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

R

R - Variable in class org.simBio.bio.faber_rudy_2000.current.ICaL

R - Variable in class org.simBio.bio.faber_rudy_2000.current.IKs

R - Variable in class org.simBio.bio.faber_rudy_2000.current.INaCa

R - Variable in class org.simBio.bio.faber_rudy_2000.current.INaK

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.ICab

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.IK1

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.IKr

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.IKs

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.INa

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.INab

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.INaCa

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.INaK

R - Variable in class org.simBio.bio.kurata_et_al_2005.current.Ito

R - Variable in class org.simBio.bio.kuratomi_et_al_2003.current.carrier.INaCa

gas constant default value is 8.3143[C*mV/K/mmol]

R - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK

gas constant default value is 8.3143[C*mV/K/mmol]

R - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaCa

gas constant default value is 8.3143[C*mV/K/mmol]

R - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK

gas constant default value is 8.3143[C*mV/K/mmol]

R - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.ConstantField

Gas constant

R - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.ReversalPotential

Gas constant

R - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.Zvalue

R - Variable in class org.simBio.bio.negroni_lascano_1996.exp.Model

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

R - Variable in class org.simBio.bio.takeuchi_et_al_2006.current.INaCa

gas constant default value is 8.3143[C*mV/K/mmol]

R - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.carrier.INaCa

R - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.carrier.INaK

R - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.ICa

r - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito

r - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito_endo

R - Variable in class org.simBio.bio.tenTusscher_et_al_2004.function.ReversalPotential2

r1 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponin

r2 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponin

adjusted by 2.5 * r1

radius - Variable in class org.simBio.bio.faber_rudy_2000.structure.Cell

ramda - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK

relative depth of access channel

ramda - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK

relative depth of access channel

Rate - Class in org.simBio.bio.sarai_et_al_2006.function

Rate.

Rate() - Constructor for class org.simBio.bio.sarai_et_al_2006.function.Rate

RateConstant - Class in org.simBio.bio.matsuoka_et_al_2003.function

function, c1/(c2*exp((x+c3)/c4)+c5*exp((x+c6)/c7))

RateConstant() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.RateConstant

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

Calculate the forward and backward rate constans of two-state model by using time constant, pKd and Hill coefficient

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

RateConstantK - Class in org.simBio.bio.matsuoka_et_al_2003.function

RateConstantK() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.RateConstantK

RateConstantVm - Class in org.simBio.bio.matsuoka_et_al_2003.function

RateConstantVm() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.RateConstantVm

RateGraph - Class in org.simBio.sim.analyzer.graph.simple

sample graph for bio.function

RateGraph() - Constructor for class org.simBio.sim.analyzer.graph.simple.RateGraph

RateGraph_KA - Class in org.simBio.sim.analyzer.graph.simple

sample graph for bio.function

RateGraph_KA() - Constructor for class org.simBio.sim.analyzer.graph.simple.RateGraph_KA

ratio - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK

ratio - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.Volume

ratio

ratio - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.PartialPotential

ratio of partial potential

ratio - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.VolumeRatio

volume ratio

Ratio - Class in org.simBio.bio.sarai_et_al_2006.function

Ratio.

Ratio() - Constructor for class org.simBio.bio.sarai_et_al_2006.function.Ratio

ratio - Variable in class org.simBio.bio.terashima_et_al_2006.function.Volume

ratio

ratio() - Method in class org.simBio.sim.analyzer.StopWatch

rbuffermito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase

buffering capacity for proton in mitochondrial matrix

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

buffering capacity for proton in mitochondrial matrix

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

buffering capacity for proton in mitochondrial matrix

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

buffering capacity for proton in mitochondrial matrix

rbuffermito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ProtonLeak

buffering capacity for proton in mitochondrial matrix

RCI - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.PKA

RCI concentration (mM)

Rcm - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi

volume ratio between cytosol and mitochondrial matrix

Rcm - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase

ratio of cytosol volume and mitochondria volume

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

ratio of cytosol volume and mitochondria volume

Rcm - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.SubstrateDehydrogenation

ratio of cytosol active volume and mitochondria volume

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

ratio of cytosol volume and mitochondria volume

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

ratio of cytosol volume and mitochondria volume

Rcm - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ProtonLeak

ratio of cytosol volume and mitochondria volume

Reactor - Class in org.simBio.core

set of equations.

Reactor() - Constructor for class org.simBio.core.Reactor

ReactorList - Class in org.simBio.core

List of the Reactors

ReactorList() - Constructor for class org.simBio.core.ReactorList

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

list of reactors

read() - Method in interface org.simBio.serialize.Serializer

deserialize.

read() - Method in class org.simBio.serialize.xml.XMLSerializer

Deserialize from xml file.

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

readToolBarConfig(Properties, JFrame, String) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

ツールバーの設定を Properties から復元する。

rebuild() - Method in class org.simBio.sim.analyzer.graph.GraphReplotBuffer

Rebuilds the redrawing buffer. From a TimeSeriesValues object, get the calculation results of the time to be displayed in Graph.AxisX, and rebuild the internal redrawing buffer.

Receipt - Class in org.simBio.sim.js.entry

Receipt

Receipt(String, String) - Constructor for class org.simBio.sim.js.entry.Receipt

Receipt() - Constructor for class org.simBio.sim.js.entry.Receipt

default

rectangleBounds - Variable in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

rectanglePage - Variable in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

rectangleView - Variable in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

rectPrintableArea - Variable in class org.simBio.sim.gui.GUI.JPrintablePanel

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

Calculation of the redox potential.

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

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

Calculation of the redox potential of cytochrome a

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

referenceHeight - Variable in class org.simBio.sim.analyzer.graph.simple.Viewer

referenceHeight - Variable in class org.simBio.sim.analyzer.graph.Viewer

referenceWidth - Variable in class org.simBio.sim.analyzer.graph.simple.Viewer

referenceWidth - Variable in class org.simBio.sim.analyzer.graph.Viewer

register(Map) - Static method in class org.simBio.util.taglets.EnOff

Register this Taglet.

register(Map) - Static method in class org.simBio.util.taglets.EnOn

Register this Taglet.

register(Map) - Static method in class org.simBio.util.taglets.JaOff

Register this Taglet.

register(Map) - Static method in class org.simBio.util.taglets.JaOn

Register this Taglet.

RelationGraph - Class in org.simBio.sim.analyzer.graph

2D graph of relation between two parameters.

RelationGraph() - Constructor for class org.simBio.sim.analyzer.graph.RelationGraph

RelationGraph - Class in org.simBio.sim.analyzer.graph.simple

2D graph of relation between two parameters

RelationGraph() - Constructor for class org.simBio.sim.analyzer.graph.simple.RelationGraph

RelationGraph_LP - Class in org.simBio.sim.analyzer.graph.simple

2D graph of relation between two parameters for org.simBio.sim.analyzer.measure.LeadPotential.

RelationGraph_LP() - Constructor for class org.simBio.sim.analyzer.graph.simple.RelationGraph_LP

relativeP - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.Ito

relative permeability of sodium to potassium

relativePK - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.ILCCa

ratio of K+ conductance to Na+ conductance

relativePK - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Ist

relativePNa - Variable in class org.simBio.bio.himeno_et_al_2008.IKs

the permeability ratio of K⁺ and Na⁺

relativePNa - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.IKs

the permeability ratio of K⁺ and Na⁺

relativePNa - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKs

the permeabilities ratio of K+ and Na+

relativePNa - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Ito

relative

relativePNa - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKs

the permeability ratio of K⁺ and Na⁺

Release - Variable in class org.simBio.bio.kurata_et_al_2005.complex.SR

Release - Class in org.simBio.bio.kurata_et_al_2005.flux

Release() - Constructor for class org.simBio.bio.kurata_et_al_2005.flux.Release

Release - Class in org.simBio.bio.tenTusscher_et_al_2004.flux

The calcium induced calcium release (CICR) current.

Release() - Constructor for class org.simBio.bio.tenTusscher_et_al_2004.flux.Release

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

オープンしているファイルを再読み込みする。

RemoteConstant - Class in org.simBio.tools.remote

simBio RemoteClientパッケージ定数クラス

RemoteConstant() - Constructor for class org.simBio.tools.remote.RemoteConstant

RemoteGui - Class in org.simBio.tools.remote

simBio

remove(int) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

ツールバーのボタンを削除する。
削除しただけでは、画面に残ってしまうので、再配置・再描画も行います。

remove(Component) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

ツールバーのボタンを削除する。

removeCalculationObserver(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削除します。

removeCellEditorListener(CellEditorListener) - Method in class org.simBio.sim.gui.CheckedJTree.CheckedJTreeCellRenderer

repaint() - Method in class org.simBio.sim.analyzer.graph.Viewer

repaint() - Method in class org.simBio.sim.analyzer.VisualizeAnalyzer

再描画パラメータの取り込みと、再描画を行う.

replotBuffer - Variable in class org.simBio.sim.analyzer.graph.Graph

Redrawing buffer

Request - Class in org.simBio.sim.js.entry

Request

Request() - Constructor for class org.simBio.sim.js.entry.Request

Request(String) - Constructor for class org.simBio.sim.js.entry.Request

Request(String, String) - Constructor for class org.simBio.sim.js.entry.Request

Request(String, Integer, String) - Constructor for class org.simBio.sim.js.entry.Request

Request(String, Integer, String, byte[], String, URL[]) - Constructor for class org.simBio.sim.js.entry.Request

rerativePK - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.INa

ratio of K+ conductance to Na+ conductance

rerativePK - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.INa

ratio of K+ conductance to Na+ conductance

reset() - Method in interface org.simBio.sim.analyzer.graph.simple.ICanvas

get graphics and clear.

reset() - Method in class org.simBio.sim.analyzer.graph.simple.Viewer

get graphics and clear.

reset() - Method in class org.simBio.sim.analyzer.StopWatch

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

resetBuffer() - Method in class org.simBio.sim.analyzer.graph.BasicGraph

resetBuffer() - Method in class org.simBio.sim.analyzer.graph.Graph

Resets the screen state.

resetBuffer() - Method in class org.simBio.sim.analyzer.VisualizeAnalyzer

画面状態をリセットする.

resize(IPlot) - Method in class org.simBio.sim.analyzer.graph.AbstractGraph

Recalculates the Graph size, based on the size of the current parent window.

resize(IPlot) - Method in class org.simBio.sim.analyzer.graph.BasicGraph

resize(IPlot) - Method in class org.simBio.sim.analyzer.graph.Graph

Recalculates the Graph size, based on the size of the parent window.

resolveEntity(String, String, String, String) - Method in class org.simBio.serialize.xml.LogSax2

Maps references to external entities into input sources.

resolveEntity(String, String) - Method in class org.simBio.serialize.xml.LogSax2

Calls the EntityResolver2 resolveEntity method.

resting - Variable in class org.simBio.sim.analyzer.measure.APD

Result - Class in org.simBio.sim.js.entry

Result

Result() - Constructor for class org.simBio.sim.js.entry.Result

Result(String) - Constructor for class org.simBio.sim.js.entry.Result

Result(String, byte[], String) - Constructor for class org.simBio.sim.js.entry.Result

Result - Class in org.simBio.sim.ps

一つの結果には、 - パラメータの値 double[] - 評価値 double[] - 時系列データ XYSeriesCollection が含まれる。 TODO beanにする？ commons digesterで読み込む？

Result() - Constructor for class org.simBio.sim.ps.Result

ResultGenerator - Class in org.simBio

Apply different protocols to a model, and change the parameters such as magnitude of the currents.

ResultGenerator() - Constructor for class org.simBio.ResultGenerator

Retriever - Class in org.simBio.sim.js

Workerを生成して、直前にJSEntryから投げられたRequestを全て回収する。 To execute, add VM argument as: -Djava.security.policy=policy.all -Djava.rmi.server.codebase=http://10.238.63.14:8083/simBio_JavaSpaces-1.0.jar but replace the codebase with current values.

Retriever() - Constructor for class org.simBio.sim.js.Retriever

reversalPotential - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.PureKchannel

reversal potential

reversalPotential - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.RateConstantK

ReversalPotential - Class in org.simBio.bio.matsuoka_et_al_2003.function

calculate reversal potential of the specific ion.

ReversalPotential() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.ReversalPotential

reversalPotential - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.PureKchannel

reversal potential

ReversalPotential2 - Class in org.simBio.bio.tenTusscher_et_al_2004.function

calculate reversal potential of the specific Ion.

ReversalPotential2() - Constructor for class org.simBio.bio.tenTusscher_et_al_2004.function.ReversalPotential2

RG - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.BetaAR_Gs

receptor-gs_protein complex concentration

rinfi - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito

rinfi - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito_endo

rNaCa - Variable in class org.simBio.bio.kurata_et_al_2005.current.INaCa

rtau - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito

rtau - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito_endo

run() - Method in class org.simBio.core.Conductor

main entry of this thread.

run() - Method in class org.simBio.JSEntry

Thread that loops, taking & saving results.

Run - Class in org.simBio

Automatically calculates models.

Run() - Constructor for class org.simBio.Run

run() - Method in class org.simBio.sim.js.Taker

run() - Method in class org.simBio.sim.js.Worker

RungeKutta - Class in org.simBio.core.integrator

RungeKutta法で計算される変数
the variable calculated by RungeKutta method

RungeKutta() - Constructor for class org.simBio.core.integrator.RungeKutta

RungeKuttaList - Class in org.simBio.core.integrator

Runge-Kutta engine (& dt adjuster)

RungeKuttaList() - Constructor for class org.simBio.core.integrator.RungeKuttaList

RunGUI - Class in org.simBio

Main entry of simBio with GUI.

RunGUI() - Constructor for class org.simBio.RunGUI

RyR - Class in org.simBio.bio.faber_rudy_2000.current

Calcium release channel on SR

RyR() - Constructor for class org.simBio.bio.faber_rudy_2000.current.RyR

ryr - Variable in class org.simBio.bio.faber_rudy_2000.structure.JSR