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Uses of Class
org.simBio.core.Component

Packages that use Component
org.simBio.bio for the biologists. 
org.simBio.bio.cor   
org.simBio.bio.faber_rudy_2000.current   
org.simBio.bio.faber_rudy_2000.function   
org.simBio.bio.faber_rudy_2000.molecule   
org.simBio.bio.faber_rudy_2000.structure   
org.simBio.bio.function   
org.simBio.bio.henriquez_et_al_2001   
org.simBio.bio.himeno_et_al_2008   
org.simBio.bio.hodgkin_huxley_1952 Modifyed Hodgkin Huxley Squid Axon Model 1952 
org.simBio.bio.kurata_et_al_2005.complex   
org.simBio.bio.kurata_et_al_2005.current   
org.simBio.bio.kurata_et_al_2005.flux   
org.simBio.bio.kurata_et_al_2005.molecule   
org.simBio.bio.kuratomi_et_al_2003.current.carrier   
org.simBio.bio.kuzumoto_et_al_2007.contraction   
org.simBio.bio.kuzumoto_et_al_2007.current   
org.simBio.bio.kuzumoto_et_al_2007.current.carrier   
org.simBio.bio.kuzumoto_et_al_2007.current.cf   
org.simBio.bio.kuzumoto_et_al_2007.function   
org.simBio.bio.kuzumoto_et_al_2007.molecule   
org.simBio.bio.matsuoka_et_al_2003.complex   
org.simBio.bio.matsuoka_et_al_2003.current   
org.simBio.bio.matsuoka_et_al_2003.current.cf   
org.simBio.bio.matsuoka_et_al_2003.current.channel   
org.simBio.bio.matsuoka_et_al_2003.current.pipette   
org.simBio.bio.matsuoka_et_al_2003.current.potassium   
org.simBio.bio.matsuoka_et_al_2003.function The common functions among models 
org.simBio.bio.matsuoka_et_al_2003.molecule.buffer   
org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca   
org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme   
org.simBio.bio.matsuoka_et_al_2004.exp   
org.simBio.bio.matsuoka_et_al_2004.function   
org.simBio.bio.matsuoka_et_al_2004.function.chemical   
org.simBio.bio.matsuoka_et_al_2004.molecule   
org.simBio.bio.matsuoka_et_al_2004.molecule.buffer   
org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme   
org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain   
org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter   
org.simBio.bio.negroni_lascano_1996 The contraction model proposed by Negroni and Lascano, 1996. 
org.simBio.bio.negroni_lascano_1996.exp   
org.simBio.bio.oka_et_al_2006.function   
org.simBio.bio.oka_et_al_2006.function.kinetics   
org.simBio.bio.oka_et_al_2006.structure   
org.simBio.bio.sarai_et_al_2006.function   
org.simBio.bio.sarai_noma_2004 Single Na channel model, Sarai and Noma, 2004. 
org.simBio.bio.sarai_noma_2004.fourState   
org.simBio.bio.takeuchi_et_al_2006.current   
org.simBio.bio.takeuchi_et_al_2006.function   
org.simBio.bio.tenTusscher_et_al_2004.current   
org.simBio.bio.tenTusscher_et_al_2004.flux   
org.simBio.bio.tenTusscher_et_al_2004.function   
org.simBio.bio.terashima_et_al_2006.complex   
org.simBio.bio.terashima_et_al_2006.current.carrier   
org.simBio.bio.terashima_et_al_2006.current.cf   
org.simBio.bio.terashima_et_al_2006.current.potassium   
org.simBio.bio.terashima_et_al_2006.experiment Classes for experimental manipulation. 
org.simBio.bio.terashima_et_al_2006.function The common functions among models 
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   
org.simBio.serialize serializer
直列化と復元 
org.simBio.serialize.xml XML serializer
 
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 CSV maker
計算結果をCSV形式で書き出します。 
org.simBio.sim.analyzer.csv.keep   
org.simBio.sim.analyzer.csv.result   
org.simBio.sim.analyzer.graph   
org.simBio.sim.analyzer.graph.results   
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   
org.simBio.sim.gui Graphical user interface
 
org.simBio.util.numerical   
 

Uses of Component in org.simBio.bio
 

Subclasses of Component in org.simBio.bio
 class Compartment
          Nodes folder, contain no equation.
 class parabola
          for test.
 

Uses of Component in org.simBio.bio.cor
 

Subclasses of Component in org.simBio.bio.cor
 class Hodgkin_huxley_squid_axon_1952_modified
          Conversion from CellML 1.0 to Java was done using COR (0.9.31.28)
Copyright (c) 2002-2005 Oxford Cardiac Electrophysiology Group
 class Vanderpol_model_1928
          Conversion from CellML 1.0 to Java was done using COR (0.9.31.28)
Copyright (c) 2002-2005 Oxford Cardiac Electrophysiology Group
 

Uses of Component in org.simBio.bio.faber_rudy_2000.current
 

Subclasses of Component in org.simBio.bio.faber_rudy_2000.current
 class Current
          sodium background current.
 class ICaL
          L-type Calcium channnel.
 class ICaT
          T-Type Calcium Channel.
 class IK1
          time indipendent potassium channel
 class IKpl
          plateau potassium channel
 class IKr
          Rapidly Activating Potassium channel
 class IKs
          slow time dependent potassium channel
 class INa
          fast sodium channel
 class INaCa
          Sodium Calcium exchanger
 class INaK
          sodium potassium pump current
 class IpCa
          Sarcolemmal Ca Pump Current
 class NSRLeak
          leak current from NSR
 class RyR
          Calcium release channel on SR
 class SRCA
          SR calcium pump.
 

Uses of Component in org.simBio.bio.faber_rudy_2000.function
 

Subclasses of Component in org.simBio.bio.faber_rudy_2000.function
 class Diffusion
          diffusion.
 class Stimulus
          Constructor for Stimulus.
 

Uses of Component in org.simBio.bio.faber_rudy_2000.molecule
 

Subclasses of Component in org.simBio.bio.faber_rudy_2000.molecule
 class CaBuffer
          analytic equation of Calcium buffering.
 class DualCaBuffer
           Faber GM, Rudy Y.
Action potential and contractility changes in [Na+]i overloaded cardiac myocytes: a simulation study.
Biophy J 2000;78:2392-2404
 

Uses of Component in org.simBio.bio.faber_rudy_2000.structure
 

Subclasses of Component in org.simBio.bio.faber_rudy_2000.structure
 class Cell
          Cell.
 class JSR
           Faber GM, Rudy Y.
Action potential and contractility changes in [Na+]i overloaded cardiac myocytes: a simulation study.
Biophy J 2000;78:2392-2404
 class NSR
           Faber GM, Rudy Y.
Action potential and contractility changes in [Na+]i overloaded cardiac myocytes: a simulation study.
Biophy J 2000;78:2392-2404
 

Uses of Component in org.simBio.bio.function
 

Subclasses of Component in org.simBio.bio.function
 class Analytic2state
          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.
 class Function
          Abstract super class of function format.
 

Fields in org.simBio.bio.function declared as Component
 Component StepChanger.times
          
 Component StepChanger.values
          
 

Uses of Component in org.simBio.bio.henriquez_et_al_2001
 

Subclasses of Component in org.simBio.bio.henriquez_et_al_2001
 class GapJunction
          Voltage-dependent gap junction model developed by Vogel and Weingart.
 

Uses of Component in org.simBio.bio.himeno_et_al_2008
 

Subclasses of Component in org.simBio.bio.himeno_et_al_2008
 class IKACh
          ACh channel.
 

Fields in org.simBio.bio.himeno_et_al_2008 declared as Component
 Component IKs.Phosphorylation
           
 

Uses of Component in org.simBio.bio.hodgkin_huxley_1952
 

Subclasses of Component in org.simBio.bio.hodgkin_huxley_1952
 class I_K
          Potassium Channel.
 class I_L
          leak component.
 class I_Na
          Sodium channel.
 class I_stim
          Stimulus current.
 class Membrane
          Membrane.
 

Uses of Component in org.simBio.bio.kurata_et_al_2005.complex
 

Subclasses of Component in org.simBio.bio.kurata_et_al_2005.complex
 class SR
           
 

Uses of Component in org.simBio.bio.kurata_et_al_2005.current
 

Subclasses of Component in org.simBio.bio.kurata_et_al_2005.current
 class ICab
           
 class INab
           
 class Ito
           
 

Uses of Component in org.simBio.bio.kurata_et_al_2005.flux
 

Subclasses of Component in org.simBio.bio.kurata_et_al_2005.flux
 class Leak
          leak flux (Jleak) from the uptake site of SRnet (mM/ms).
 class Release
           
 class Transfer
           
 class Uptake
           
 

Uses of Component in org.simBio.bio.kurata_et_al_2005.molecule
 

Subclasses of Component in org.simBio.bio.kurata_et_al_2005.molecule
 class CaBuffer_RK
          Calculate using ordinary differential equation, working with analytic buffer.
 

Uses of Component in org.simBio.bio.kuratomi_et_al_2003.current.carrier
 

Subclasses of Component in org.simBio.bio.kuratomi_et_al_2003.current.carrier
 class Carrier
          Abstract class for ping-pong model of the carrier.
 

Uses of Component in org.simBio.bio.kuzumoto_et_al_2007.contraction
 

Subclasses of Component in org.simBio.bio.kuzumoto_et_al_2007.contraction
 class CrossBridgeForce
          Cross bridge force of NL contraction model, Negroni JA and Lascano EC.
 class CrossBridgeLength
          Length of cross bridge of NL contraction model, Negroni JA and Lascano EC.
 class ForceEquilibrium
          Calculation of force equilibrium.
 class IsotonicContraction
          Calculation of half sarcomere length in isotonic experiments.
 class ParallelElementForce
          Parallel element force of NL contraction model, Negroni JA and Lascano EC.
 class Troponin
          troponin of Negroni and Lascano contraction model.
 class Troponinmit
          Troponin state transition of Cardiac Muscle Model by Negroni and Lascano.
 

Uses of Component in org.simBio.bio.kuzumoto_et_al_2007.current
 

Subclasses of Component in org.simBio.bio.kuzumoto_et_al_2007.current
 class IRyR
          Calcium releasing channel on SR.
 

Uses of Component in org.simBio.bio.kuzumoto_et_al_2007.current.carrier
 

Subclasses of Component in org.simBio.bio.kuzumoto_et_al_2007.current.carrier
 class ICaPump
          Ca pump on network SR.
 class IPMCA
          Ca pump on cell membrane.
 

Fields in org.simBio.bio.kuzumoto_et_al_2007.current.carrier declared as Component
 Component IPMCA.Phosphorylation
           
 

Uses of Component in org.simBio.bio.kuzumoto_et_al_2007.current.cf
 

Subclasses of Component in org.simBio.bio.kuzumoto_et_al_2007.current.cf
 class ICFTR
          Cystic fibrosis transmembrane conductance regulator Cl- channel current.
 

Fields in org.simBio.bio.kuzumoto_et_al_2007.current.cf declared as Component
 Component IKs.Phosphorylation
           
 

Uses of Component in org.simBio.bio.kuzumoto_et_al_2007.function
 

Subclasses of Component in org.simBio.bio.kuzumoto_et_al_2007.function
 class Average
           
 class ConcentrationAMP
          calculation of AMP concentration (conformed to mass conservation law).
 class KoDependency_IK1
          Updated [K]o dependency calculation for IK1.
 class PA2MS
          Average and Convert pA to M/S.
 

Uses of Component in org.simBio.bio.kuzumoto_et_al_2007.molecule
 

Subclasses of Component in org.simBio.bio.kuzumoto_et_al_2007.molecule
 class BetaAR_Gs
          betaAR and Gs signaling module.
 class CAMP
          cAMP module.
 class PKA
          PKA module.
 class PLB
          Phospholamban module.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.complex
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.complex
 class ATPsynthesis
          The lumped model of ATP synthesis.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.current
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.current
 class MembraneTransporter
          Abstract class of membrane transporters.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.current.cf
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.current.cf
 class CfChannel
          calculate current component of Na, K, Ca ion according to the constant field theory.
 class Iha
          Hyperpolarization-activated cation current, Iha.
 class ILCCa
          Calcium activated Non-Selective Cation current.
 class Ist
          Sustained inward current for pacemaker model.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.current.channel
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.current.channel
 class Channel
          template of Channel.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.current.pipette
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.current.pipette
 class CurrentClamp
          current clamp, external current in the RC membrane model.
 class Pipette
          external current in the RC membrane model.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.current.potassium
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.current.potassium
 class PureKchannel
          calculate pure potassium channel current.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.function
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.function
 class Charge
          keep whole cell current from external solution.
 class ConstantField
          calculate constant field.
 class Diffusion_a
          The first order ordinary differential equation is solved using analytic equation.
 class Diffusion_t
          The first order ordinary differential equation is solved using analytic equation.
 class KoDependency
          dependency of extracellular potassium concentration.
 class RateConstant
          function, c1/(c2*exp((x+c3)/c4)+c5*exp((x+c6)/c7))
 class RateConstantK
           
 class RateConstantVm
           
 class ReversalPotential
          calculate reversal potential of the specific ion.
 class Volume
           
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer
 class Buffer
          abstract of buffer
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca
 class Analytic
          instantaneous Ca buffer, using analytic equation as for Zeng et al, 1995 J.
 class Analytic_RK
          instantaneous Ca buffer using analytic equation as for Zeng et al, 1995.
 class InstantCaBuffer
          instantaneous Ca buffer, iterative method.
 class TroponinNL
          Troponin state transition of Cardiac Muscle Model by Negroni and Lascano.
 class TroponinNL_RK
          Troponin state transition of Negroni and Lascano contraction model for Runge-Kutta.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme
 class CrossBridgeNL
          Cross bridge kinetics of Cardiac Muscle Model by Negroni and Lascano.
 class IsometricContraction
          Isometric Contraction
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.exp
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.exp
 class Anoxia
          Anoxia condition on ventricular cell model was occured to regulate the oxygen concentration.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.function
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.function
 class Acidity
          calculation of pH (acidity) of the optional solution.
 class ConcentrationCyta2
          Calculation of the concentration of Cytochrome a2+
 class ConcentrationPi
          calculation of iorganic phosphate concentration (conformed to mass conservation law)
 class GradientP
          proton driving force
 class GradientpH
          proton gradient on mitochondrial inner membrane.
 class MassConservation
          calculation of molecular concentration conformed to mass conservation law
 class MassConservation2
          calculation of molecular concentration conformed to mass conservation law
 class MembranePotential
          membrane potential on mitochondrial inner membrane.
 class MetalFreeConcentration
          free concentration of metal affinity molecule
 class PartialPotential
          calcuration of partial potential.
 class PressureToConcentration
          calculation of concentration of gas-molecule from partial pressure.
 class RedoxPotential
          Calculation of the redox potential.
 class RedoxPotentialCyta
          Calculation of the redox potential of cytochrome a
 class VolumeRatio
          Calculation of volume ratio between cell and organella.
 class Zvalue
          calculation of z value.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.function.chemical
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.function.chemical
 class CN
          effect of CN addition.
 class FCCP
          effect of FCCP addition.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule
 class SubstrateDehydrogenation
          NADH dehydrogenation.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.buffer
 class HBuffering
          Buffering capacity coefficient for H+ (rbuffer).
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme
 class AK
          Adenylate Kinase (AK) System
 class CK
          Creatine Kinase (CK) System.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain
 class ATPsynthase
          Mitochondrial F1/F0 ATP Synthase.
 class ComplexI
          NADH-Ubiquinone oxidoreductase (complex I).
 class ComplexIII
          Cytochrome bc1 Complex (complex III).
 class ComplexIV
          Cytochrome c Oxidase (complex IV).
 class OxidativePhosphorylation
          Differential equation for reactions of oxidattive phosphorylation.
 

Uses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter
 

Subclasses of Component in org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter
 class ANT
          ADP/ATP carrier, ADP/ATP translocase, SLC25A4.
 class PhosphateCarrier
          Phosphate Transporter.
 class ProtonLeak
          Proton leak from cytosol to intremitochondoria.
 

Uses of Component in org.simBio.bio.negroni_lascano_1996
 

Subclasses of Component in org.simBio.bio.negroni_lascano_1996
 class CrossBridge
          Cross bridge kinetics of Cardiac Muscle Model by Negroni and Lascano.
 class Qpump
          equation 8 in the Negroni and Lascano, 1996 Qpump=Kp/(1+(Km/[Ca2+])^2)
 class Qrel
          equation 9 in the Negroni and Lascano, 1996
 

Uses of Component in org.simBio.bio.negroni_lascano_1996.exp
 

Subclasses of Component in org.simBio.bio.negroni_lascano_1996.exp
 class LChange
          muscle length is set with the controlled step and duration
 class Model
          Cardiac Muscle Model by Negroni and Lascano.
 

Uses of Component in org.simBio.bio.oka_et_al_2006.function
 

Subclasses of Component in org.simBio.bio.oka_et_al_2006.function
 class JunctionalConductance
          Calculate the junctional conductance (nS).
 class JunctionalPotential
          Calculate the trans-junctional potential between neighbouring two cells.
 

Uses of Component in org.simBio.bio.oka_et_al_2006.function.kinetics
 

Subclasses of Component in org.simBio.bio.oka_et_al_2006.function.kinetics
 class IndependentGate
          Calculate the mean open probability of the gating model consisting of multiple independent gates.
 class MultiStateModel
          Ligand-operated multi transition model.
 class RateConstantCaGate
          Calculate the forward and backward rate constans of two-state model by using time constant, pKd and Hill coefficient
 class TwoStateModel
          Two-state model.
 

Uses of Component in org.simBio.bio.oka_et_al_2006.structure
 

Subclasses of Component in org.simBio.bio.oka_et_al_2006.structure
 class GapJunctionK
          Gap junction model.
 

Uses of Component in org.simBio.bio.sarai_et_al_2006.function
 

Subclasses of Component in org.simBio.bio.sarai_et_al_2006.function
 class Rate
          Rate.
 class Ratio
          Ratio.
 

Uses of Component in org.simBio.bio.sarai_noma_2004
 

Subclasses of Component in org.simBio.bio.sarai_noma_2004
 class VoltageClamp
          apply square voltage pulse
 

Uses of Component in org.simBio.bio.sarai_noma_2004.fourState
 

Subclasses of Component in org.simBio.bio.sarai_noma_2004.fourState
 class MonteCarlo
           
 class NaChannel
          4 state gate of fast Sodium channel calculated by Monte Carlo method and ordinary differential Equations.
 class ODE
          Created on 2003/10/30
 

Uses of Component in org.simBio.bio.takeuchi_et_al_2006.current
 

Subclasses of Component in org.simBio.bio.takeuchi_et_al_2006.current
 class PMCA
          sarcolemmal Ca2+ pump.
 

Uses of Component in org.simBio.bio.takeuchi_et_al_2006.function
 

Subclasses of Component in org.simBio.bio.takeuchi_et_al_2006.function
 class Electroneutrality
          Calculate difference between total amounts of cations and anions.
 class ENaCa
          equilibrium potential for Na+/Ca2+ exchanger.
 class Ouabain
          Calculate ouabain effect on amplitude of INaK.
 

Uses of Component in org.simBio.bio.tenTusscher_et_al_2004.current
 

Subclasses of Component in org.simBio.bio.tenTusscher_et_al_2004.current
 class IbCa
          Background Ca2+ current.
 class IbNa
          Background Na+ current.
 class ICa
          L-type Ca2+ current.
 class IpK
          Plateau K current.
 class Ito_endo
          Transient outward current.
 

Uses of Component in org.simBio.bio.tenTusscher_et_al_2004.flux
 

Subclasses of Component in org.simBio.bio.tenTusscher_et_al_2004.flux
 class UpTake
          Pump current taking up calcium into SR.
 

Uses of Component in org.simBio.bio.tenTusscher_et_al_2004.function
 

Subclasses of Component in org.simBio.bio.tenTusscher_et_al_2004.function
 class ReversalPotential2
          calculate reversal potential of the specific Ion.
 

Uses of Component in org.simBio.bio.terashima_et_al_2006.complex
 

Subclasses of Component in org.simBio.bio.terashima_et_al_2006.complex
 class WaterFlux
          Water flux across the cell membrane [um3/ms].
 

Uses of Component in org.simBio.bio.terashima_et_al_2006.current.carrier
 

Subclasses of Component in org.simBio.bio.terashima_et_al_2006.current.carrier
 class NKCC
          Flux via Na+-K+-2Cl- cotransporter [amol/msec].
 

Uses of Component in org.simBio.bio.terashima_et_al_2006.current.cf
 

Subclasses of Component in org.simBio.bio.terashima_et_al_2006.current.cf
 class IClb
           
 class IVRCC
          volume-regulated Cl- current.
 

Uses of Component in org.simBio.bio.terashima_et_al_2006.current.potassium
 

Subclasses of Component in org.simBio.bio.terashima_et_al_2006.current.potassium
 class IKATP
          ATP-sensitive potassium current.
 

Uses of Component in org.simBio.bio.terashima_et_al_2006.experiment
 

Subclasses of Component in org.simBio.bio.terashima_et_al_2006.experiment
 class StepChanger
          Change the value in a step manner.
 class StepChanger2
          step change
 class TonicityChange
          Change extracellular fluid tonicity
 

Uses of Component in org.simBio.bio.terashima_et_al_2006.function
 

Subclasses of Component in org.simBio.bio.terashima_et_al_2006.function
 class AmplitudeNaK
          Calculate volume-dependency of INaK amplitude.
 class KoDependency2
          Calculate Ko dependency for IKATP.
 class Tonicity
          Tonicity of extracellular fluid .
 class TotalVolume
          Calculate total cell volume from cell volume accessible for ion diffusion.
 

Uses of Component in org.simBio.core
 

Subclasses of Component in org.simBio.core
 class Analyzer
          Please inherit this Class to manipulate every Node.
 class Composite
          Composite Pattern.
 class Conductor
          root instance to conduct integration.
 class Link
          making Link
 class Parameter
          labeled public double, Component of the Composite Pattern.
 class Reactor
          set of equations.
 

Methods in org.simBio.core with parameters of type Component
 void Visitor.visit(Component component)
           
 void Conductor.visit(Component component)
          Add Variables to the list.
 

Uses of Component in org.simBio.core.integrator
 

Subclasses of Component in org.simBio.core.integrator
 class Concentration
          The amount of ion (or molecule) is hold as value.
 class Euler
          the variable calculated by euler method
オイラー法で計算される変数
 class Positive
          keep the value positive.
 class PositiveRK
          Keep the value positive, for Runge-Kutta.
 class Probability
          Keep the value between 0 and 1.
 class RungeKutta
          RungeKutta法で計算される変数
the variable calculated by RungeKutta method
 

Uses of Component in org.simBio.serialize
 

Methods in org.simBio.serialize that return Component
 Component Serializer.read()
          deserialize.
 

Methods in org.simBio.serialize with parameters of type Component
 void Serializer.update(Component component, java.io.OutputStream stream, org.xml.sax.InputSource source)
          update serialized.
 void Collector.visit(Component component)
           
 void Serializer.write(Component component, java.lang.String uri)
          serialize.
 

Constructors in org.simBio.serialize with parameters of type Component
Collector(Component component, java.util.List list)
          Collect values.
 

Uses of Component in org.simBio.serialize.xml
 

Methods in org.simBio.serialize.xml that return Component
 Component XMLSerializer.getComponent(java.lang.String className)
          Return Class instance designated by the complete class name.
 Component XMLSerializer.read()
          Deserialize from xml file.
 

Methods in org.simBio.serialize.xml with parameters of type Component
 void XMLSerializer.update(Component component, java.io.OutputStream stream, org.xml.sax.InputSource original)
          Updates an XML file.
 void XMLSerializer.update(Component component, java.lang.String uri, java.io.Reader reference)
          Updates an XML file.
 void XMLSerializer.write(Component component)
          Serialize to the xml file.
 void XMLSerializer.write(Component component, java.lang.String uri)
          Serializes a component to the xml file.
 

Uses of Component in org.simBio.sim.analyzer
 

Subclasses of Component in org.simBio.sim.analyzer
 class StopWatch
           
 class VisualizeAnalyzer
          base class for visualized Node(Viewer, Graph, Axis).
 

Uses of Component in org.simBio.sim.analyzer.csv
 

Subclasses of Component in org.simBio.sim.analyzer.csv
 class CsvMaker
          Writes values to a file in csv format. If a directory which does not exist is included in the file path, the directory is created.
 class Siblings
          should be placed into the xml file of the parent node from which one wants to get the childrens' parameters
親Reactorの持つ全てのVariableとReactorの値をcsv形式で書き出す
 class Total
          writes values of all parameters, variables and nodes to csv file
親Reactor以下のTreeに存在する全てのReactorとParameterの値をcsv fileに書き出す
 

Fields in org.simBio.sim.analyzer.csv declared as Component
 Component CsvMaker.fileName
           
 Component CsvMaker.isActive
           
 

Methods in org.simBio.sim.analyzer.csv with parameters of type Component
 void Total.visit(Component data)
           
 

Uses of Component in org.simBio.sim.analyzer.csv.keep
 

Subclasses of Component in org.simBio.sim.analyzer.csv.keep
 class ParamEvalKeeper
          Keep changing parameters and evaluaion values and write to csv.
 class TimeSeriesKeeper
          Keep time series data and write to csv.
 

Fields in org.simBio.sim.analyzer.csv.keep declared as Component
 Component ParamEvalKeeper.evalPrefix
          評価値名の頭に付ける親の名前の数
 Component ParamEvalKeeper.parameters
          targetsの中の最初にある、変化させてるパラメータの数。残りのtargetは評価値と見なす。
 Component ParamEvalKeeper.paramPrefix
          parameter名の頭に付ける親の名前の数
 

Uses of Component in org.simBio.sim.analyzer.csv.result
 

Subclasses of Component in org.simBio.sim.analyzer.csv.result
 class AbstractAppender
          append the parameters to CSV file at the end of calculation.
 class ALaCarte
          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。
 

Uses of Component in org.simBio.sim.analyzer.graph
 

Subclasses of Component in org.simBio.sim.analyzer.graph
 class AbstractGraph
          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.
 class AxisXLog
          x axis by log scale.
 class AxisYLog
          y axis by log scale.
 class BasicGraph
          Graph which displays time series data.
 

Uses of Component in org.simBio.sim.analyzer.graph.results
 

Methods in org.simBio.sim.analyzer.graph.results that return Component
 Component TimeSeriesSingle.getNode()
          対応するNodeを取得する.
 

Constructors in org.simBio.sim.analyzer.graph.results with parameters of type Component
TimeSeriesSingle(TimeSeriesValues values, int series, java.lang.String name, Component node)
          時系列をカプセル化する。
 

Uses of Component in org.simBio.sim.analyzer.graph.simple
 

Subclasses of Component in org.simBio.sim.analyzer.graph.simple
 class Axis
           
 class AxisX
          x axis
 class AxisXFix
           
 class AxisY
          y axis
 class Graph
          2D graph.
 class Graph4State
           
 class RateGraph
          sample graph for bio.function
 class RateGraph_KA
          sample graph for bio.function
 class RelationGraph
          2D graph of relation between two parameters
 class RelationGraph_LP
          2D graph of relation between two parameters for org.simBio.sim.analyzer.measure.LeadPotential.
 class StepChart
          targetをずらして表示する。
 class Viewer
          graph viewer.
 

Uses of Component in org.simBio.sim.analyzer.measure
 

Subclasses of Component in org.simBio.sim.analyzer.measure
 class AbstractMeasure
          Measuring.
 class Amplitude
          get the difference between the maximum and minimum value of the target.
 class AmplitudeInCycle
          get the difference between the maximum and minimum value of the target in a cycle.
 class APD
          Measuring Action Potential Duration.
 class APDforSA
          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。
 class APDforSA2
          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。
 class HR
          心拍数を計測する。
 class LeadPotential
          Calculate Lead Potential.
 class Limitter
          targetの値が設定値を超えたら計算を終了する。
 class PeakDetect
          
 class Sum
          targetsの和を求める。
 class Vmax
          Measuring dV/dt max.
 class VmaxTime
          measure Vmax and timing of Vmax.
 

Uses of Component in org.simBio.sim.gui
 

Methods in org.simBio.sim.gui with parameters of type Component
 void ValueChangeObserver.update(Component component)
          値が変更された時に、このメソッドが呼び出されます。
 void GUI.visit(Component data)
          Visitor Pattern Interface : do nothing
 void DataListTable.visit(Component d)
           
 

Uses of Component in org.simBio.util.numerical
 

Subclasses of Component in org.simBio.util.numerical
 class MathFunction
          This abstract class represents a mathematical function on a simBio model tree.
 class MathMultivariableFunction
          This abstract class represents a mathematical function on a simBio model tree (light-weight version).
 class MathUnivariableFunction
          This abstract class represents a mathematical function on a simBio model tree (light-weight version).
 

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