The Modelers Workspace Current Design Plans and Status

1
The Modelers WorkspaceCurrent Design Plans and
Status

• Current project members
• Michael Hucka
• Kavita Shankar
• Sara Emardson
• David Beeman
• James Bower
• Original design implementation by Jenny Forss
• Division of Biology
• California Institute of Technology
• Pasadena, CA

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Goals for the Modelers Workspace

• Software tool to assist computational
  neuroscientists
• Provide facilities for
• Interacting with databases of models and other
  objects
• Creating, editing and visualizing models
• Interacting with simulation systems such as
  GENESIS
• Managing a personal database of models other
  objects
• Collaborating with other scientists using shared
  editing and viewing of database contents

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Components in the System

• 3 main components
• User Interface
• Downloadable Java JavaScript program
• Run either as separate app or within a web
  browser
• Communication with Workspace Database over
  network
• Roaming user can access Workspace from anywhere
• Workspace Database
• Stand-alone server, waits for network connections
• Private repository for users work (models,
  notebooks, etc.)
• Rendezvous point for collaborative activities
• Modelers Workspace Directory
• Global registry of databases, users, model
  templates

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Example of the User Interface the Search Pane
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Multiple User Access to Workspace Database
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Objects in Workspace Databases

• A Workspace Database contains objects
  representing different types of entities models,
  bib references, etc.
• Each object is structured according to a template
• A template ( schema) defines the format of an
  object
• Different templates are used for different types
  of objects
• E.g. Neuron Model, Ion Channel Model, Reference
• A Base Template is the root of the template
  hierarchy
• New templates defined by starting from either the
  base template or an existing template
• Only addition of attributes is allowed, not
  deletion
• Objects encoded in XML templates are XML Schemas

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Example

• Segment structure
• --------------------------------------
• type string
• name string
• geometry
  SegmentGeometry structure
• .numberOfCompartments integer
• .symmetric boolean
• .parentSegment integer
  
• .relativeOrAbsolute string
• .x float
• .y float
• .z float
• .startDiameter float
• .endDiameter float
• passiveProperties
  PassiveProperties structure
• .specificResistanceRm float
• .specificCapacitanceCm float
• .specificAxialResistanceRa float
• .membraneRestingPotentialErest float

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Generic Inspector
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Interaction with Neuronal Simulation Programs
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The Modelers Workspace Directory

• Server located at a known network address
• Contacted by User Interface component
• Supports Modelers Workspace users
• Maintains real-time updated list of databases
• Also information about each known database
• Templates used
• Database interface plug-in (mediator)
• Maintains global collection of templates used by
  databases
• Maintains real-time updated list of users
• Helps in setting up collaboration meetings

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Creating Publicly-Accessible Databases

• Provides facility to take existing Workspace
  Database, clone it, and set it up as a
  stand-alone server
• Includes (1) registering the database with the
  Modelers Workspace Directory and (2) uploading
  templates used
• Goal is to help promote
• Sharing of models
• Evolution and sharing of templates

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Summary

• Modelers Workspace is intended to be a tool for
  assisting computational neuroscientists
• Will run on any Java-enabled networked computer
• Current status
• Completed specifications for behavior of system
• Major modules defined
• Have started coding user interface
• Web site www.modelersworkspace.org