neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo| 1. The help command line option |
| 2. The help command and its topics |
| 3. List commands |
| 4. Backward compatibility list commands |
| 1. Expected output |
GENESIS 3 shell.
options:
--batch-mode batch mode, means that interactive mode is disabled.
--execute execute this string, may be given multiple times.
--help print usage information.
--output-tags Adds XML-like tags to diagnostic messages.
--verbose set verbosity level ('errors', 'warnings', 'information', 'debug', default is 'warnings').
--version give version information.
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| 1. Expected output | GENESIS 3 shell |
| 1. Executed command | help |
| 2. Expected output | synopsis: help <topic> synopsis: <topic> must be one of commands, components, documentation, variables, libraries |
| 1. Executed command | help command |
| 2. Expected output | description: help on a specific command synopsis: 'help command <command_name>' all commands: |
| 1. Executed command | help command output_add |
| 2. Expected output | description: add a variable to the output file. synopsis: output_add <element_name> <field_name> |
| 1. Executed command | help component |
| 2. Expected output | description: help on a specific software component synopsis: 'help component <component_name>' Core components: |
| 1. Executed command | help component ssp |
| 2. Expected output |
description: simple scheduler in perl
usage: |-
The simple scheduler in perl binds together software components for
running simulations. It is based on services and solvers: services
provide functionality to assist the solvers to construct an
efficient simulation run-time environment, solvers apply algorithms
to solve the problem posed, numerically or otherwise.
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| 1. Expected output | GENESIS 3 shell |
| 1. Executed command | list |
| 2. Expected output | synopsis: list <type> synopsis: <type> must be one of commands, components, documentation, functions, inputclass_templates, inputclasses, physical, section, structure, verbose synopsis: (you gave ) |
| 1. Executed command | list commands |
| 2. Expected output | all commands: - ce - check - chemesis3_set_timestep - component_load - create - delete - echo - exit - explore - heccer_set_timestep - help - input_add - input_delete - input_show - inputbinding_add - inputclass_add - inputclass_delete - inputclass_show - inputclass_template_show - library_show - list - list_elements - model_parameter_add - model_parameter_show - model_state_load - model_state_save - morphology_list_spine_heads - morphology_summarize - ndf_load - ndf_save - npl_load - npy_load - output_add - output_filename - output_format - output_mode - output_resolution - output_show - parameter_scaled_show - parameter_show - pwe - py_diagnose - pynn_load - querymachine - quit - reset - run - runtime_parameter_add - runtime_parameter_delete - runtime_parameters_show - set_verbose - sh - show_global_time - show_verbose - sli_listcommands - sli_listobjects - sli_load - sli_printcommandlist - sli_run - sli_script - ssp_load - ssp_save - swc_load - tabulate - xml_load - xml_save |
| 1. Executed command | list components |
| 2. Expected output |
Core components:
chemesis3:
description: biochemical pathway solver
disabled: 'experimental, working on it'
module: Chemesis3
status: 'disabled (experimental, working on it)'
type:
description: simulation object
layer: 1
exchange:
description: NeuroML and NineML exchange
disabled: immature and by default not loaded
integrator: Neurospaces::Exchange::Commands
module: Neurospaces::Exchange
status: disabled (immature and by default not loaded)
type:
description: 'intermediary, model-container interface'
layer: 2
experiment:
description: Simulation objects implementing experiments
disabled: immature and by default not loaded
module: Experiment
status: disabled (immature and by default not loaded)
type:
description: simulation objects for I/O
layer: 1
gshell:
description: the GENESIS 3 shell allows convenient interaction with other components
disabled: 0
module: GENESIS3
status: loaded
type:
description: scriptable user interface
layer: 3
heccer:
description: single neuron equation solver
module: Heccer
status: loaded
type:
description: simulation object
layer: 1
model-container:
description: internal storage for neuronal models
integrator: Neurospaces::Integrators::Commands
module: Neurospaces
status: loaded
type:
description: intermediary
layer: 2
sli:
description: GENESIS 2 backward compatible scripting interface
integrator: SLI::Integrators::Commands
module: SLI
status: loaded
type:
description: scriptable user interface
layer: 2
ssp:
description: binds the software components of a simulation together
integrator: SSP::Integrators::Commands
module: SSP
status: loaded
type:
description: simulation controller
layer: 1
studio:
description: Graphical interface that allows to explore models
disabled: "the Neurospaces studio is an experimental feature, try loading it with the 'component_load' command"
module: Neurospaces::Studio
status: "disabled (the Neurospaces studio is an experimental feature, try loading it with the 'component_load' command)"
type:
description: graphical user interface
layer: 4
Other components:
python:
description: interface to python scripting
module: GENESIS3::Python
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| 1. Executed command | list functions |
| 2. Expected output | NERNST |
| 1. Executed command | list physical |
| 2. Expected output | all physical tokens: - ALGORITHM - ATTACHMENT - AXON_HILLOCK - CELL - CHANNEL - CONCENTRATION_GATE_KINETIC - CONNECTION - CONNECTION_GROUP - CONTOUR_GROUP - CONTOUR_POINT - EM_CONTOUR - EQUATION_EXPONENTIAL - FIBER - GATE_KINETIC - GROUP - GROUPED_PARAMETERS - HH_GATE - IZHIKEVICH - KINETICS - NETWORK - NEURON - POOL - POPULATION - PROJECTION - PULSE_GEN - RANDOMVALUE - REACTION - SEGMENT - SEGMENT_GROUP |
| 1. Executed command | list section |
| 2. Expected output | all section tokens: - IMPORT - PRIVATE_MODELS - PUBLIC_MODELS |
| 1. Expected output | GENESIS 3 shell |
| 1. Executed command | sli_listcommands |
| 2. Expected output | Available commands: abort abs acos addaction addalias addclass addescape addfield addforwmsg addglobal addjob addmsg addmsgdef addobject addtask argc arglist argv asin atan call cd ce check chr clearerrors closefile copy cos countchar countelementlist cpu create createmap debug debugfunc delete deleteaction deleteall deleteclass deletefield deleteforwmsg deletejob deletemsg deletemsgdef deletetasks disable echo el enable enddump eof error exists exit exp findchar findsolvefield floatformat flushfile gaussian gctrace getarg getclock getdate getdefault getelementlist getenv getfield getfieldnames getglobal getmsg getpath getstat gftrace h help initdump input isa le listactions listclasses listcommands listescape listfiles listglobals listobjects log logfile max maxerrors maxwarnings min mkdir move msgsubstitute notes objsubstitute openfile pope position pow printargs printenv pushe putevent pwe quit rand randseed readcell readfile reclaim resched reset restore round save set_nsintegrator_verbose_level setclock setdefault setenv setfield setfieldprot setglobal setmethod setpriority setprompt setrand setupalpha sh showclocks showcommand showfield showjobs showmsg showobject showsched showstat silent simdump simobjdump simundump sin sqrt stack step stop strcat strcmp strlen strncmp strsub substituteinfo substring swapdump tan trunc tset tweakalpha tweaktau useclock version volumeconnect warning where writefile |
| 1. Executed command | sli_listobjects |
| 2. Expected output | AVAILABLE OBJECTS: asc_file hsolve neurospaces neutral nsintegrator |