommandServer

main(String[]) - Static method in class org.simBio.tools.remote.RemoteGui

main(String[]) - Static method in class org.simBio.XmlGenerator

Main_epsilon - Variable in class org.simBio.bio.cor.Vanderpol_model_1928

Main_epsilon (dimensionless).

Main_x - Variable in class org.simBio.bio.cor.Vanderpol_model_1928

Main_x (dimensionless).

Main_y - Variable in class org.simBio.bio.cor.Vanderpol_model_1928

Main_y (dimensionless).

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.ALaCarte

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.CsvMaker

Label line

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.keep.TimeSeriesKeeper

prepare XYSeries for each target.

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.result.AbstractAppender

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.result.ALaCarte

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.Siblings

MakeLabelLine() - Method in class org.simBio.sim.analyzer.csv.Total

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.ALaCarte

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.CsvMaker

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.keep.TimeSeriesKeeper

set target value at the XYSeries.

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.result.AbstractAppender

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.result.ALaCarte

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.Siblings

MakeValueLine() - Method in class org.simBio.sim.analyzer.csv.Total

mark(int) - Method in class org.simBio.sim.dm.util.StringInputStream

markSupported() - Method in class org.simBio.sim.dm.util.StringInputStream

MassConservation - Class in org.simBio.bio.matsuoka_et_al_2004.function

calculation of molecular concentration conformed to mass conservation law

MassConservation() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation

MassConservation2 - Class in org.simBio.bio.matsuoka_et_al_2004.function

calculation of molecular concentration conformed to mass conservation law

MassConservation2() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation2

MathFunction - Class in org.simBio.util.numerical

This abstract class represents a mathematical function on a simBio model tree.

MathFunction() - Constructor for class org.simBio.util.numerical.MathFunction

MathMultivariableFunction - Class in org.simBio.util.numerical

This abstract class represents a mathematical function on a simBio model tree (light-weight version).

MathMultivariableFunction() - Constructor for class org.simBio.util.numerical.MathMultivariableFunction

MathUnivariableFunction - Class in org.simBio.util.numerical

This abstract class represents a mathematical function on a simBio model tree (light-weight version).

MathUnivariableFunction() - Constructor for class org.simBio.util.numerical.MathUnivariableFunction

max - Variable in class org.simBio.bio.himeno_et_al_2008.ICaL

max - Variable in class org.simBio.bio.himeno_et_al_2008.Ist

PKA phosphorylate

MAX - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.ICaL

max - Variable in class org.simBio.bio.takeuchi_et_al_2006.function.Ouabain

maximum amplitude [A/F]

max - Variable in class org.simBio.sim.analyzer.graph.Axis

max - Variable in class org.simBio.sim.analyzer.graph.simple.Axis

max - Variable in class org.simBio.sim.analyzer.graph.simple.RateGraph_KA

maxFactor - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.IVRCC

factor to define maximum VRCC activation by swelling

maxFactor - Variable in class org.simBio.bio.terashima_et_al_2006.function.AmplitudeNaK

factor to define maximum INaK activation by swelling

maximum - Variable in class org.simBio.sim.analyzer.measure.Amplitude

maximum value of the target

maximum - Variable in class org.simBio.sim.analyzer.measure.AmplitudeInCycle

maximum value of the target

maximum - Variable in class org.simBio.sim.analyzer.measure.Limitter

上限

maximums - Static variable in class org.simBio.sim.ps.view.PlotContour

maximums for z-axis of each evaluation

maxProducingRate - Variable in class org.simBio.bio.matsuoka_et_al_2003.complex.ATPsynthesis

max rate of ATP production (/msec).

maxTime - Variable in class org.simBio.sim.analyzer.graph.AbstractGraph

maximum time until now

MDP - Variable in class org.simBio.sim.analyzer.measure.APDforSA2

最大分極電位 (mV)

measure(double) - Method in class org.simBio.sim.analyzer.csv.keep.TimeSeriesKeeper

measure(double) - Method in class org.simBio.sim.analyzer.graph.simple.RelationGraph_LP

plot targets.

measure(double) - Method in class org.simBio.sim.analyzer.measure.AbstractMeasure

measure(double) - Method in class org.simBio.sim.analyzer.measure.Amplitude

keep the maximum and the minimum value of the target.

measure(double) - Method in class org.simBio.sim.analyzer.measure.AmplitudeInCycle

keep the maximum and the minimum value of the target.

measure(double) - Method in class org.simBio.sim.analyzer.measure.APDforSA

Vmがthresholdを超えている時間を計測する。

measure(double) - Method in class org.simBio.sim.analyzer.measure.APDforSA2

Vmがthresholdを超えている時間を計測する。 一つ前のAPからthresholdを求める。

measure(double) - Method in class org.simBio.sim.analyzer.measure.HR

総電流が負から正に変化した時間を計測する。 前回との差を取ってAP間隔を計測する。 1 minをAP間隔で除する。

measure(double) - Method in class org.simBio.sim.analyzer.measure.LeadPotential

measure(double) - Method in class org.simBio.sim.analyzer.measure.Limitter

measure(double) - Method in class org.simBio.sim.analyzer.measure.PeakDetect

measure(double) - Method in class org.simBio.sim.analyzer.measure.Sum

measure(double) - Method in class org.simBio.sim.analyzer.measure.VmaxTime

Membrane - Class in org.simBio.bio.hodgkin_huxley_1952

Membrane.

Membrane() - Constructor for class org.simBio.bio.hodgkin_huxley_1952.Membrane

membrane_Cm - Variable in class org.simBio.bio.cor.Hodgkin_huxley_squid_axon_1952_modified

membrane_Cm (microF_per_cm2).

membrane_E_R - Variable in class org.simBio.bio.cor.Hodgkin_huxley_squid_axon_1952_modified

membrane_E_R (millivolt).

membrane_V - Variable in class org.simBio.bio.cor.Hodgkin_huxley_squid_axon_1952_modified

membrane_V (millivolt).

MembranePotential - Class in org.simBio.bio.matsuoka_et_al_2004.function

membrane potential on mitochondrial inner membrane.

MembranePotential() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.MembranePotential

MembraneTransporter - Class in org.simBio.bio.matsuoka_et_al_2003.current

Abstract class of membrane transporters.

MembraneTransporter() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.current.MembraneTransporter

MembraneTransporter - Class in org.simBio.bio.terashima_et_al_2006.current

abstract class of membrane transporters.

MembraneTransporter() - Constructor for class org.simBio.bio.terashima_et_al_2006.current.MembraneTransporter

metal - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.MetalFreeConcentration

metal ion concentration

MetalFreeConcentration - Class in org.simBio.bio.matsuoka_et_al_2004.function

free concentration of metal affinity molecule

MetalFreeConcentration() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.MetalFreeConcentration

Mg - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.IK1

the concentration of Mg2+ (mM)

min - Variable in class org.simBio.sim.analyzer.graph.Axis

min - Variable in class org.simBio.sim.analyzer.graph.simple.Axis

min - Variable in class org.simBio.sim.analyzer.graph.simple.RateGraph_KA

minDt - Variable in class org.simBio.core.VariableList

minimum dt

minfi - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.INa

minimum - Variable in class org.simBio.sim.analyzer.measure.Amplitude

minimum value of the target

minimum - Variable in class org.simBio.sim.analyzer.measure.AmplitudeInCycle

minimum value of the target

minimum - Variable in class org.simBio.sim.analyzer.measure.Limitter

下限

minimums - Static variable in class org.simBio.sim.ps.view.PlotContour

minimums for z-axis of each evaluation

mode - Variable in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

MODE_AUTOSCALE - Variable in class org.simBio.sim.analyzer.graph.Axis

Action mode: autoscale mode

MODE_AUTOSCROLL - Variable in class org.simBio.sim.analyzer.graph.Axis

Action mode: autoscroll mode

MODE_FIXED - Variable in class org.simBio.sim.analyzer.graph.Axis

Action mode: fixed mode

MODE_LOAD - Static variable in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

MODE_OPERATED - Static variable in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

MODE_OPERATING - Static variable in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

MODE_WAIT - Static variable in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

Model - Class in org.simBio.bio.negroni_lascano_1996.exp

Cardiac Muscle Model by Negroni and Lascano.

Model() - Constructor for class org.simBio.bio.negroni_lascano_1996.exp.Model

Model - Class in org.simBio.bio.noble_et_al_1998

Noble98 Guinea-Pig Ventricular Cell Model by courtesy of Penny Noble.

Model() - Constructor for class org.simBio.bio.noble_et_al_1998.Model

modelBufferClear - Variable in class org.simBio.sim.gui.GUI

計算開始時に、Viewer の再計算バッファをクリアするためのフラグ

modeLoading() - Method in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

動作モードを読込中にする。

modeOperated() - Method in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

動作モードを演算後にする。

modeOperating() - Method in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

動作モードを演算中にする。

modeWait() - Method in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

動作モードを入力待ちにする。

MonteCarlo - Class in org.simBio.bio.sarai_noma_2004.fourState

MonteCarlo() - Constructor for class org.simBio.bio.sarai_noma_2004.fourState.MonteCarlo

mouseDragged(MouseEvent) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDMouseMotionListener

mousePressed(MouseEvent) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDMouseMotionListener

mouseReleased(MouseEvent) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDMouseMotionListener

MSG_ERROR - Static variable in class org.simBio.tools.remote.RemoteConstant

汎用メッセージ value "error"

MSG_FAIL - Static variable in class org.simBio.tools.remote.RemoteConstant

汎用メッセージ value "fail"

MSG_SUCCESS - Static variable in class org.simBio.tools.remote.RemoteConstant

汎用メッセージ value "success"

mtau - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.INa

MultiStateModel - Class in org.simBio.bio.oka_et_al_2006.function.kinetics

Ligand-operated multi transition model.

MultiStateModel() - Constructor for class org.simBio.bio.oka_et_al_2006.function.kinetics.MultiStateModel

myu - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.GradientP

u value

myu - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.RedoxPotentialCyta

u value

myu - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexIII

u value

myu - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.OxidativePhosphorylation

u value

myu - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT

u value (=0.861)

myu - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.PhosphateCarrier

u value (=0.861)