Events - Past Events

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Identified Neuron Database Workshop

Dec 15th -17th, 2004

Group Photo

Workshop Presentations:

Thursday Dec 16th
Friday Dec 17th

The purpose of this workshop is to bring together Computer Scientists and
Neuroscientists interested in the problem of creating a database of
identified neurons and connections.  The immediate goal is to increase the
communication among three groups of people:

  1. Experimental neuroscientists who represent communities that might need such a database,
  2. Experts who have created related databases, and
  3. Computer scientists who have expertise in related areas of data management and manipulation.
    The ultimate goal is to create a web-based tool where information about identified neurons or neuronal classes and synapses can be published.

Download a copy of the Final Program (PDF)


Thurs. Dec 16th Workshop Sessions

Morning Session: Reports on Neuroinformatics Efforts. What are issues of database design? What’s out there already? Presentations will be on existing neuronal databases, highlighting their features. These presentations will discuss how these databases are used by the various communities. They will also discuss current problems that need to be worked on.
Speakers Presentations
Paul Katz
(Georgia State University)
Introductory remarks (ppt)
Gwen Jacobs
(Montana State University)

Overview of activity at NIH, SFN and the neuroscience community with respect to data sharing, ontologies and ongoing efforts in other communities. (ppt)

Maryann Martone
(University of California San Diego)

Federation of distributed multiscale data: the BIRN and CCDB projects (ppt)

Daniel Gardner
(Cornell Medical College)

Neurodatabase.org and BrainML.org: open databases for neuroscience (pdf)

Luis Marenco
(Yale University School of Medicine)
The EAV/CR WebDB Toolkit: An open source application framework for building evolvable neuroscience databases (ppt)
Christopher Comer
(University of Illinois at Chicago)

Identified neuron database for insect segmental ganglion (ppt)

Nirav Merchant
(University of Arizona)

Community Databases: Flat files to semantic web

General Discussion What can we achieve with this workshop?
Afternoon Session: Database Needs of the Invertebrate Neuroscience Community These talks will be by potential users of a database of identified neurons describing what their needs would be. What types of data are collected by experimentalists? How are neurons identified?
Speakers Presentations
Paul Katz
(Georgia State University)

Developing a database of identified neurons for the mollusc, Tritonia (ppt)

Klaudiusz Weiss
(Mt. Sinai School of Medicine)

Identified neurons in Aplysia
Leonid Moroz
(University of Florida)

Single neuron gene expression profiling and the Aplysia transcriptome project

W. Otto Friesen
(University of Virginia)

Identified neurons in the CNS of the medicinal leech.

Dirk Bucher
(Brandeis University)

Identified neurons in the crustacean stomatogastric system (ppt)

Donald Edwards
(Georgia State University)

Identified neurons in the crustacean segmental nervous system (ppt)


Friday Dec 17th Workshop Sessions

Database Implementation Issues These talks will bring together the issues surrounding the implementation of database design.
Speakers Presentations
Gwen Jacobs
(Montana State University)
Neurosys: Hierarchical database project (ppt)
Monte Westerfield
(University of Oregon)

How to get started building a database (ppt)

Daniel Gardner
(Cornell Medical College)

Towards interoperable databases: relatable terms and compatible interfaces (pdf)

Mihai Bota
(University of Southern California)

The Brain Architecture Management System

Raymond Lee
(California Institute of Technology)

Connections, functions and genes-integrating neuronal information in WormBase (ppt)

Scott Emmons
(Albert Einstein College of Medicine)

Computer software for nervous system reconstruction from serial section electron micrographs.

Ying Zhu
(Georgia State University)

A plan for visualization and mapping neurons (ppt)

Raj Sunderraman
(Georgia State University)
Issues of design and implementation (ppt)

Roundtable Discussion - Building identified neuron databases. What should the structure of the databases be? What is the relative value of detail vs. searchability? What features should the user interface have? How much time should it take to enter data for a cell? What features should be included in the search engine? What steps should be taken? Where do we go from here? Create Action Plan.