Genesis 2 Backwards Compatibility Bridge

Index of group ./specifications/conversions

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G-2 to G-3 model conversion

1. Single compartment conversion

2. Converted single compartment run from ssp

3. Single compartment conversion, with sodium channel

4. Converted single compartment run from ssp

1. Single compartment conversion

Startup command : src/ns-sli

(No model has been loaded for the following set of commands.)

1.1. Can we set the main simulation clock?

1. Executed command	setclock 0 5e-5
2. Expected output

1.2. Can we create a compartment container?

1. Executed command	create neutral /n
2. Expected output

1.3. Can we create a compartment?

1. Executed command	create compartment /n/c
2. Expected output

1.4. Can we set the fields of the compartment?

1. Executed command	setfield /n/c Cm 4.57537e-11 Rm 3.58441e+08 Ra 360502 len 1 dia 1 initVm -0.068 Eleak -0.080
2. Expected output

1.5. What model components do we find in the model container, including fixed libraries?

1. Executed command	call model_container NEUROSPACES_COMMAND "expand /**"
2. Expected output	- /proto - /output - /n - /n/c

1.6. What model components do we find in the model container, selected output?

1. Executed command	call model_container NEUROSPACES_COMMAND "expand /n/**"
2. Expected output	- /n - /n/c

1.7. What does this look like in NDF (1)?

1. Executed command

call model_container NEUROSPACES_COMMAND "export library ndf STDOUT /n/**"

2. Expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

PRIVATE_MODELS
  GROUP "proto_3_3"
  END GROUP
  CHILD "proto_3_3" "proto_inserted_3"
  END CHILD
  GROUP "output_4_4"
  END GROUP
  CHILD "output_4_4" "output_inserted_4"
  END CHILD
  SEGMENT "c_6_6"
    PARAMETERS
      PARAMETER ( ELEAK = -0.08 ),
      PARAMETER ( Vm_init = -0.068 ),
      PARAMETER ( DIA = 1 ),
      PARAMETER ( LENGTH = 1 ),
      PARAMETER ( RA = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 360502 ),
          ), ),
      PARAMETER ( RM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 3.58441e+08 ),
          ), ),
      PARAMETER ( CM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 4.57537e-11 ),
          ), ),
    END PARAMETERS
  END SEGMENT
  CHILD "c_6_6" "c_inserted_6"
  END CHILD
  GROUP "n_5_5"
    CHILD "c_6_6" "c"
    END CHILD
  END GROUP
  CHILD "n_5_5" "n_inserted_5"
  END CHILD
END PRIVATE_MODELS
PUBLIC_MODELS
  CHILD "proto_3_3" "proto"
  END CHILD
  CHILD "output_4_4" "output"
  END CHILD
  CHILD "n_5_5" "n"
  END CHILD
END PUBLIC_MODELS

1.8. Can we set the inject field?

1. Executed command	setfield /n/c inject 1e-9
2. Expected output

1.9. What does this look like in NDF (2), does it include the inject field?

1. Executed command

call model_container NEUROSPACES_COMMAND "export library ndf STDOUT /n/**"

2. Expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

PRIVATE_MODELS
  GROUP "proto_3_3"
  END GROUP
  CHILD "proto_3_3" "proto_inserted_3"
  END CHILD
  GROUP "output_4_4"
  END GROUP
  CHILD "output_4_4" "output_inserted_4"
  END CHILD
  SEGMENT "c_6_6"
    PARAMETERS
      PARAMETER ( INJECT = 1e-09 ),
      PARAMETER ( ELEAK = -0.08 ),
      PARAMETER ( Vm_init = -0.068 ),
      PARAMETER ( DIA = 1 ),
      PARAMETER ( LENGTH = 1 ),
      PARAMETER ( RA = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 360502 ),
          ), ),
      PARAMETER ( RM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 3.58441e+08 ),
          ), ),
      PARAMETER ( CM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 4.57537e-11 ),
          ), ),
    END PARAMETERS
  END SEGMENT
  CHILD "c_6_6" "c_inserted_6"
  END CHILD
  GROUP "n_5_5"
    CHILD "c_6_6" "c"
    END CHILD
  END GROUP
  CHILD "n_5_5" "n_inserted_5"
  END CHILD
END PRIVATE_MODELS
PUBLIC_MODELS
  CHILD "proto_3_3" "proto"
  END CHILD
  CHILD "output_4_4" "output"
  END CHILD
  CHILD "n_5_5" "n"
  END CHILD
END PUBLIC_MODELS

1.10. Can we save the NDF to a file?

1. Executed command	call model_container NEUROSPACES_COMMAND "export library ndf /tmp/conversion1.ndf /n/**"
2. Expected output

1.11. Can we create an output element (1)?

1. Executed command	create asc_file /out
2. Expected output

1.12. Can we initialize the output element (1)?

1. Executed command	setfield /out filename "/tmp/conversion1.txt" flush 1
2. Expected output

1.13. Can we connect the output element with the model?

1. Executed command	addmsg /n/c /out SAVE Vm
2. Expected output

1.14. Can we reset the simulation (1)?

1. Executed command	reset
2. Expected output

1.15. Can we set the options for the DUMP command (1)?

1. Executed command

setfield /neurospaces_integrator heccer_dump_selection { HECCER_DUMP_INDEXERS_SUMMARY + HECCER_DUMP_INDEXERS_STRUCTURE + HECCER_DUMP_INTERMEDIARY_COMPARTMENT_SUMMARY + HECCER_DUMP_INTERMEDIARY_MECHANISM_SUMMARY + HECCER_DUMP_INTERMEDIARY_STRUCTURE + HECCER_DUMP_INTERMEDIARY_SUMMARY + HECCER_DUMP_INTERMEDIARY_COMPARTMENTS_PARAMETERS + HECCER_DUMP_VM_COMPARTMENT_MATRIX + HECCER_DUMP_VM_COMPARTMENT_DATA + HECCER_DUMP_VM_COMPARTMENT_OPERATIONS + HECCER_DUMP_VM_CHANNEL_POOL_FLUXES + HECCER_DUMP_VM_MECHANISM_DATA + HECCER_DUMP_VM_MECHANISM_OPERATIONS + HECCER_DUMP_VM_SUMMARY }

2. Expected output

genesis

1.16. Can we dump the model from heccer (1)?

1. Executed command

call /neurospaces_integrator NSINTEGRATOR_DUMP

2. Expected output

Heccer (pcName) : (/n)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0)
Heccer (dStep) : (5e-05)
Intermediary (iCompartments) : (1)
Compartment (mc.iType) : (1)
Compartment (iParent) : (-1)
Compartment (dCm) : (4.57537e-11)
Compartment (dEm) : (-0.08)
Compartment (dInitVm) : (-0.068)
Compartment (dInject) : (1e-09)
Compartment (dRa) : (360502)
Compartment (dRm) : (3.58441e+08)
MinimumDegree (iEntries) : (1)
MinimumDegree (piChildren[0]) : (0)
MinimumDegree (piForward[0]) : (0)
MinimumDegree (piBackward[0]) : (0)
Tables (iTabulatedGateCount) : (0)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -2.23189e-10 1e-09 546404 1.00152
00001 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00152)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)

1.17. Synchronize the simulator with the test specification

1. Executed command	echo "ready to go"
2. Expected output	ready to go

1.18. Can we run the simulation (1)?

1. Executed command	step 0.01 -time
2. Expected output	completed

1.19. Can we quit the simulator?

1. Executed command	quit
2. Expected output

1.20. Can we find the output, no sodium channel?

1. Expected output

application_output_file: /tmp/conversion1.txt
expected_output_file: ..//tests/specifications/strings/conversion1.txt

2. Converted single compartment run from ssp

Startup command : /usr/local/bin/ssp --time 0.01 --time-step 5e-5 --cell /tmp/conversion1.ndf --model-name n --output-fields /n/c->Vm --optimize --verbose --dump

Comments, Preparation, Reparation

1. Preparation needed before the commands below :	Create the output/ directory
2. And repared afterwards using :	Remove the generated output files in the output/ directory

2.1. Can we compile the converted model description from SSP ?

1. Expected output


Heccer (pcName) : (unnamed test)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0)
Heccer (dStep) : (5e-05)
Intermediary (iCompartments) : (1)
Compartment (mc.iType) : (1)
Compartment (iParent) : (-1)
Compartment (dCm) : (4.57537e-11)
Compartment (dEm) : (-0.08)
Compartment (dInitVm) : (-0.068)
Compartment (dInject) : (1e-09)
Compartment (dRa) : (360502)
Compartment (dRm) : (3.58441e+08)
MinimumDegree (iEntries) : (1)
MinimumDegree (piChildren[0]) : (0)
MinimumDegree (piForward[0]) : (0)
MinimumDegree (piBackward[0]) : (0)
Tables (iTabulatedGateCount) : (0)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -2.23189e-10 1e-09 546404 1.00152
00001 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00152)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)

2.2. Does the simulation produce the correct output ?

1. Expected output

application_output_file: ..//output/n.out
expected_output_file: ..//tests/specifications/strings/conversion1-ssp.txt

3. Single compartment conversion, with sodium channel

Startup command : src/ns-sli

(No model has been loaded for the following set of commands.)

3.1. Can we set the main simulation clock?

1. Executed command	setclock 0 5e-5
2. Expected output

3.2. Can we create a compartment container?

1. Executed command	create neutral /n
2. Expected output

3.3. Can we create a compartment?

1. Executed command	create compartment /n/c
2. Expected output

3.4. Can we set the fields of the compartment?

1. Executed command	setfield /n/c Cm 4.57537e-11 Rm 3.58441e+08 Ra 360502 len 1 dia 1 initVm -0.068 Eleak -0.080
2. Expected output

3.5. Can we create a sodium conductance?

1. Executed command	create tabchannel /n/c/naf
2. Expected output

3.6. Can we configure the sodium conductance (1)?

1. Executed command	setfield /n/c/naf Ek 0.045 Gbar 0.0002092393115 Ik 0.0 Gk 0.0 Xpower 3.0 Ypower 1.0 Zpower 0.0
2. Expected output

3.7. Can we configure the sodium conductance (2)?

1. Executed command	setupalpha /n/c/naf X 35.0e3 0.0 0.0 0.005 -10.0e-3 7.0e3 0.0 0.0 0.065 20.0e-3 -size 3000 -range -0.1 0.05
2. Expected output

3.8. Can we configure the sodium conductance (3)?

1. Executed command	setupalpha /n/c/naf Y 0.225e3 0.0 1.0 0.08 10.0e-3 7.5e3 0.0 0.0 -0.003 -18.0e-3 -size 3000 -range -0.1 0.05
2. Expected output

3.9. Can we configure the sodium conductance (4)?

1. Executed command	addmsg /n/c /n/c/naf VOLTAGE Vm addmsg /n/c/naf /n/c CHANNEL Gk Ek
2. Expected output

3.10. What model components do we find in the model container, including fixed libraries?

1. Executed command

call model_container NEUROSPACES_COMMAND "expand /**"

2. Expected output


- /proto
- /output
- /n
- /n/c
- /n/c/naf
- /n/c/naf/HH_activation
- /n/c/naf/HH_activation/A
- /n/c/naf/HH_activation/B
- /n/c/naf/HH_inactivation
- /n/c/naf/HH_inactivation/A
- /n/c/naf/HH_inactivation/B

3.11. What model components do we find in the model container, selected output?

1. Executed command

call model_container NEUROSPACES_COMMAND "expand /n/**"

2. Expected output


- /n
- /n/c
- /n/c/naf
- /n/c/naf/HH_activation
- /n/c/naf/HH_activation/A
- /n/c/naf/HH_activation/B
- /n/c/naf/HH_inactivation
- /n/c/naf/HH_inactivation/A
- /n/c/naf/HH_inactivation/B

3.12. What does this look like in NDF (1)?

1. Executed command

call model_container NEUROSPACES_COMMAND "export library ndf STDOUT /n/**"

2. Expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

PRIVATE_MODELS
  GROUP "proto_3_3"
  END GROUP
  CHILD "proto_3_3" "proto_inserted_3"
  END CHILD
  GROUP "output_4_4"
  END GROUP
  CHILD "output_4_4" "output_inserted_4"
  END CHILD
  GATE_KINETIC "A_9_9"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = -0.01 ),
      PARAMETER ( HH_AB_Offset_E = 0.005 ),
      PARAMETER ( HH_AB_Add = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 35000 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "A_9_9" "A_inserted_9"
  END CHILD
  GATE_KINETIC "B_10_10"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = 0.02 ),
      PARAMETER ( HH_AB_Offset_E = 0.065 ),
      PARAMETER ( HH_AB_Add = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 7000 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "B_10_10" "B_inserted_10"
  END CHILD
  HH_GATE "HH_activation_8_8"
    PARAMETERS
      PARAMETER ( POWER = 3 ),
      PARAMETER ( state_init = -1 ),
    END PARAMETERS
    CHILD "A_9_9" "A"
    END CHILD
    CHILD "B_10_10" "B"
    END CHILD
  END HH_GATE
  CHILD "HH_activation_8_8" "HH_activation_inserted_8"
  END CHILD
  GATE_KINETIC "A_12_12"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = 0.01 ),
      PARAMETER ( HH_AB_Offset_E = 0.08 ),
      PARAMETER ( HH_AB_Add = 1 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 225 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "A_12_12" "A_inserted_12"
  END CHILD
  GATE_KINETIC "B_13_13"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = -0.018 ),
      PARAMETER ( HH_AB_Offset_E = -0.003 ),
      PARAMETER ( HH_AB_Add = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 7500 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "B_13_13" "B_inserted_13"
  END CHILD
  HH_GATE "HH_inactivation_11_11"
    PARAMETERS
      PARAMETER ( POWER = 1 ),
      PARAMETER ( state_init = -1 ),
    END PARAMETERS
    CHILD "A_12_12" "A"
    END CHILD
    CHILD "B_13_13" "B"
    END CHILD
  END HH_GATE
  CHILD "HH_inactivation_11_11" "HH_inactivation_inserted_11"
  END CHILD
  CHANNEL "naf_7_7"
    BINDABLES
      INPUT Vm,
      OUTPUT G,
      OUTPUT I,
    END BINDABLES
    BINDINGS
      INPUT ..-&gt;Vm,
    END BINDINGS
    PARAMETERS
      PARAMETER ( G_MAX = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 0.000209239 ),
          ), ),
      PARAMETER ( Erev = 0.045 ),
    END PARAMETERS
    CHILD "HH_activation_8_8" "HH_activation"
    END CHILD
    CHILD "HH_inactivation_11_11" "HH_inactivation"
    END CHILD
  END CHANNEL
  CHILD "naf_7_7" "naf_inserted_7"
  END CHILD
  SEGMENT "c_6_6"
    BINDINGS
      INPUT naf-&gt;I,
    END BINDINGS
    PARAMETERS
      PARAMETER ( ELEAK = -0.08 ),
      PARAMETER ( Vm_init = -0.068 ),
      PARAMETER ( DIA = 1 ),
      PARAMETER ( LENGTH = 1 ),
      PARAMETER ( RA = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 360502 ),
          ), ),
      PARAMETER ( RM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 3.58441e+08 ),
          ), ),
      PARAMETER ( CM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 4.57537e-11 ),
          ), ),
    END PARAMETERS
    CHILD "naf_7_7" "naf"
    END CHILD
  END SEGMENT
  CHILD "c_6_6" "c_inserted_6"
  END CHILD
  GROUP "n_5_5"
    CHILD "c_6_6" "c"
    END CHILD
  END GROUP
  CHILD "n_5_5" "n_inserted_5"
  END CHILD
END PRIVATE_MODELS
PUBLIC_MODELS
  CHILD "proto_3_3" "proto"
  END CHILD
  CHILD "output_4_4" "output"
  END CHILD
  CHILD "n_5_5" "n"
  END CHILD
END PUBLIC_MODELS

3.13. Can we set the inject field?

1. Executed command	setfield /n/c inject 1e-9
2. Expected output

3.14. What does this look like in NDF (2), does it include the inject field?

1. Executed command

call model_container NEUROSPACES_COMMAND "export library ndf STDOUT /n/**"

2. Expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

PRIVATE_MODELS
  GROUP "proto_3_3"
  END GROUP
  CHILD "proto_3_3" "proto_inserted_3"
  END CHILD
  GROUP "output_4_4"
  END GROUP
  CHILD "output_4_4" "output_inserted_4"
  END CHILD
  GATE_KINETIC "A_9_9"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = -0.01 ),
      PARAMETER ( HH_AB_Offset_E = 0.005 ),
      PARAMETER ( HH_AB_Add = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 35000 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "A_9_9" "A_inserted_9"
  END CHILD
  GATE_KINETIC "B_10_10"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = 0.02 ),
      PARAMETER ( HH_AB_Offset_E = 0.065 ),
      PARAMETER ( HH_AB_Add = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 7000 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "B_10_10" "B_inserted_10"
  END CHILD
  HH_GATE "HH_activation_8_8"
    PARAMETERS
      PARAMETER ( POWER = 3 ),
      PARAMETER ( state_init = -1 ),
    END PARAMETERS
    CHILD "A_9_9" "A"
    END CHILD
    CHILD "B_10_10" "B"
    END CHILD
  END HH_GATE
  CHILD "HH_activation_8_8" "HH_activation_inserted_8"
  END CHILD
  GATE_KINETIC "A_12_12"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = 0.01 ),
      PARAMETER ( HH_AB_Offset_E = 0.08 ),
      PARAMETER ( HH_AB_Add = 1 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 225 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "A_12_12" "A_inserted_12"
  END CHILD
  GATE_KINETIC "B_13_13"
    PARAMETERS
      PARAMETER ( HH_AB_Tau = -0.018 ),
      PARAMETER ( HH_AB_Offset_E = -0.003 ),
      PARAMETER ( HH_AB_Add = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -0 ),
      PARAMETER ( HH_AB_Scale = 7500 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "B_13_13" "B_inserted_13"
  END CHILD
  HH_GATE "HH_inactivation_11_11"
    PARAMETERS
      PARAMETER ( POWER = 1 ),
      PARAMETER ( state_init = -1 ),
    END PARAMETERS
    CHILD "A_12_12" "A"
    END CHILD
    CHILD "B_13_13" "B"
    END CHILD
  END HH_GATE
  CHILD "HH_inactivation_11_11" "HH_inactivation_inserted_11"
  END CHILD
  CHANNEL "naf_7_7"
    BINDABLES
      INPUT Vm,
      OUTPUT G,
      OUTPUT I,
    END BINDABLES
    BINDINGS
      INPUT ..-&gt;Vm,
    END BINDINGS
    PARAMETERS
      PARAMETER ( G_MAX = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 0.000209239 ),
          ), ),
      PARAMETER ( Erev = 0.045 ),
    END PARAMETERS
    CHILD "HH_activation_8_8" "HH_activation"
    END CHILD
    CHILD "HH_inactivation_11_11" "HH_inactivation"
    END CHILD
  END CHANNEL
  CHILD "naf_7_7" "naf_inserted_7"
  END CHILD
  SEGMENT "c_6_6"
    BINDINGS
      INPUT naf-&gt;I,
    END BINDINGS
    PARAMETERS
      PARAMETER ( INJECT = 1e-09 ),
      PARAMETER ( ELEAK = -0.08 ),
      PARAMETER ( Vm_init = -0.068 ),
      PARAMETER ( DIA = 1 ),
      PARAMETER ( LENGTH = 1 ),
      PARAMETER ( RA = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 360502 ),
          ), ),
      PARAMETER ( RM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 3.58441e+08 ),
          ), ),
      PARAMETER ( CM = 
        GENESIS2
          (
              PARAMETER ( scale = 1 ),
              PARAMETER ( value = 4.57537e-11 ),
          ), ),
    END PARAMETERS
    CHILD "naf_7_7" "naf"
    END CHILD
  END SEGMENT
  CHILD "c_6_6" "c_inserted_6"
  END CHILD
  GROUP "n_5_5"
    CHILD "c_6_6" "c"
    END CHILD
  END GROUP
  CHILD "n_5_5" "n_inserted_5"
  END CHILD
END PRIVATE_MODELS
PUBLIC_MODELS
  CHILD "proto_3_3" "proto"
  END CHILD
  CHILD "output_4_4" "output"
  END CHILD
  CHILD "n_5_5" "n"
  END CHILD
END PUBLIC_MODELS

3.15. Can we save the NDF to a file?

1. Executed command	call model_container NEUROSPACES_COMMAND "export library ndf /tmp/conversion2.ndf /n/**"
2. Expected output

3.16. Can we create an output element (1)?

1. Executed command	create asc_file /out
2. Expected output

3.17. Can we initialize the output element (1)?

1. Executed command	setfield /out filename "/tmp/conversion2.txt" flush 1
2. Expected output

3.18. Can we connect the output element with the model?

1. Executed command	addmsg /n/c /out SAVE Vm
2. Expected output

3.19. Can we reset the simulation (1)?

1. Executed command	reset
2. Expected output

3.20. Can we set the options for the DUMP command (1)?

1. Executed command

setfield /neurospaces_integrator heccer_dump_selection { HECCER_DUMP_INDEXERS_SUMMARY + HECCER_DUMP_INDEXERS_STRUCTURE + HECCER_DUMP_INTERMEDIARY_COMPARTMENT_SUMMARY + HECCER_DUMP_INTERMEDIARY_MECHANISM_SUMMARY + HECCER_DUMP_INTERMEDIARY_STRUCTURE + HECCER_DUMP_INTERMEDIARY_SUMMARY + HECCER_DUMP_INTERMEDIARY_COMPARTMENTS_PARAMETERS + HECCER_DUMP_VM_COMPARTMENT_MATRIX + HECCER_DUMP_VM_COMPARTMENT_DATA + HECCER_DUMP_VM_COMPARTMENT_OPERATIONS + HECCER_DUMP_VM_CHANNEL_POOL_FLUXES + HECCER_DUMP_VM_MECHANISM_DATA + HECCER_DUMP_VM_MECHANISM_OPERATIONS + HECCER_DUMP_VM_SUMMARY }

2. Expected output

genesis

3.21. Can we dump the model from heccer (1)?

1. Executed command

call /neurospaces_integrator NSINTEGRATOR_DUMP

2. Expected output

Heccer (pcName) : (/n)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0)
Heccer (dStep) : (5e-05)
Intermediary (iCompartments) : (1)
Compartment (mc.iType) : (1)
Compartment (iParent) : (-1)
Compartment (dCm) : (4.57537e-11)
Compartment (dEm) : (-0.08)
Compartment (dInitVm) : (-0.068)
Compartment (dInject) : (1e-09)
Compartment (dRa) : (360502)
Compartment (dRm) : (3.58441e+08)
MinimumDegree (iEntries) : (1)
MinimumDegree (piChildren[0]) : (0)
MinimumDegree (piForward[0]) : (0)
MinimumDegree (piBackward[0]) : (0)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -2.23189e-10 1e-09 546404 1.00152
00001 :: INITIALIZECHANNEL 0.045 0.000209239
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 3 (nil)							 0.00778252
00004 :: CONCEPTGATE 1 1 (nil)							 0.265266
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00152)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)

3.22. Synchronize the simulator with the test specification

1. Executed command	echo "ready to go"
2. Expected output	ready to go

3.23. Can we run the simulation (1)?

1. Executed command	step 0.01 -time
2. Expected output	completed

3.24. Can we quit the simulator?

1. Executed command	quit
2. Expected output

3.25. Can we find the output, with sodium channel?

1. Expected output

application_output_file: /tmp/conversion2.txt
expected_output_file: ..//tests/specifications/strings/conversion2.txt

4. Converted single compartment run from ssp

Startup command : /usr/local/bin/ssp --time 0.01 --time-step 5e-5 --cell /tmp/conversion2.ndf --model-name n --output-fields /n/c->Vm --optimize --verbose --dump

Comments, Preparation, Reparation

1. Preparation needed before the commands below :	Create the output/ directory
2. And repared afterwards using :	Remove the generated output files in the output/ directory

4.1. Can we compile the converted model description from SSP ?

1. Expected output

Heccer (pcName) : (unnamed test)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0)
Heccer (dStep) : (5e-05)
Intermediary (iCompartments) : (1)
Compartment (mc.iType) : (1)
Compartment (iParent) : (-1)
Compartment (dCm) : (4.57537e-11)
Compartment (dEm) : (-0.08)
Compartment (dInitVm) : (-0.068)
Compartment (dInject) : (1e-09)
Compartment (dRa) : (360502)
Compartment (dRm) : (3.58441e+08)
MinimumDegree (iEntries) : (1)
MinimumDegree (piChildren[0]) : (0)
MinimumDegree (piForward[0]) : (0)
MinimumDegree (piBackward[0]) : (0)
Tables (iTabulatedGateCount) : (2)
Tabulated gate 0, interval (dStart) : (-0.1)
Tabulated gate 0, interval (dEnd) : (0.05)
Tabulated gate 0, interval (dStep) : (5e-05)
Tabulated gate 0, interpolation (iShape) : (0)
Tabulated gate 0, (iEntries) : (3000)
Tabulated gate 1, interval (dStart) : (-0.1)
Tabulated gate 1, interval (dEnd) : (0.05)
Tabulated gate 1, interval (dStep) : (5e-05)
Tabulated gate 1, interpolation (iShape) : (0)
Tabulated gate 1, (iEntries) : (3000)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -2.23189e-10 1e-09 546404 1.00152
00001 :: INITIALIZECHANNEL 0.045 0.000209239
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 3 (nil)							 0.00778252
00004 :: CONCEPTGATE 1 1 (nil)							 0.265266
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00152)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)

4.2. Does the simulation produce the correct output ?

1. Expected output

application_output_file: ..//output/n.out
expected_output_file: ..//tests/specifications/strings/conversion2-ssp.txt