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

Index of group ./specifications/xml

Index
Up

importing and processing of a model encoded in xml

1. Import and export of a model in xml

Startup command : bin/genesis-g3

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

1.1. Is startup successful ?

1. Expected output

Welcome to the GENESIS 3 shell

1.2. Can we load a xml model ?

1. Executed command	xml_load channels/gaba.xml
2. Expected output	genesis

1.3. Can we export the model to an NDF file ?

1. Executed command	ndf_save /** /tmp/1.ndf
2. Expected output	genesis

1.4. Does the exported NDF file contain the correct model ?

1. Expected output

application_output_file: /tmp/1.ndf
#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

PRIVATE_MODELS
  ATTACHMENT "Synapse_7_7"
    BINDABLES
      INPUT spike,
      OUTPUT activation,
    END BINDABLES
    ATTRIBUTES       weight,       delay, END ATTRIBUTES
  END ATTACHMENT
  CHILD "Synapse_7_7" "Synapse_7_8"
  END CHILD
  CHILD "Synapse_7_8" "synapse_7_10"
  END CHILD
  CHILD "synapse_7_10" "synapse_inserted_10"
  END CHILD
  EQUATION_EXPONENTIAL "exp2_11_11"
    BINDABLES
      INPUT activation,
      OUTPUT G,
    END BINDABLES
    BINDINGS
      INPUT ../synapse-&gt;activation,
    END BINDINGS
    PARAMETERS
      PARAMETER ( TAU1 = 0.00093 ),
      PARAMETER ( TAU2 = 0.0265 ),
    END PARAMETERS
  END EQUATION_EXPONENTIAL
  CHILD "exp2_11_11" "exp2_inserted_11"
  END CHILD
  CHANNEL "Purk_GABA_9_9"
    BINDABLES
      INPUT Vm,
      OUTPUT I,
    END BINDABLES
    PARAMETERS
      PARAMETER ( G_MAX = 1.077 ),
      PARAMETER ( Erev = -0.08 ),
    END PARAMETERS
    CHILD "synapse_inserted_10" "synapse"
    END CHILD
    CHILD "exp2_11_11" "exp2"
    END CHILD
  END CHANNEL
  CHILD "Purk_GABA_9_9" "Purk_GABA_inserted_9"
  END CHILD
END PRIVATE_MODELS
PUBLIC_MODELS
  CHILD "Purk_GABA_9_9" "Purk_GABA"
  END CHILD
END PUBLIC_MODELS

1.5. Can we export the model to an XML file ?

1. Executed command	xml_save /** /tmp/1.xml
2. Expected output	genesis

1.6. Does the exported XML file contain the correct model ?

1. Expected output

application_output_file: /tmp/1.xml
&lt;neurospaces type="ndf"/&gt;

&lt;private_models&gt;
  &lt;ATTACHMENT&gt; &lt;name&gt;Synapse_7_7&lt;/name&gt;
    &lt;bindables&gt;
      &lt;input&gt; &lt;name&gt;spike&lt;/name&gt; &lt;/input&gt;
      &lt;output&gt; &lt;name&gt;activation&lt;/name&gt; &lt;/output&gt;
    &lt;/bindables&gt;
    &lt;attributes&gt;       &lt;name&gt;weight&lt;/name&gt;       &lt;name&gt;delay&lt;/name&gt; &lt;/attributes&gt;
  &lt;/ATTACHMENT&gt;
  &lt;child&gt; &lt;prototype&gt;Synapse_7_7&lt;/prototype&gt; &lt;name&gt;Synapse_7_8&lt;/name&gt;
  &lt;/child&gt;
  &lt;child&gt; &lt;prototype&gt;Synapse_7_8&lt;/prototype&gt; &lt;name&gt;synapse_7_10&lt;/name&gt;
  &lt;/child&gt;
  &lt;child&gt; &lt;prototype&gt;synapse_7_10&lt;/prototype&gt; &lt;name&gt;synapse_inserted_10&lt;/name&gt;
  &lt;/child&gt;
  &lt;EQUATION_EXPONENTIAL&gt; &lt;name&gt;exp2_11_11&lt;/name&gt;
    &lt;bindables&gt;
      &lt;input&gt; &lt;name&gt;activation&lt;/name&gt; &lt;/input&gt;
      &lt;output&gt; &lt;name&gt;G&lt;/name&gt; &lt;/output&gt;
    &lt;/bindables&gt;
    &lt;bindings&gt;
      &lt;input&gt; &lt;name&gt;../synapse-&gt;activation&lt;/name&gt; &lt;/input&gt;
    &lt;/bindings&gt;
    &lt;parameters&gt;
      &lt;parameter&gt; &lt;name&gt;TAU1&lt;/name&gt;&lt;value&gt;0.00093&lt;/value&gt; &lt;/parameter&gt;
      &lt;parameter&gt; &lt;name&gt;TAU2&lt;/name&gt;&lt;value&gt;0.0265&lt;/value&gt; &lt;/parameter&gt;
    &lt;/parameters&gt;
  &lt;/EQUATION_EXPONENTIAL&gt;
  &lt;child&gt; &lt;prototype&gt;exp2_11_11&lt;/prototype&gt; &lt;name&gt;exp2_inserted_11&lt;/name&gt;
  &lt;/child&gt;
  &lt;CHANNEL&gt; &lt;name&gt;Purk_GABA_9_9&lt;/name&gt;
    &lt;bindables&gt;
      &lt;input&gt; &lt;name&gt;Vm&lt;/name&gt; &lt;/input&gt;
      &lt;output&gt; &lt;name&gt;I&lt;/name&gt; &lt;/output&gt;
    &lt;/bindables&gt;
    &lt;parameters&gt;
      &lt;parameter&gt; &lt;name&gt;G_MAX&lt;/name&gt;&lt;value&gt;1.077&lt;/value&gt; &lt;/parameter&gt;
      &lt;parameter&gt; &lt;name&gt;Erev&lt;/name&gt;&lt;value&gt;-0.08&lt;/value&gt; &lt;/parameter&gt;
    &lt;/parameters&gt;
    &lt;child&gt; &lt;prototype&gt;synapse_inserted_10&lt;/prototype&gt; &lt;name&gt;synapse&lt;/name&gt;
    &lt;/child&gt;
    &lt;child&gt; &lt;prototype&gt;exp2_11_11&lt;/prototype&gt; &lt;name&gt;exp2&lt;/name&gt;
    &lt;/child&gt;
  &lt;/CHANNEL&gt;
  &lt;child&gt; &lt;prototype&gt;Purk_GABA_9_9&lt;/prototype&gt; &lt;name&gt;Purk_GABA_inserted_9&lt;/name&gt;
  &lt;/child&gt;
&lt;/private_models&gt;
&lt;public_models&gt;
  &lt;child&gt; &lt;prototype&gt;Purk_GABA_9_9&lt;/prototype&gt; &lt;name&gt;Purk_GABA&lt;/name&gt;
  &lt;/child&gt;
&lt;/public_models&gt;

2. Comment

xml to html conversion fails when converting this test to html