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

O

O1 - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Iha

O2 - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexIV

oxygen concentration

O2 - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Iha

O3 - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Iha

observedCurrent - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.pipette.VoltageClamp

current through the cell membrane

observedCurrent - Variable in class org.simBio.bio.sarai_et_al_2003.VoltageClamp

total current through the cell membrane (pA)

ODE - Class in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca

Ca buffer, using ordinary differential equation (ODE).

ODE() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.ODE

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

Created on 2003/10/30

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

offset - Variable in class org.simBio.bio.faber_rudy_2000.function.Stimulus

offset - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_stim

stimulus onset (milliS)

offset - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.pipette.Pipette

offset (msec) of the test pulse

offset - Variable in class org.simBio.bio.matsuoka_et_al_2004.exp.Anoxia

offset - Variable in class org.simBio.bio.sarai_noma_2004.VoltageClamp

offset - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.pipette.Pipette

offset (msec) of the test pulse

offset - Variable in class org.simBio.bio.terashima_et_al_2006.experiment.StepChanger

offset - Variable in class org.simBio.bio.terashima_et_al_2006.experiment.StepChanger2

offset - Variable in class org.simBio.sim.analyzer.csv.CsvMaker

offset - Variable in class org.simBio.sim.analyzer.measure.AbstractMeasure

offsetTime - Variable in class org.simBio.bio.terashima_et_al_2006.experiment.TonicityChange

OneTimeListExchanger - Class in org.simBio.sim.dm.exchange

毎回子ExchangerもExchangeさせるListExchangerクラス。

OneTimeListExchanger(Node) - Constructor for class org.simBio.sim.dm.exchange.OneTimeListExchanger

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

Graph window on screen

OnScreen(IViewer, String) - Constructor for class org.simBio.sim.analyzer.graph.OnScreen

Constractor

onset - Variable in class org.simBio.bio.faber_rudy_2000.function.Stimulus

onset - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_stim

stimulus onset (milliS)

onset - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.pipette.Pipette

onset (msec) of the test pulse

onset - Variable in class org.simBio.bio.matsuoka_et_al_2004.exp.Anoxia

onset - Variable in class org.simBio.bio.negroni_lascano_1996.exp.LChange

start time for shortning

onset - Variable in class org.simBio.bio.sarai_et_al_2003.VoltageClamp

onset (msec) of the clump

onset - Variable in class org.simBio.bio.sarai_noma_2004.VoltageClamp

onset - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.pipette.Pipette

onset (msec) of the test pulse

onset - Variable in class org.simBio.bio.terashima_et_al_2006.experiment.StepChanger

onset - Variable in class org.simBio.bio.terashima_et_al_2006.experiment.StepChanger2

onset - Variable in class org.simBio.sim.analyzer.csv.CsvMaker

onset - Variable in class org.simBio.sim.analyzer.measure.AbstractMeasure

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

onset - Variable in class org.simBio.sim.analyzer.measure.Vmax

onsetTime - Variable in class org.simBio.bio.terashima_et_al_2006.experiment.TonicityChange

open - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.IRyR

open state probability

open - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.channel.IRyR

open state probability

open - Variable in class org.simBio.bio.oka_et_al_2006.function.kinetics.MultiStateModel

open state probability

open - Variable in class org.simBio.bio.oka_et_al_2006.function.kinetics.TwoStateModel

open state probability

open - Variable in class org.simBio.bio.takeuchi_et_al_2006.current.IRyR

open state probability

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

ファイル名を指定してオープンする

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

ファイルを開くための、ダイアログボックスを開く

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

ダイアログを開き、ファイル名を指定してオープンする

openState1 - Variable in class org.simBio.bio.himeno_et_al_2008.Iha

openState1 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.Iha

openState2 - Variable in class org.simBio.bio.himeno_et_al_2008.Iha

openState2 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.Iha

optimumHSL - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme.CrossBridgeNL

org.simBio - package org.simBio

simBio: biological DYNAMIC simulation platform.

org.simBio.bio - package org.simBio.bio

for the biologists.

org.simBio.bio.cor - package org.simBio.bio.cor

org.simBio.bio.faber_rudy_2000.current - package org.simBio.bio.faber_rudy_2000.current

org.simBio.bio.faber_rudy_2000.function - package org.simBio.bio.faber_rudy_2000.function

org.simBio.bio.faber_rudy_2000.molecule - package org.simBio.bio.faber_rudy_2000.molecule

org.simBio.bio.faber_rudy_2000.structure - package org.simBio.bio.faber_rudy_2000.structure

org.simBio.bio.function - package org.simBio.bio.function

org.simBio.bio.henriquez_et_al_2001 - package org.simBio.bio.henriquez_et_al_2001

org.simBio.bio.himeno_et_al_2008 - package org.simBio.bio.himeno_et_al_2008

org.simBio.bio.hodgkin_huxley_1952 - package org.simBio.bio.hodgkin_huxley_1952

Modifyed Hodgkin Huxley Squid Axon Model 1952

org.simBio.bio.kurata_et_al_2005.complex - package org.simBio.bio.kurata_et_al_2005.complex

org.simBio.bio.kurata_et_al_2005.current - package org.simBio.bio.kurata_et_al_2005.current

org.simBio.bio.kurata_et_al_2005.flux - package org.simBio.bio.kurata_et_al_2005.flux

org.simBio.bio.kurata_et_al_2005.molecule - package org.simBio.bio.kurata_et_al_2005.molecule

org.simBio.bio.kuratomi_et_al_2003.current.carrier - package org.simBio.bio.kuratomi_et_al_2003.current.carrier

org.simBio.bio.kuzumoto_et_al_2007.contraction - package org.simBio.bio.kuzumoto_et_al_2007.contraction

org.simBio.bio.kuzumoto_et_al_2007.current - package org.simBio.bio.kuzumoto_et_al_2007.current

org.simBio.bio.kuzumoto_et_al_2007.current.carrier - package org.simBio.bio.kuzumoto_et_al_2007.current.carrier

org.simBio.bio.kuzumoto_et_al_2007.current.cf - package org.simBio.bio.kuzumoto_et_al_2007.current.cf

org.simBio.bio.kuzumoto_et_al_2007.function - package org.simBio.bio.kuzumoto_et_al_2007.function

org.simBio.bio.kuzumoto_et_al_2007.molecule - package org.simBio.bio.kuzumoto_et_al_2007.molecule

org.simBio.bio.matsuoka_et_al_2003 - package org.simBio.bio.matsuoka_et_al_2003

The cardiac cell model proposed by Matsuoka et al, 2003.

org.simBio.bio.matsuoka_et_al_2003.complex - package org.simBio.bio.matsuoka_et_al_2003.complex

org.simBio.bio.matsuoka_et_al_2003.current - package org.simBio.bio.matsuoka_et_al_2003.current

org.simBio.bio.matsuoka_et_al_2003.current.carrier - package org.simBio.bio.matsuoka_et_al_2003.current.carrier

org.simBio.bio.matsuoka_et_al_2003.current.cf - package org.simBio.bio.matsuoka_et_al_2003.current.cf

org.simBio.bio.matsuoka_et_al_2003.current.channel - package org.simBio.bio.matsuoka_et_al_2003.current.channel

org.simBio.bio.matsuoka_et_al_2003.current.pipette - package org.simBio.bio.matsuoka_et_al_2003.current.pipette

org.simBio.bio.matsuoka_et_al_2003.current.potassium - package org.simBio.bio.matsuoka_et_al_2003.current.potassium

org.simBio.bio.matsuoka_et_al_2003.function - package org.simBio.bio.matsuoka_et_al_2003.function

The common functions among models

org.simBio.bio.matsuoka_et_al_2003.molecule.buffer - package org.simBio.bio.matsuoka_et_al_2003.molecule.buffer

org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca - package org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca

org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme - package org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme

org.simBio.bio.matsuoka_et_al_2004.current.carrier - package org.simBio.bio.matsuoka_et_al_2004.current.carrier

org.simBio.bio.matsuoka_et_al_2004.exp - package org.simBio.bio.matsuoka_et_al_2004.exp

org.simBio.bio.matsuoka_et_al_2004.function - package org.simBio.bio.matsuoka_et_al_2004.function

org.simBio.bio.matsuoka_et_al_2004.function.chemical - package org.simBio.bio.matsuoka_et_al_2004.function.chemical

org.simBio.bio.matsuoka_et_al_2004.molecule - package org.simBio.bio.matsuoka_et_al_2004.molecule

org.simBio.bio.matsuoka_et_al_2004.molecule.buffer - package org.simBio.bio.matsuoka_et_al_2004.molecule.buffer

org.simBio.bio.matsuoka_et_al_2004.molecule.buffer.Ca - package org.simBio.bio.matsuoka_et_al_2004.molecule.buffer.Ca

org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme - package org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme

org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain - package org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain

org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter - package org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter

org.simBio.bio.negroni_lascano_1996 - package org.simBio.bio.negroni_lascano_1996

The contraction model proposed by Negroni and Lascano, 1996.

org.simBio.bio.negroni_lascano_1996.exp - package org.simBio.bio.negroni_lascano_1996.exp

org.simBio.bio.noble_et_al_1998 - package org.simBio.bio.noble_et_al_1998

org.simBio.bio.oka_et_al_2006.function - package org.simBio.bio.oka_et_al_2006.function

org.simBio.bio.oka_et_al_2006.function.kinetics - package org.simBio.bio.oka_et_al_2006.function.kinetics

org.simBio.bio.oka_et_al_2006.structure - package org.simBio.bio.oka_et_al_2006.structure

org.simBio.bio.sarai_et_al_2003 - package org.simBio.bio.sarai_et_al_2003

org.simBio.bio.sarai_et_al_2003.figure - package org.simBio.bio.sarai_et_al_2003.figure

org.simBio.bio.sarai_et_al_2006.current.carrier - package org.simBio.bio.sarai_et_al_2006.current.carrier

org.simBio.bio.sarai_et_al_2006.current.cf - package org.simBio.bio.sarai_et_al_2006.current.cf

org.simBio.bio.sarai_et_al_2006.figure - package org.simBio.bio.sarai_et_al_2006.figure

org.simBio.bio.sarai_et_al_2006.function - package org.simBio.bio.sarai_et_al_2006.function

org.simBio.bio.sarai_noma_2004 - package org.simBio.bio.sarai_noma_2004

Single Na channel model, Sarai and Noma, 2004.

org.simBio.bio.sarai_noma_2004.fourState - package org.simBio.bio.sarai_noma_2004.fourState

org.simBio.bio.sarai_noma_2004.structure - package org.simBio.bio.sarai_noma_2004.structure

org.simBio.bio.takeuchi_et_al_2006.current - package org.simBio.bio.takeuchi_et_al_2006.current

org.simBio.bio.takeuchi_et_al_2006.function - package org.simBio.bio.takeuchi_et_al_2006.function

org.simBio.bio.tenTusscher_et_al_2004.complex - package org.simBio.bio.tenTusscher_et_al_2004.complex

org.simBio.bio.tenTusscher_et_al_2004.current - package org.simBio.bio.tenTusscher_et_al_2004.current

org.simBio.bio.tenTusscher_et_al_2004.current.carrier - package org.simBio.bio.tenTusscher_et_al_2004.current.carrier

org.simBio.bio.tenTusscher_et_al_2004.current.pipette - package org.simBio.bio.tenTusscher_et_al_2004.current.pipette

org.simBio.bio.tenTusscher_et_al_2004.flux - package org.simBio.bio.tenTusscher_et_al_2004.flux

org.simBio.bio.tenTusscher_et_al_2004.function - package org.simBio.bio.tenTusscher_et_al_2004.function

org.simBio.bio.terashima_et_al_2006.complex - package org.simBio.bio.terashima_et_al_2006.complex

org.simBio.bio.terashima_et_al_2006.current - package org.simBio.bio.terashima_et_al_2006.current

Classes for membrane currents.

org.simBio.bio.terashima_et_al_2006.current.carrier - package org.simBio.bio.terashima_et_al_2006.current.carrier

org.simBio.bio.terashima_et_al_2006.current.cf - package org.simBio.bio.terashima_et_al_2006.current.cf

org.simBio.bio.terashima_et_al_2006.current.channel - package org.simBio.bio.terashima_et_al_2006.current.channel

org.simBio.bio.terashima_et_al_2006.current.potassium - package org.simBio.bio.terashima_et_al_2006.current.potassium

org.simBio.bio.terashima_et_al_2006.experiment - package org.simBio.bio.terashima_et_al_2006.experiment

Classes for experimental manipulation.

org.simBio.bio.terashima_et_al_2006.function - package org.simBio.bio.terashima_et_al_2006.function

The common functions among models

org.simBio.core - package org.simBio.core

The basal Classes of the simBio
simBioの基盤クラス群。
他のクラスは全て、ここにあるクラスを参照もしくは継承もしくは利用しています。

org.simBio.core.integrator - package org.simBio.core.integrator

org.simBio.serialize - package org.simBio.serialize

serializer
直列化と復元

org.simBio.serialize.xml - package org.simBio.serialize.xml

XML serializer

org.simBio.sim.analyzer - package org.simBio.sim.analyzer

analyzers which inherit core.Analyzer,
core.Analyserを継承するクラス群

org.simBio.sim.analyzer.csv - package org.simBio.sim.analyzer.csv

CSV maker
計算結果をCSV形式で書き出します。

org.simBio.sim.analyzer.csv.keep - package org.simBio.sim.analyzer.csv.keep

org.simBio.sim.analyzer.csv.result - package org.simBio.sim.analyzer.csv.result

org.simBio.sim.analyzer.graph - package org.simBio.sim.analyzer.graph

org.simBio.sim.analyzer.graph.plot - package org.simBio.sim.analyzer.graph.plot

org.simBio.sim.analyzer.graph.results - package org.simBio.sim.analyzer.graph.results

org.simBio.sim.analyzer.graph.simple - package org.simBio.sim.analyzer.graph.simple

2D Graph maker
計算結果を2次元グラフで表示する。

org.simBio.sim.analyzer.measure - package org.simBio.sim.analyzer.measure

org.simBio.sim.dm - package org.simBio.sim.dm

Database Manager
created by Hido.

org.simBio.sim.dm.exchange - package org.simBio.sim.dm.exchange

org.simBio.sim.dm.util - package org.simBio.sim.dm.util

org.simBio.sim.gui - package org.simBio.sim.gui

Graphical user interface

org.simBio.sim.gui.toolKit - package org.simBio.sim.gui.toolKit

org.simBio.sim.gui.toolKit.dndmenu - package org.simBio.sim.gui.toolKit.dndmenu

org.simBio.sim.js - package org.simBio.sim.js

org.simBio.sim.js.entry - package org.simBio.sim.js.entry

org.simBio.sim.js.jini - package org.simBio.sim.js.jini

org.simBio.sim.ps - package org.simBio.sim.ps

org.simBio.sim.ps.serialize - package org.simBio.sim.ps.serialize

org.simBio.sim.ps.view - package org.simBio.sim.ps.view

org.simBio.tools.remote - package org.simBio.tools.remote

org.simBio.tools.remote.process - package org.simBio.tools.remote.process

org.simBio.util - package org.simBio.util

org.simBio.util.numerical - package org.simBio.util.numerical

org.simBio.util.numerical.methods - package org.simBio.util.numerical.methods

org.simBio.util.taglets - package org.simBio.util.taglets

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

origin location & Length (0.01mm)

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

other - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation

other concentration of the same molecular group

other1 - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation2

other concentration of the same molecular group

other2 - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation2

other concentration of the same molecular group

Ouabain - Class in org.simBio.bio.takeuchi_et_al_2006.function

Calculate ouabain effect on amplitude of INaK.

Ouabain() - Constructor for class org.simBio.bio.takeuchi_et_al_2006.function.Ouabain

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

concentration of extracellular ouabain [mM]

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

extracellular ion concentration (mM)

out - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.Current

external ion concentration (mM)

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

extracellular ion concentration (mM)

out_ - Variable in class org.simBio.tools.remote.process.AbstractAfterProcess

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

活動電位のピーク (mV)

OxidativePhosphorylation - Class in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain

Differential equation for reactions of oxidattive phosphorylation.

OxidativePhosphorylation() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.OxidativePhosphorylation

oxygen - Variable in class org.simBio.bio.matsuoka_et_al_2004.exp.Anoxia

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

oxygen concentration