Upload
valdemar-astrid
View
27
Download
0
Tags:
Embed Size (px)
DESCRIPTION
OpenCMISS + CellML. David Nickerson & Chris Bradley Auckland Bioengineering Institute University of Auckland New Zealand. OpenCMISS. Re-engineering of CMISS Main website http://www.opencmiss.org/ Open source on github https:// github.com/organizations/OpenCMISS. - PowerPoint PPT Presentation
Citation preview
OpenCMISS + CellML
David Nickerson & Chris BradleyAuckland Bioengineering InstituteUniversity of AucklandNew Zealand
OpenCMISS
• Re-engineering of CMISS• Main website
– http://www.opencmiss.org/
• Open source on github– https://github.com/organizations/OpenCMISS
OpenCMISS(Iron) libraryIron librarycore library
openCMISS
(cm)Field
ML
API
CellM
L A
PIopenCMIS
S(cm)Fi
eld
ML
API
CellM
L A
PIopenCMIS
S(cm)
CellM
L A
PI
Field
ML
API
FieldML file
CellML file
Proc
esso
rs
History file
Language
BindingsFortran
C/C++
Python
Etc.
Language
BindingsFortran
C/C++
Python
Etc.
Language
BindingsFortran
C/C++
Python
Etc.
Language
BindingsFortran
C/C++
Python
Etc.
OpenCMISS(iron)
Field
ML
API
CellM
L A
PI
External Program or script
External Program or script
External Program or script
External Program or script
OpenCMISS application
openCMISS
(cm)Field
ML
API
CellM
L A
PI
Com
La
yer
Com
La
yer
openCMISS
(cm)Field
ML
API
CellM
L A
PI
openCMISS
(cm)
CellM
L A
PI
Field
ML
API
Com
La
yer
FieldML file
CellML fileOpenCOR
Proc
esso
rs
CellM
L A
PI
Field
ML
API
Com
La
yer
History fileFi
eld
ML
API
CellM
L A
PI
Com
La
yer
Iron
Zinc Network
Example – Electrical Activation (Bidomain representation)
Cell Membrane
Intracellular Spacei, i
Extracellular Spacee, e
Iion
Cell model =
Bidomain equations
Where:– Vm = transmembrane potential– i = intracellular potential– e = extracellular potential– Am = membrane surface/volume ratio– Cm = membrane capacitance– e = intracellular conductivity tensor– i = intracellular conductivity tensor– Iion = ionic source current from cellular model– Im = transmembrane stimulus current– ii = current injection per volume intro intracellular space– ie = current injection per volume intro extracellular space
eimieie
imionmeimim
mm
eim
iiV
iIIAVt
VCA
V
σσσ
σσ
Cellular processes
ATP
IKr2
K+
K+
K+ K
+ K+ K
+
IKATP
IK1IKto
IKr1
IKs
INa-stretch
IAn-stretch
INS-stretch
IK-stretch
ICa-stretch
H2PO-4
2Na+
H+Lac
Na+
H+
HCO-3
Cl-
CBEOH-
Cl-
CHE
HCO-3Na
+
NBCNHELAT NPE
MgADP Mg2+
MgATP
MgPi
Magnesium Buffering
K+ Ca2+
MgADP+Pi+H+ MgATPOxPhos
ImKATP
3H+H+
2Lac
3MgATP
3MgADP+3Pi
Glycogenolysis Contraction
AK
CK
ADP
AMP
MgADP
MgATP
Cr
PCr ADP+H+
VCO2transport
CO2H+
H2PO4-
Intrinsic Buffers
Ca2+TropC
Calmodulin
Calcium Buffering
3Na+
NCE Ca2+
IpNa
Na+
IbNa
INa
DS
Na+
Na+
NSRJSR
MgATP Ca2+
Ca2+Vtr
Ca2+
Ca2+
Vleak
Vrel
VupCa2+
Na+K+
Vdecay
IbCa
3Na+
2K+
MgATP+
Problem/Field description
ATP
IKr2
K+
K+
K+
K+K+
K+
IKATP
IK1
IKto
IKr1
IKs
I
N
a-
st
re
tc
h
I
A
n-
st
re
tc
h
I
N
S-
st
re
tc
h
I
K
-
st
re
tc
h
I
C
a-
st
re
tc
h
H2PO-4
2Na+
H+Lac
Na+
H+
HCO-3
Cl-
CBE
OH-
Cl-
CHE
HCO-3
Na+
NBCNHELAT
NPE
MgADP Mg2+
MgATP
MgPi
K+Ca2+
MgADP+Pi+H+ MgATP
OxPhos
ImKATP
3H+H+
2Lac
3MgATP
3MgADP+3Pi
AK
CK
ADP
AMP
MgADP
MgATP
Cr
PCr ADP+H+
VCO2transport
CO2H+
H2PO4-
Intrinsic Buffers
Ca2+
TropC
Calmodulin
3Na+
NCE
Ca2+
IpNa
Na+
IbNa
INa
DS
Na+
Na+
NSR
JSR
MgATP Ca2+
Ca2+
Vtr
Ca2+
Ca2+
Vleak
Vrel
Vup
Ca2+
Na+
K+
Vdecay
IbCa
3Na+
2K+
MgATP+
Fields:• Geometric• Fibre• Material (i, e, Am, Cm etc.)
• Potential (Vm, e, etc.)
• Source (Iion, etc.)
• Cellular state variables• Cellular intermediate
variables• Cellular parameter variables
Field parameter vector
12 3
4 56 7
89 10 11 12
13 1415
16 17 18 19
20 2122
2324 25 26
272829 30
3132
33 34
35
13
57
1517
19
21
29
3133
35
Fieldvariable,
u
Component,u1
Component,u2
Parameter vector,
x
GlobalDOFs
Electrophysiology - CellML300%
100%
gNa Distribution
+50 mV
-85 mV
Stimulus off
+50 mV
-85 mV
Normal activation
+50 mV
-85 mV
gNa activation
Finite Elasticity – Breast Mechanics
Courtesy of Prasad Gamage
Skin
Breast Tissue
Undeformed
DeformedUnder gravityloading
Fluid Mechanics – 3D NSCarotid Artery Flow, Re=100
Mesh Velocity Pressure
Courtesy of David Ladd
CellML as a DOF black box
Fieldvariable
ParameterDOF Vector
Component1
Component2
Component3
Inputs Outputs
OpenCMISS CellML Import
void computeRates( double VOI, double *PARAMETERS, double *RATES, double *STATES, double
*INTERMEDIATE);{
const double FIXED[..];
::
}
State Parameters Intermediate
ATP
IKr2
K+
K+
K+
K+
K+
K+
I
K
A
T
P
IK1
IKto
IKr1
IKs
INa-stretch
IAn-stretch
INS-stretch
IK-stretch
ICa-stretch
H2
PO-
4
2Na+
H+Lac
Na+
H+
HCO-3
Cl-
CBE
OH-
Cl-
CHE
HCO-3
Na+
NBCNHE
LAT
NPE
MgADP Mg2+
MgATP
MgPi
K+
Ca2+
MgADP+Pi+H+ MgATP
OxPhos
ImKATP
3H+
H+
2Lac
3MgATP
3MgADP+3Pi
AK
CK
ADP
AMP
MgADP
MgATP
Cr
PCr ADP+H+
VCO2transport
CO2H+
H2PO4-
Intrinsic Buffers
Ca2+
TropC
Calmodulin
3Na+
NCE
Ca2+
IpNa
Na+
IbNa
INa
DS
Na+
Na+
NSR
JSR
MgATP Ca2+
Ca2+
Vtr
Ca2+
Ca2+
Vleak
Vrel
Vup
Ca2+
Na+
K+
Vdecay
IbCa
3Na+
2K+
MgATP+
StateParametersIntermediate
CellML Variables
CellML Environment
CellML Model
Import
Set as known
Set as wanted
Set as known and wanted
CellML Interface
ATP
IKr2
K+
K+
K+
K+K+ K+
IKATP
IK1
IKto
IKr1
IKs
INa-stretch
IAn-stretch
INS-stretch
IK-stretch
ICa-stretch
H2PO-4
2Na+
H+Lac
Na+
H+
HCO-3
Cl-
CBE
OH-
Cl-
CHE
HCO-3
Na+
NBCNHELAT
NPE
MgADP Mg2+
MgATP
MgPi
K+Ca2+
MgADP+Pi+H+ MgATP
OxPhos
ImKATP
3H+H+
2Lac
3MgATP
3MgADP+3Pi
AK
CK
ADP
AMP
MgADP
MgATP
Cr
PCr ADP+H+
VCO2transport
CO2H+
H2PO4-
Intrinsic Buffers
Ca2+
TropC
Calmodulin
3Na+
NCE
Ca2+
IpNa
Na+
IbNa
INa
DS
Na+
Na+
NSR
JSR
MgATP Ca2+
Ca2+Vtr
Ca2+
Ca2+
Vleak
Vrel
VupCa2+
Na+
K+
Vdecay
IbCa
3Na+
2K+
MgATP+ ModelsState ParametersIntermediate
CellM
Len
vir
on
OpenCMISSField
CellMLFields
CellML/Field Maps
ModelsState ParametersIntermediate
CellM
Len
vir
on
CellML to field MapField to CellML MapCellML integrate
Cellular model
TransmembraneVoltage Field
CellML/Field Maps
ModelsState ParametersIntermediate
CellM
Len
vir
on
StrainField
StressField
CellML to field MapField to CellML MapCellML evaluate
Constitutive
Law