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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.
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。
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
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.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
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
- Class in
org.simBio
Automatically calculates models.
Run()
- Constructor for class org.simBio.
Run
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
Overview
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Copyright © 2005 Cell/Biodinamics simulation project. All Rights Reserved.