Main Neurospaces logo neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo

Index of group ./specifications/structure

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internal data structures

1. Serial and parent context parsing
2. IO and treemodel structure correctness

1. Serial and parent context parsing

Startup command : ./neurospacesparse -v 1 -q legacy/networks/network-test.ndf

1.1. Is neurospaces startup successful ?

1. Part of expected output 
./neurospacesparse: No errors for .+?/legacy/networks/network-test.ndf.

1.2. Is the Golgi cell loaded in an appropriate namespace ?

1. Executed command
printinfo Golgi::G::Golgi/Golgi_soma
2. Part of expected output 
    Name, index (Golgi_soma,-1)
    Type (T_sym_segment)
    segmenName, index (Golgi_soma,-1)
        PARA  Name (ELEAK)
        PARA  Type (TYPE_PARA_FIELD), Value : ..->ELEAK
        PARA  Name (DIA)
        PARA  Type (TYPE_PARA_NUMBER), Value(3.000000e-05)
        PARA  Name (Vm_init)
        PARA  Type (TYPE_PARA_NUMBER), Value(-6.500000e-02)
        PARA  Name (RM)
        PARA  Type (TYPE_PARA_NUMBER), Value(3.030000e+00)
        PARA  Name (RA)
        PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
        PARA  Name (CM)
        PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e-02)
    segmen{-- begin HIER sections ---
        Name, index (spikegen,-1)
        Type (T_sym_attachment)
        attachName, index (spikegen,-1)
            PARA  Name (THRESHOLD)
            PARA  Type (TYPE_PARA_NUMBER), Value(2.000000e-02)
            PARA  Name (REFRACTORY)
            PARA  Type (TYPE_PARA_NUMBER), Value(2.000000e-03)
        attach{-- begin HIER sections ---
        attach}--  end  HIER sections ---
            attachName, index (SpikeGen,-1)
            attach{-- begin HIER sections ---
            attach}--  end  HIER sections ---
                attachName, index (SpikeGen,-1)
                attach{-- begin HIER sections ---
                attach}--  end  HIER sections ---
        Name, index (Ca_pool,-1)
        Type (T_sym_pool)
        pool  Name, index (Ca_pool,-1)
        pool  {-- begin HIER sections ---
        pool  }--  end  HIER sections ---
            pool  Name, index (Ca_concen,-1)
            pool  {-- begin HIER sections ---
            pool  }--  end  HIER sections ---
                pool  Name, index (Ca_concen,-1)
                pool  {-- begin HIER sections ---
                pool  }--  end  HIER sections ---
                    pool  Name, index (Ca_concen,-1)
                        PARA  Name (concen_init)
                        PARA  Type (TYPE_PARA_NUMBER), Value(7.550000e-05)
                        PARA  Name (BASE)
                        PARA  Type (TYPE_PARA_NUMBER), Value(7.550000e-05)
                        PARA  Name (TAU)
                        PARA  Type (TYPE_PARA_NUMBER), Value(2.000000e-01)
                        PARA  Name (VAL)
                        PARA  Type (TYPE_PARA_NUMBER), Value(2.000000e+00)
                        PARA  Name (DIA)
                        PARA  Type (TYPE_PARA_FIELD), Value : ..->DIA
                        PARA  Name (LENGTH)
                        PARA  Type (TYPE_PARA_FIELD), Value : ..->LENGTH
                        PARA  Name (THICK)
                        PARA  Type (TYPE_PARA_NUMBER), Value(6.000000e-07)
                        PARA  Name (BETA)
                        PARA  Type (TYPE_PARA_FUNCTION), Value(FIXED)
                            FUNC  Name (FIXED)
                                PARA  Name (value)
                                PARA  Type (TYPE_PARA_NUMBER), Value(2.023795e+10)
                                PARA  Name (scale)
                                PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    pool  {-- begin HIER sections ---
                    pool  }--  end  HIER sections ---
        Name, index (CaHVA,-1)
        Type (T_sym_channel)
        channeName, index (CaHVA,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_FIELD), Value : ../..->G_MAX
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_FUNCTION), Value(NERNST)
                FUNC  Name (NERNST)
                    PARA  Name (Cin)
                    PARA  Type (TYPE_PARA_FIELD), Value : ../Ca_pool->concen
                    PARA  Name (Cout)
                    PARA  Type (TYPE_PARA_NUMBER), Value(2.400000e+00)
                    PARA  Name (valency)
                    PARA  Type (TYPE_PARA_FIELD), Value : ../Ca_pool->VAL
                    PARA  Name (T)
                    PARA  Type (TYPE_PARA_NUMBER), Value(3.700000e+01)
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (CaHVA,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (CaHVA,-1)
                    PARA  Name (Xpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(2.000000e+00)
                    PARA  Name (Ypower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    PARA  Name (Zpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (H,-1)
        Type (T_sym_channel)
        channeName, index (H,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(1.714963e+00)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(-4.200000e-02)
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (H,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (H,-1)
                    PARA  Name (Xpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    PARA  Name (Ypower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                    PARA  Name (Zpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (InNa,-1)
        Type (T_sym_channel)
        channeName, index (InNa,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(4.001580e+02)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(5.500000e-02)
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (InNa,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (InNa,-1)
                    PARA  Name (Xpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(3.000000e+00)
                    PARA  Name (Ypower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    PARA  Name (Zpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (KA,-1)
        Type (T_sym_channel)
        channeName, index (KA,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(5.244928e+00)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(-9.000000e-02)
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (KA,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (KA,-1)
                    PARA  Name (Xpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(3.000000e+00)
                    PARA  Name (Ypower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    PARA  Name (Zpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (KDr,-1)
        Type (T_sym_channel)
        channeName, index (KDr,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(6.788394e+01)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(-9.000000e-02)
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (KDr,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (KDr,-1)
                    PARA  Name (Xpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(4.000000e+00)
                    PARA  Name (Ypower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    PARA  Name (Zpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (Moczyd_KC,-1)
        Type (T_sym_channel)
        channeName, index (Moczyd_KC,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(5.716543e+00)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(-9.000000e-02)
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (Moczyd_KC,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (Moczyd_KC,-1)
                    PARA  Name (Xindex)
                    PARA  Type (TYPE_PARA_NUMBER), Value(-1.000000e+00)
                    PARA  Name (Xpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(1.000000e+00)
                    PARA  Name (Ypower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                    PARA  Name (Zpower)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (mf_AMPA,-1)
        Type (T_sym_channel)
        channeName, index (mf_AMPA,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(3.577338e-01)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
            PARA  Name (NORMALIZE)
            PARA  Type (TYPE_PARA_FUNCTION), Value(SUM)
                FUNC  Name (SUM)
                    PARA  Name (COUNT)
                    PARA  Type (TYPE_PARA_SYMBOLIC), Value : synapse
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (AMPA,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (AMPA,-1)
                    PARA  Name (G_MAX)
                    PARA  Type (TYPE_PARA_NUMBER), Value(3.577338e-01)
                    PARA  Name (Erev)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                    Name, index (synapse,-1)
                    Type (T_sym_attachment)
                    attachName, index (synapse,-1)
                    attach{-- begin HIER sections ---
                    attach}--  end  HIER sections ---
                        attachName, index (Synapse,-1)
                        attach{-- begin HIER sections ---
                        attach}--  end  HIER sections ---
                            attachName, index (Synapse,-1)
                                PARA  Name (weight)
                                PARA  Type (TYPE_PARA_ATTRIBUTE), 
                                PARA  Name (delay)
                                PARA  Type (TYPE_PARA_ATTRIBUTE), 
                            attach{-- begin HIER sections ---
                            attach}--  end  HIER sections ---
                    Name, index (exp2,-1)
                    Type (T_sym_equation_exponential)
                    equatiName, index (exp2,-1)
                        PARA  Name (TAU1)
                        PARA  Type (TYPE_PARA_NUMBER), Value(1.500000e-03)
                        PARA  Name (TAU2)
                        PARA  Type (TYPE_PARA_NUMBER), Value(9.000000e-05)
                    equati{-- begin HIER sections ---
                    equati}--  end  HIER sections ---
                channe}--  end  HIER sections ---
        Name, index (pf_AMPA,-1)
        Type (T_sym_channel)
        channeName, index (pf_AMPA,-1)
            PARA  Name (G_MAX)
            PARA  Type (TYPE_PARA_NUMBER), Value(3.577338e-01)
            PARA  Name (Erev)
            PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
            PARA  Name (NORMALIZE)
            PARA  Type (TYPE_PARA_FUNCTION), Value(SUM)
                FUNC  Name (SUM)
                    PARA  Name (COUNT)
                    PARA  Type (TYPE_PARA_SYMBOLIC), Value : synapse
        channe{-- begin HIER sections ---
        channe}--  end  HIER sections ---
            channeName, index (AMPA,-1)
            channe{-- begin HIER sections ---
            channe}--  end  HIER sections ---
                channeName, index (AMPA,-1)
                    PARA  Name (G_MAX)
                    PARA  Type (TYPE_PARA_NUMBER), Value(3.577338e-01)
                    PARA  Name (Erev)
                    PARA  Type (TYPE_PARA_NUMBER), Value(0.000000e+00)
                channe{-- begin HIER sections ---
                    Name, index (synapse,-1)
                    Type (T_sym_attachment)
                    attachName, index (synapse,-1)
                    attach{-- begin HIER sections ---
                    attach}--  end  HIER sections ---
                        attachName, index (Synapse,-1)
                        attach{-- begin HIER sections ---
                        attach}--  end  HIER sections ---
                            attachName, index (Synapse,-1)
                                PARA  Name (weight)
                                PARA  Type (TYPE_PARA_ATTRIBUTE), 
                                PARA  Name (delay)
                                PARA  Type (TYPE_PARA_ATTRIBUTE), 
                            attach{-- begin HIER sections ---
                            attach}--  end  HIER sections ---
                    Name, index (exp2,-1)
                    Type (T_sym_equation_exponential)
                    equatiName, index (exp2,-1)
                        PARA  Name (TAU1)
                        PARA  Type (TYPE_PARA_NUMBER), Value(1.500000e-03)
                        PARA  Name (TAU2)
                        PARA  Type (TYPE_PARA_NUMBER), Value(9.000000e-05)
                    equati{-- begin HIER sections ---
                    equati}--  end  HIER sections ---
                channe}--  end  HIER sections ---
    segmen}--  end  HIER sections ---

1.3. What is the treespaces ID of a synaptic channel on a spine of the second Purkinje cell ?

1. Executed command
serialID /CerebellarCortex/Purkinjes/1 /CerebellarCortex/Purkinjes/1/segments/b3s46[15]/Purkinje_spine_0/head/par
2. Part of expected output 
serial ID = 25523

1.4. What is the serial mapping for the fifth Purkine cell ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes/5
2. Part of expected output 
Traversal serial ID = 265341
Principal serial ID = 265341 of 439542 Principal successors

1.5. What is the serial mapping for the fifth Purkine cell when referenced with a parent reference ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes/5/segments/..
2. Part of expected output 
Traversal serial ID = 265341
Principal serial ID = 265341 of 439542 Principal successors

1.6. What is the serial mapping for the fifth Purkine cell segments ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes/5/segments
2. Part of expected output 
Traversal serial ID = 265343
Principal serial ID = 265343 of 439542 Principal successors

1.7. What is the serial mapping for the fifth Purkine cell segments when referenced using a parent reference ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes/5/segments/../segments
2. Part of expected output 
Traversal serial ID = 265343
Principal serial ID = 265343 of 439542 Principal successors

1.8. What is the serial mapping for the fifth Purkine cell when referenced using two parent references ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes/5/segments/soma/../..
2. Part of expected output 
Traversal serial ID = 265341
Principal serial ID = 265341 of 439542 Principal successors

1.9. Do we get an error if we try to reference a symbol that does not exist using parent references ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes/5/segments/soma/../../soma
2. Part of expected output 
symbol not found

1.10. What is the serial mapping for a symbol that does exist using parent references, yet with one intermediate reference to a symbol that does not exist ?

1. Executed command
serialMapping /CerebellarCortex/a_non_existent_population/../Purkinjes/5
2. Part of expected output 
Traversal serial ID = 265341
Principal serial ID = 265341 of 439542 Principal successors

1.11. What is the serial mapping for a symbol that does exist using parent references, yet with intermediate references to symbols that do not exist ?

1. Executed command
serialMapping /a_non_existent_network/a_non_existent_population/../../CerebellarCortex/Purkinjes/5
2. Part of expected output 
Traversal serial ID = 265341
Principal serial ID = 265341 of 439542 Principal successors
3. Comment
this behaviour is undefined, but tested

1.12. What is the serial mapping for a symbol that does exist using parent references, yet with intermediate references to symbols that do not exist and using the root namespace operator ?

1. Executed command
serialMapping ::/a_non_existent_network/a_non_existent_population/../../CerebellarCortex/Purkinjes/5
2. Part of expected output 
symbol is not an ancestor
3. Comment
this behaviour is undefined, but tested

2. IO and treemodel structure correctness

Startup command : ./neurospacesparse -v 1 -q legacy/networks/network-test.ndf

2.1. Is neurospaces startup successful ?

1. Part of expected output 
./neurospacesparse: No errors for .+?/legacy/networks/network-test.ndf.

2.2. Describe the children of the soma of the first granule cell.

1. Executed command
childreninfo /CerebellarCortex/Granules/0/Granule_soma
2. Part of expected output 
children (if any) :
Child 0 : spikegen,T_sym_attachment
Child 1 : InNa,T_sym_channel
Child 2 : Ca_pool,T_sym_pool
Child 3 : CaHVA,T_sym_channel
Child 4 : H,T_sym_channel
Child 5 : KA,T_sym_channel
Child 6 : KDr,T_sym_channel
Child 7 : Moczyd_KC,T_sym_channel
Child 8 : mf_AMPA,T_sym_channel
Child 9 : mf_NMDA,T_sym_channel
Child 10 : GABAA,T_sym_channel
Child 11 : GABAB,T_sym_channel
inputs (if any) :
Input 0 : CaHVA/I,T_sym_channel
Input 1 : H/I,T_sym_channel
Input 2 : InNa/I,T_sym_channel
Input 3 : KA/I,T_sym_channel
Input 4 : KDr/I,T_sym_channel
Input 5 : mf_NMDA/I,T_sym_channel
Input 6 : mf_AMPA/I,T_sym_channel
Input 7 : GABAA/I,T_sym_channel
Input 8 : GABAB/I,T_sym_channel

2.3. Describe the children of the soma of the first Purkinje cell.

1. Executed command
childreninfo /CerebellarCortex/Purkinjes/0/segments/soma
2. Part of expected output 
children (if any) :
inputs (if any) :

2.4. Describe the children of the cerebellar cortex network.

1. Executed command
childreninfo /CerebellarCortex
2. Part of expected output 
children (if any) :
Child 0 : BackwardProjectionA_algorithm,T_sym_algorithm
Child 1 : BackwardProjectionB_algorithm,T_sym_algorithm
Child 2 : ForwardProjection_algorithm,T_sym_algorithm
Child 3 : Mossies2Golgis_algorithm,T_sym_algorithm
Child 4 : Mossies2Granules_NMDA_algorithm,T_sym_algorithm
Child 5 : Mossies2Granules_AMPA_algorithm,T_sym_algorithm
Child 6 : Granules2Golgis_algorithm,T_sym_algorithm
Child 7 : Golgis2Granules_GABAA_algorithm,T_sym_algorithm
Child 8 : Golgis2Granules_GABAB_algorithm,T_sym_algorithm
Child 9 : MossyFibers,T_sym_population
Child 10 : Granules,T_sym_population
Child 11 : Golgis,T_sym_population
Child 12 : Purkinjes,T_sym_population
Child 13 : MossyFiberProjection,T_sym_projection
Child 14 : ForwardProjection,T_sym_projection
Child 15 : BackwardProjection,T_sym_projection
Child 16 : ParallelFiberProjection,T_sym_projection
inputs (if any) :

2.5. Describe the root namespaces, default arguments.

1. Executed command
namespaces
2. Part of expected output 
File (/tmp/neurospaces/test/models/fibers/mossyfiber.ndf) --> Namespace (Fibers::)
File (/tmp/neurospaces/test/models/legacy/populations/golgi.ndf) --> Namespace (Golgi::)
File (/tmp/neurospaces/test/models/legacy/populations/granule.ndf) --> Namespace (Granule::)
File (/tmp/neurospaces/test/models/legacy/populations/purkinje.ndf) --> Namespace (Purkinje::)

2.6. Describe the root namespaces, namespace explicitly given.

1. Executed command
namespaces ::
2. Part of expected output 
File (/tmp/neurospaces/test/models/fibers/mossyfiber.ndf) --> Namespace (Fibers::)
File (/tmp/neurospaces/test/models/legacy/populations/golgi.ndf) --> Namespace (Golgi::)
File (/tmp/neurospaces/test/models/legacy/populations/granule.ndf) --> Namespace (Granule::)
File (/tmp/neurospaces/test/models/legacy/populations/purkinje.ndf) --> Namespace (Purkinje::)

2.7. Describe the root namespaces, root explicitly given.

1. Executed command
namespaces ::/
2. Part of expected output 
File (/tmp/neurospaces/test/models/fibers/mossyfiber.ndf) --> Namespace (Fibers::)
File (/tmp/neurospaces/test/models/legacy/populations/golgi.ndf) --> Namespace (Golgi::)
File (/tmp/neurospaces/test/models/legacy/populations/granule.ndf) --> Namespace (Granule::)
File (/tmp/neurospaces/test/models/legacy/populations/purkinje.ndf) --> Namespace (Purkinje::)

2.8. What are the forestspace IDs for the spine neck ?

1. Executed command
serialMapping /CerebellarCortex/Purkinjes /CerebellarCortex/Purkinjes/0/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output 
Traversal serial ID = 1141
Principal serial ID = 1141 of 153157 Principal successors