Databasing the brain

Workshop - Oslo, June 25 – 27, 2006


MONDAY June 26:

08.30 – 10.00 Genes to neurons

Chair: Giorgio Ascoli

  • Robert Williams: Neurogenomic databases and The Gene Network
  • Nicolas Le Novere: BioModels Database: Curation and exchange of quantitative models
  • Maryann Martone: 3-D neuron centered database
  • Jean Pierre Changeux: Role of nicotinic receptors in cognition

10.00 10.30 Coffe break

10.30 – 11.15 Senselab databases: integrated, multidisciplinary models of neurons and neural systems

Chair: Philippe Cupers

  • Gordon Shepherd: Senselab overview
  • Jorn Hounsgaard: Senselab user perspective

11.30 – 12.45 Panel 2: Role of journals in promoting data sharing and supporting databases

Chair: Gordon Shepherd

This session will explore the possible role of journals in providing information about databasing initiatives and in encouraging scientists to share persistent data via databases. While databases represent novel approaches for data sharing and analysis, journals provide the only established mechanism for peer-review and proper referencing of data and interpretations. Mechanisms for publication in journals and simultaneous posting of data in data repositories have been established. Beyond the fields of genomics and proteomics, such mechanisms are rarely used, although examples exist in the brain imaging community. In addition, journals are in a position to communicate and emphasize new developments and encourage the establishment of new routes for the dissemination and sharing of data.The panel will present challenges and problems as well as example success stories where they exist.

  • Maryann Martone: SfN Neuroinformatics committee: Data sharing standards
  • Giorgio Ascoli: Neuroinformatics
  • John D. Van Horn: Journal of Cognitive Neuroscience
  • Timo Hannay: Nature Web Publishing
  • Ole Petter Ottersen: Neuroscience
  • Terje Sagvolden: Open Access Journals
  • Gordon Shepherd: SfN Neuroinformatics committee: Journal relations

12.45 14.30 Lunch

14.30 – 16.00 Neurons to systems

Chair: August Smit

  • Erik De Schutter: Modeling the cerebellar system – importance of variability
  • Jan Bjaalie: The Rodent Brain Workbench
  • Rolf Kötter: CoCoMac and related databases for primate brain data
  • David Van Essen: Surface Management System Database for primate cortical data

16.15 - 17.30 Panel 3: Preparing data and metadata - role of companies

Chair: Erik De Schutter

This session will explore how the industry (companies producing software and equipment for data acquisition, storage, and data management) can help establish data and metadata formats via interactions with the scientific communities. Standardized data formats and standardized schemes for assigning information to a given data set (experimental conditions, manipulations performed, chemicals used, etc.) represent the basis for any database effort. Future use of data made available via a database can only be successful if a) data of the same category are comparable, b) data of one category is defined in relationship to data of other categories, and c) sufficient amount of metadata is stored. Practical aspects related to data and metadata formats and the annotation of data at the work bench, are therefore of crucial importance for data sharing, tools sharing, and the integration of multiple categories of data.

  • Erik De Schutter: Metadata starts at the workbench
  • Reinhard Braul, MicroBrightField Europe, E.K.
  • Greg Smith, Cambridge Electronic Design Limited
  • Lucas Noldus, Noldus Information Technology bv.
  • Jaak Vilo, EGeen Inc., Estonian division
  • Ad Aertsen: Annotation of simulation data
  • Jaap van Pelt: Challenges of combining experiments

19.30 Dinner at the Centre for Sustainability, Soria Moria