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

Index of group ./specifications/algorithms

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algorithms

1. Network model : algorithm instantiation and reporting.

1. Network model : algorithm instantiation and reporting.

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. How many granule cells do we have ?

1. Executed command
cellcount /CerebellarCortex/Granules
2. Part of expected output 
Number of cells : 6240

1.3. How many compartments do the granule cells have in total ?

1. Executed command
segmentcount /CerebellarCortex/Granules
2. Part of expected output 
Number of segments : 6240

1.4. How does neurospaces react if we try to access parameters that are not defined ?

1. Executed command
printparameter /CerebellarCortex/Golgis/0/Golgi_soma/KDr Emax
2. Part of expected output 
parameter not found in symbol

1.5. What do the algorithm classes and instances report of what they have done, ConnectionCheckerClass ?

1. Executed command
algorithmclass ConnectionChecker
2. Part of expected output 
---
name: ConnectionCheckerClass
report:
    number_of_created_instances: 3

1.6. What do the algorithm classes and instances report of what they have done, RandomizeClass ?

1. Executed command
algorithmclass Randomize
2. Part of expected output 
---
name: RandomizeClass
report:
    number_of_created_instances: 2

1.7. What do the algorithm classes and instances report of what they have done, SpinesClass ?

1. Executed command
algorithmclass Spines
2. Part of expected output 
---
name: SpinesClass
report:
    number_of_created_instances: 1

1.8. What do the algorithm classes and instances report of what they have done, ProjectionRandomizedClass ?

1. Executed command
algorithmclass ProjectionRandomized
2. Part of expected output 
---
name: ProjectionRandomizedClass
report:
    number_of_created_instances: 0

1.9. What do the algorithm classes and instances report of what they have done, ProjectionVolumeClass ?

1. Executed command
algorithmclass ProjectionVolume
2. Part of expected output 
---
name: ProjectionVolumeClass
report:
    number_of_created_instances: 6

1.10. What do the algorithm classes and instances report of what they have done, Grid3DClass ?

1. Executed command
algorithmclass Grid3D
2. Part of expected output 
---
name: Grid3DClass
report:
    number_of_created_instances: 4

1.11. What do the algorithm classes and instances report of what they have done, DendrogramClass ?

1. Executed command
algorithmclass Dendrogram
2. Part of expected output 
---
name: DendrogramClass
report:
    number_of_created_instances: 0

1.12. What do the algorithm classes and instances report of what they have done, Golgis2Granules_GABAB ?

1. Executed command
algorithminstance Golgis2Granules_GABAB
2. Part of expected output 
---
name: ProjectionVolumeInstance Golgis2Granules_GABAB_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 6240
    number_of_tries_adding_connections: 6240
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: GABAB
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: GABAB
    ProjectionVolumeInstance_weight: 9.000000

1.13. What do the algorithm classes and instances report of what they have done, Golgis2Granules_GABAA ?

1. Executed command
algorithminstance Golgis2Granules_GABAA
2. Part of expected output 
---
name: ProjectionVolumeInstance Golgis2Granules_GABAA_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 6240
    number_of_tries_adding_connections: 6240
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: GABAA
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: GABAA
    ProjectionVolumeInstance_weight: 45.000000

1.14. What do the algorithm classes and instances report of what they have done, Granules2Golgis ?

1. Executed command
algorithminstance Granules2Golgis
2. Part of expected output 
---
name: ProjectionVolumeInstance Granules2Golgis_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 98112
    number_of_tries_adding_connections: 98112
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: ForwardProjection
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: pf_AMPA
    ProjectionVolumeInstance_weight: 45.000000

1.15. What do the algorithm classes and instances report of what they have done, Mossies2Granules_AMPA ?

1. Executed command
algorithminstance Mossies2Granules_AMPA
2. Part of expected output 
---
name: ProjectionVolumeInstance Mossies2Granules_AMPA_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 18734
    number_of_tries_adding_connections: 18734
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: AMPA
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 0.306100
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: mf_AMPA
    ProjectionVolumeInstance_weight: 6.000000

1.16. What do the algorithm classes and instances report of what they have done, Mossies2Granules_NMDA ?

1. Executed command
algorithminstance Mossies2Granules_NMDA
2. Part of expected output 
---
name: ProjectionVolumeInstance Mossies2Granules_NMDA_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 18734
    number_of_tries_adding_connections: 18734
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: NMDA
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 0.306100
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: mf_NMDA
    ProjectionVolumeInstance_weight: 4.000000

1.17. What do the algorithm classes and instances report of what they have done, Mossies2Golgis ?

1. Executed command
algorithminstance Mossies2Golgis
2. Part of expected output 
---
name: ProjectionVolumeInstance Mossies2Golgis_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 600
    number_of_tries_adding_connections: 600
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: GolgiComponent
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: mf_AMPA
    ProjectionVolumeInstance_weight: 0.000000

1.18. What do the algorithm classes and instances report of what they have done, ForwardProjection ?

1. Executed command
algorithminstance ForwardProjection
2. Part of expected output 
---
name: ConnectionCheckerInstance ForwardProjection_algorithm
report:
    number_of_checked_connection_groups: 0
    number_of_checked_connections: 98112
    average_weight: 45.000000
    average_delay: 0.001967
    ConnectionCheckerInstance_network: CerebellarCortex
    ConnectionCheckerInstance_projection: ForwardProjection

1.19. What do the algorithm classes and instances report of what they have done, BackwardProjectionB ?

1. Executed command
algorithminstance BackwardProjectionB
2. Part of expected output 
---
name: ConnectionCheckerInstance BackwardProjectionB_algorithm
report:
    number_of_checked_connection_groups: 0
    number_of_checked_connections: 6240
    average_weight: 9.000000
    average_delay: 0.000000
    ConnectionCheckerInstance_network: CerebellarCortex
    ConnectionCheckerInstance_projection: GABAB

1.20. What do the algorithm classes and instances report of what they have done, BackwardProjectionA ?

1. Executed command
algorithminstance BackwardProjectionA
2. Part of expected output 
---
name: ConnectionCheckerInstance BackwardProjectionA_algorithm
report:
    number_of_checked_connection_groups: 0
    number_of_checked_connections: 6240
    average_weight: 45.000000
    average_delay: 0.000000
    ConnectionCheckerInstance_network: CerebellarCortex
    ConnectionCheckerInstance_projection: GABAA

1.21. What do the algorithm classes and instances report of what they have done, PurkinjeGrid ?

1. Executed command
algorithminstance PurkinjeGrid
2. Part of expected output 
---
name: Grid3DInstance PurkinjeGrid
report:
    number_of_created_components: 6
    Grid3DInstance_prototype: Purkinje_cell
    Grid3DInstance_options: 3 0.000100 2 0.000200 1 0.900000

1.22. What do the algorithm classes and instances report of what they have done, SpinesNormal_13_1 ?

1. Executed command
algorithminstance SpinesNormal_13_1
2. Part of expected output 
---
name: SpinesInstance SpinesNormal_13_1
report:
    number_of_added_spines: 1474
    number_of_virtual_spines: 142982.466417
    number_of_spiny_segments: 1474
    number_of_failures_adding_spines: 0
    SpinesInstance_prototype: Purkinje_spine
    SpinesInstance_surface: 1.33079e-12

1.23. What do the algorithm classes and instances report of what they have done, GranuleGrid ?

1. Executed command
algorithminstance GranuleGrid
2. Part of expected output 
---
name: Grid3DInstance GranuleGrid
report:
    number_of_created_components: 6240
    Grid3DInstance_prototype: Granule_cell
    Grid3DInstance_options: 120 0.000025 26 0.000019 2 0.000020

1.24. What do the algorithm classes and instances report of what they have done, GolgiGrid ?

1. Executed command
algorithminstance GolgiGrid
2. Part of expected output 
---
name: Grid3DInstance GolgiGrid
report:
    number_of_created_components: 20
    Grid3DInstance_prototype: Golgi_cell
    Grid3DInstance_options: 10 0.000300 2 0.000300 1 0.000040

1.25. What do the algorithm classes and instances report of what they have done, Golgi_CaHVA ?

1. Executed command
algorithminstance Golgi_CaHVA
2. Part of expected output 
---
name: RandomizeInstance Golgi_CaHVA
report:
    number_of_randomized_components: 20
    number_of_non-randomized_components_algorithm_symbols: 3
    number_of_non-randomized_components_unexpected: 0
    RandomizeInstance_prototype: CaHVA
    RandomizeInstance_options: Golgi_cell->G_MAX 213.000000 8.317569 9.317569

1.26. What do the algorithm classes and instances report of what they have done, GolgiLeak ?

1. Executed command
algorithminstance GolgiLeak
2. Part of expected output 
---
name: RandomizeInstance GolgiLeak
report:
    number_of_randomized_components: 20
    number_of_non-randomized_components_algorithm_symbols: 3
    number_of_non-randomized_components_unexpected: 0
    RandomizeInstance_prototype: Golgi_soma
    RandomizeInstance_options: Golgi_cell->ELEAK 213.000000 -0.060000 -0.050000

1.27. What do the algorithm classes and instances report of what they have done, MossyGrid ?

1. Executed command
algorithminstance MossyGrid
2. Part of expected output 
---
name: Grid3DInstance MossyGrid
report:
    number_of_created_components: 30
    Grid3DInstance_prototype: MossyFiber
    Grid3DInstance_options: 10 0.000360 3 0.000300 1 0.900000

1.28. What do the algorithm classes and instances report of what they have done ?

1. Executed command
algorithmset
2. Part of expected output 
---
number_of_algorithm_classes: 8
---
name: ConnectionCheckerClass
report:
    number_of_created_instances: 3
---
name: RandomizeClass
report:
    number_of_created_instances: 2
---
name: SpinesClass
report:
    number_of_created_instances: 1
---
name: ProjectionRandomizedClass
report:
    number_of_created_instances: 0
---
name: ProjectionVolumeClass
report:
    number_of_created_instances: 6
---
name: InserterClass
report:
    number_of_created_instances: 0
---
name: Grid3DClass
report:
    number_of_created_instances: 4
---
name: DendrogramClass
report:
    number_of_created_instances: 0
---
number_of_algorithm_instances: 16
---
name: ProjectionVolumeInstance Golgis2Granules_GABAB_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 6240
    number_of_tries_adding_connections: 6240
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: GABAB
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: GABAB
    ProjectionVolumeInstance_weight: 9.000000
---
name: ProjectionVolumeInstance Golgis2Granules_GABAA_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 6240
    number_of_tries_adding_connections: 6240
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: GABAA
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: GABAA
    ProjectionVolumeInstance_weight: 45.000000
---
name: ProjectionVolumeInstance Granules2Golgis_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 98112
    number_of_tries_adding_connections: 98112
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: ForwardProjection
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: pf_AMPA
    ProjectionVolumeInstance_weight: 45.000000
---
name: ProjectionVolumeInstance Mossies2Granules_AMPA_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 18734
    number_of_tries_adding_connections: 18734
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: AMPA
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 0.306100
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: mf_AMPA
    ProjectionVolumeInstance_weight: 6.000000
---
name: ProjectionVolumeInstance Mossies2Granules_NMDA_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 18734
    number_of_tries_adding_connections: 18734
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: NMDA
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 0.306100
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: mf_NMDA
    ProjectionVolumeInstance_weight: 4.000000
---
name: ProjectionVolumeInstance Mossies2Golgis_algorithm
report:
    number_of_added_connection_groups: 1
    number_of_added_connections: 600
    number_of_tries_adding_connections: 600
    number_of_failures_adding_connections: 0
    number_of_failures_generator_coordinates: 0
    number_of_failures_receiver_coordinates: 0
    ProjectionVolumeInstance_network: CerebellarCortex
    ProjectionVolumeInstance_projection: GolgiComponent
    ProjectionVolumeInstance_randomseed: 1212.000000
    ProjectionVolumeInstance_probability: 1.000000
    ProjectionVolumeInstance_pre: spikegen
    ProjectionVolumeInstance_post: mf_AMPA
    ProjectionVolumeInstance_weight: 0.000000
---
name: ConnectionCheckerInstance ForwardProjection_algorithm
report:
    number_of_checked_connection_groups: 0
    number_of_checked_connections: 98112
    average_weight: 45.000000
    average_delay: 0.001967
    ConnectionCheckerInstance_network: CerebellarCortex
    ConnectionCheckerInstance_projection: ForwardProjection
---
name: ConnectionCheckerInstance BackwardProjectionB_algorithm
report:
    number_of_checked_connection_groups: 0
    number_of_checked_connections: 6240
    average_weight: 9.000000
    average_delay: 0.000000
    ConnectionCheckerInstance_network: CerebellarCortex
    ConnectionCheckerInstance_projection: GABAB
---
name: ConnectionCheckerInstance BackwardProjectionA_algorithm
report:
    number_of_checked_connection_groups: 0
    number_of_checked_connections: 6240
    average_weight: 45.000000
    average_delay: 0.000000
    ConnectionCheckerInstance_network: CerebellarCortex
    ConnectionCheckerInstance_projection: GABAA
---
name: Grid3DInstance PurkinjeGrid
report:
    number_of_created_components: 6
    Grid3DInstance_prototype: Purkinje_cell
    Grid3DInstance_options: 3 0.000100 2 0.000200 1 0.900000
---
name: SpinesInstance SpinesNormal_13_1
report:
    number_of_added_spines: 1474
    number_of_virtual_spines: 142982.466417
    number_of_spiny_segments: 1474
    number_of_failures_adding_spines: 0
    SpinesInstance_prototype: Purkinje_spine
    SpinesInstance_surface: 1.33079e-12
---
name: Grid3DInstance GranuleGrid
report:
    number_of_created_components: 6240
    Grid3DInstance_prototype: Granule_cell
    Grid3DInstance_options: 120 0.000025 26 0.000019 2 0.000020
---
name: Grid3DInstance GolgiGrid
report:
    number_of_created_components: 20
    Grid3DInstance_prototype: Golgi_cell
    Grid3DInstance_options: 10 0.000300 2 0.000300 1 0.000040
---
name: RandomizeInstance Golgi_CaHVA
report:
    number_of_randomized_components: 20
    number_of_non-randomized_components_algorithm_symbols: 3
    number_of_non-randomized_components_unexpected: 0
    RandomizeInstance_prototype: CaHVA
    RandomizeInstance_options: Golgi_cell->G_MAX 213.000000 8.317569 9.317569
---
name: RandomizeInstance GolgiLeak
report:
    number_of_randomized_components: 20
    number_of_non-randomized_components_algorithm_symbols: 3
    number_of_non-randomized_components_unexpected: 0
    RandomizeInstance_prototype: Golgi_soma
    RandomizeInstance_options: Golgi_cell->ELEAK 213.000000 -0.060000 -0.050000
---
name: Grid3DInstance MossyGrid
report:
    number_of_created_components: 30
    Grid3DInstance_prototype: MossyFiber
    Grid3DInstance_options: 10 0.000360 3 0.000300 1 0.900000