global coordination in neuroinformatics

Global coordination inneuroinformatics

Jan G. Bjaalie

INCF SecretariatKarolinska InstitutetStockholm

BelgiumCzech RepublicFinlandFranceGermanyItalyJapanNetherlandsNorwayPolandSwedenSwitzerlandUnited KingdomUnited States

Structure of the INCF

Definition of INCF Neuroinformatics

Mission

Motivation

Action

INCF

International Neuroinformatics Coordinating Facility

Structure


KI: building and administrative services

KTH: HPC

Structure

Core aspects:

• Interoperable databases• Shared tools for data-

acquisition, analysis, visualization and distribution

• Environments for theoretical analyses: computational and simulation approaches

Databases

Tools Models

INCF Neuroinformatics:

Definition

At the intersection between many disciplines:

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


Databases

Tools Models

Definition

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 ForumOECD Global Science Forum


Databases

Tools Models

Definition

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

The mission of the INCF

Mission

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

Action

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

Action

Informatics applied toneuroscience

THEMES:

Knowledge management systems,semantic web

Data and metadata managementand sharing

Tools development and sharing

Computing infrastructures

Interoperability of resources

Sustainability of resources

Neurosciencecontributions toinformatics

Training forneuroinformatics


Action


ACTIVITY AREAS:

Modeling of the brain

Neuroinformatics for brain structure

Neuroinformatics for brain function

Neuroinformatics for brain diseases

Nomenclature and ontologies




Action


ACTIVITY AREAS:

Large-scale modeling

Digital atlasingNeuroimage database integration

Neuroanatomical nomenclature



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Portal

Standards

Training

Action

WORKSHOP ACTIVITY

Large-scale modeling 1. Multi Simulator Coordinator: MUSIC

1b. Project related to uniform application programming interface (API) across neural simulators

2. Standards establishment

3. Blue Gene and GRID access-brokerage

Digital atlasing 1. Allen Brain Atlas mirror

1b. Allen Brain Atlas resource integration

2. Digital brain atlasing (brain navigation) software + tools for mapping and characterization

3. Committee together with Nomenclature

4. Spatial atlas of gene expression in the rat nervous system

Neuroimage database integration

1. Expansion of existing neuroimage databases + data exchange and tools integration

Nomenclature 1. Standing committee for nomenclature

2. Interaction with BIRN and NIF ontologies

Action

10-15 invited participants

1 reporter

Members recruited from Workshops, and other

1 Program Officer

Action

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 terminologiesAction

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

From topical analyses to action

Action

Action

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

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Portal

Standards

Training

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

- Domain oriented services- Basic services

INCF Neuroinformatics Portal

Action

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


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


Action


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


Basic services

Software center

INCF Software Center

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

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

Use Case:

Who (actor)...does what (interaction) with the system...for what purpose (goal)


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

Executive Director

Executive Advisor

Administrative Assistant

Controller

Deputy Executive Director

Scientific Officer and Tech lead

Program Officer

System Developer

IT Manager

Usability and Requirem. Analyst

Administrative Assistant

(25%)

INCF Portal Team

Sci. Information and PR Officer

INCF SecretariatOrganizational chart, October 2007

INCF Secretariat

Expenses Budget 2008

52 %

2 %

26 %

20 %0 %

Staff Expenses

Running Expenses

Program Expenses

Professional Services

Secretariat Facilities

www.incf.org

INCF CongressStockholm, September 7-9, 2008

www.neuroinformatics2008.org