The Modeler’s Workspace Current Design Plans and Status

1. The Modeler’s 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

2. Goals for the Modeler’s 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

3. 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 user’s work (models, notebooks, etc.) • Rendezvous point for collaborative activities • Modeler’s Workspace Directory • Global registry of databases, users, model templates

4. Example of the User Interface: the Search Pane

5. Multiple User Access to Workspace Database

6. 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

7. 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 .membraneLeakagePotentialEleak float .equilibriumPotentialEk float .electrotonicLengthLambda float .channelConductanceGk float .membraneSurface float activeProperties list of ActiveProperties structures

8. Generic Inspector

9. Interaction with Neuronal Simulation Programs

10. The Modeler’s Workspace Directory • Server located at a known network address • Contacted by User Interface component • Supports Modeler’s 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

11. 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 Modeler’s Workspace Directory and (2) uploading templates used • Goal is to help promote • Sharing of models • Evolution and sharing of templates

12. Summary • Modeler’s 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