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Global coordination in neuroinformatics. Jan G. Bjaalie INCF Secretariat Karolinska Institutet Stockholm. Belgium Czech Republic Finland France Germany Italy Japan Netherlands Norway Poland Sweden Switzerland United Kingdom United States. INCF. Structure of the INCF

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slide1

Global coordination in

neuroinformatics

Jan G. Bjaalie

INCF Secretariat

Karolinska Institutet

Stockholm

slide2

Belgium

Czech Republic

Finland

France

Germany

Italy

Japan

Netherlands

Norway

Poland

Sweden

Switzerland

United Kingdom

United States

slide3

INCF

Structure of the INCF

Definition of INCF Neuroinformatics

Mission

Motivation

Action

slide8

International Neuroinformatics Coordinating Facility

KI: building and administrative services

KTH: HPC

Structure

slide9

INCF Neuroinformatics:

Core aspects:

  • Interoperable databases
  • Shared tools for data-acquisition, analysis, visualization and distribution
  • Environments for theoretical analyses: computational and simulation approaches

Databases

Tools

Models

Definition

slide10

INCF Neuroinformatics:

At the intersection between many disciplines:

  • medicine
  • biology
  • behavioural sciences
  • physics
  • computer science
  • mathematics
  • engineering

Databases

Tools

Models

Definition

slide11

INCF Neuroinformatics:

Neuroinformatics - an interdisciplinary research area, combining research in neuroscience and informatics (including computation) to develop and apply advanced tools and approaches needed for understanding the brain.

OECD MegaScience Forum

OECD Global Science Forum

Databases

Tools

Models

Definition

slide12

The mission of the INCF

coordinate and foster international activities in neuroinformatics

contribute to development and maintenance of database and computational infrastructure and support mechanisms for neuroscience applications

enable access to all freely accessible data and analysis resources for human brain research to the international research community

develop mechanisms for the seamless flow of information and knowledge between academia, private enterprises and the publication industry

Mission

slide13

Motivation

    • challenge to integrate data and build knowledge and understanding
  • Neuroinformatics will contribute to an improved access to and integration of data and transfer of knowledge across levels of organization, and to the development of realistic models of brain functions
  • Technology: Neuroinformatics will serve as a source of inspiration for information sciences and the development of artificial systems utilizing principles of neural processing found in the brain
  • Health: Even modest progress in treatment of brain related diseases, or delayed onset of neurodegenerative diseases, will have a huge impact on quality of life and global economy

Motivation

slide15

The INCF Secretariat offers services to the National nodes:

  • will assist the Nodes in reaching their goals
  • will play a proactive role in furthering neuroinformatics
  • will coordinate efforts among Nodes and research groups, with the aim of avoiding unnecessary duplications and facilitate dissemination of results and achievements

Action

principal work program
Principal Work Program

Informatics applied to

neuroscience

THEMES:

Knowledge management systems,

semantic web

Data and metadata management

and sharing

Tools development and sharing

Computing infrastructures

Interoperability of resources

Sustainability of resources

Neuroscience

contributions to

informatics

Training for

neuroinformatics

Action

principal work program1
Principal Work Program

Informatics applied to

neuroscience

ACTIVITY AREAS:

Modeling of the brain

Neuroinformatics for brain

structure

Neuroinformatics for brain function

Neuroinformatics for brain diseases

Nomenclature and ontologies

Neuroscience

contributions to

informatics

Training for

neuroinformatics

Action

principal work program2
Principal Work Program

Informatics applied to

neuroscience

ACTIVITY AREAS:

Large-scale modeling

Digital atlasing

Neuroimage database integration

Neuroanatomical nomenclature

Neuroscience

contributions to

informatics

Training for

neuroinformatics

Action

slide19

Neuroimage db integration

Large-scale modeling

Digital atlasing

Nomenclature

Portal

Standards

Training

Action

slide22

Members recruited from Workshops, and other

1 Program Officer

10-15 invited participants

1 reporter

Action

slide23

INCF report:

-survey

-analysis

-action points

First workshops:

Large scale modeling

Mouse and rat brain digital atlasing

Neuroimage database integration

Global portal services

Nomenclatures and terminologies

Action

slide24

From topical analyses to action

Choice of topic

Workshop scientific organizer

Workshop participants

Workshop report

Ranking of recommendations, cost-benefit analyses,

focus on infrastructure

Action coordinated by the Secretariat:

NODES -- EXTERNAL CONTRACTS -- INTERNAL

Establishment of Program

Action

music the multi simulator coordinator

Neuroimage db integration

Large-scale modeling

Digital atlasing

Nomenclature

Portal

Standards

Training

MUSIC – The Multi Simulator Coordinator
  • An interoperability standard for simulation software and a software product to support and facilitate use and adoption of the standard
  • Result of top priority recommendations from Large-Scale Modeling workshop in late 2006
  • Development of the standard itself and its supporting software product outsourced to sub-contractor
  • INCF releases MUSIC as an INCF standard and product in 2008

Allen Brain Atlas co-hosting and future data and tools resource integration

  • The worlds largest database of rodent brain image data
  • Extension of technical infrastructure for better service for clients world-wide
  • Strategic data and tools resource integration opportunity, new environment for tools developments and data sharing

Action

slide27

INCF Neuroinformatics Portal

  • Platform for providing research oriented services to the neuroscience community world-wide
  • Domain oriented services
  • Basic services

Action

slide28

INCF Neuroinformatics Portal

  • Domain oriented services
  • Will facilitate navigation and integration of distributed resources in selected domain areas
  • - data fusion and integration
  • - tools provision
  • strategic resource persistence and standardization
  • quality, referencing and availability

- international community derived authority in the context of INCF Workshops and Expert panels

Action

slide29

INCF Neuroinformatics Portal

  • Domain oriented services
  • Large-scale modeling of the nervous system
  • Mouse and rat brain digital atlasing systems
  • Integration of neuroimage data resources
  • Neuroanatomical nomenclature

Action

slide30

INCF Neuroinformatics Portal

Basic services

General community building support:

online meeting forums, blogs with emphasis on news and commentaries for the different divisions of the portal, and calendars of neuroscience and neuroinformatics events. Given the focus on domain oriented services, the above functionalities will address the different domains specifically, but also offer integration of communication across domains.

Action

slide31

INCF Neuroinformatics Portal

Basic services

Software center

Action

slide32

INCF Software Center

End user perspective

Will allow software users to efficiently find, evaluate, and successfully make use of shared software tools

Developer perspective

Will allow software developers to efficiently disseminate their software, track the use of it, and receive feedback of importance for further refining and development

slide34

INCF Software Center

Use Case:

Who (actor)...

does what (interaction) with the system...

for what purpose (goal)

slide40

Technologies

Plone, an open-source content management system, building on the Python-based web-application server Zope

Plone can easily be extended to fit specific needs, as seen e.g. by the 600 different extensions currently published on http://plone.org/products

Number of add-ons can be employed by many of the support services to be provided by the Neuroinformatics Portal

Used by organizations and institutions such as ACM SIGGRAPH, NASA / Jet Propulsion Labs, and the National Cancer Institute

slide44
www.incf.org

INCF Congress

Stockholm, September 7-9, 2008

www.neuroinformatics2008.org