Global coordination in neuroinformatics Jan G. Bjaalie INCF Secretariat Karolinska Institutet...
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![Page 1: Global coordination in neuroinformatics Jan G. Bjaalie INCF Secretariat Karolinska Institutet Stockholm.](https://reader036.fdocuments.net/reader036/viewer/2022062500/5697bf821a28abf838c85a1c/html5/thumbnails/1.jpg)
Global coordination inneuroinformatics
Jan G. Bjaalie
INCF SecretariatKarolinska InstitutetStockholm
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BelgiumCzech RepublicFinlandFranceGermanyItalyJapanNetherlandsNorwayPolandSwedenSwitzerlandUnited KingdomUnited States
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Structure of the INCF
Definition of INCF Neuroinformatics
Mission
Motivation
Action
INCF
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International Neuroinformatics Coordinating Facility
Structure
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International Neuroinformatics Coordinating Facility
Structure
![Page 6: Global coordination in neuroinformatics Jan G. Bjaalie INCF Secretariat Karolinska Institutet Stockholm.](https://reader036.fdocuments.net/reader036/viewer/2022062500/5697bf821a28abf838c85a1c/html5/thumbnails/6.jpg)
International Neuroinformatics Coordinating Facility
Structure
![Page 7: Global coordination in neuroinformatics Jan G. Bjaalie INCF Secretariat Karolinska Institutet Stockholm.](https://reader036.fdocuments.net/reader036/viewer/2022062500/5697bf821a28abf838c85a1c/html5/thumbnails/7.jpg)
International Neuroinformatics Coordinating Facility
Structure
![Page 8: Global coordination in neuroinformatics Jan G. Bjaalie INCF Secretariat Karolinska Institutet Stockholm.](https://reader036.fdocuments.net/reader036/viewer/2022062500/5697bf821a28abf838c85a1c/html5/thumbnails/8.jpg)
International Neuroinformatics Coordinating Facility
KI: building and administrative services
KTH: HPC
Structure
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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
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At the intersection between many disciplines:
• medicine• biology• behavioural sciences• physics• computer science• mathematics• engineering
INCF Neuroinformatics:
Databases
Tools Models
Definition
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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
INCF Neuroinformatics:
Databases
Tools Models
Definition
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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
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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
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Action
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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
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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
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Principal Work Program
Action
Informatics applied toneuroscience
ACTIVITY AREAS:
Modeling of the brain
Neuroinformatics for brain structure
Neuroinformatics for brain function
Neuroinformatics for brain diseases
Nomenclature and ontologies
Neurosciencecontributions toinformatics
Training forneuroinformatics
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Principal Work Program
Action
Informatics applied toneuroscience
ACTIVITY AREAS:
Large-scale modeling
Digital atlasingNeuroimage database integration
Neuroanatomical nomenclature
Neurosciencecontributions toinformatics
Training forneuroinformatics
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Larg
e-sc
ale
mod
elin
g
Digita
l atla
sing
Neuro
imag
e db
inte
grat
ion
Nomen
clatu
re
Portal
Standards
Training
Action
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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
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Action
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10-15 invited participants
1 reporter
Members recruited from Workshops, and other
1 Program Officer
Action
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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
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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
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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
Larg
e-sc
ale
mod
elin
g
Digita
l atla
sing
Neuro
imag
e db
inte
grat
ion
Nomen
clatu
re
Portal
Standards
Training
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Platform for providing research oriented services to the neuroscience community world-wide
- Domain oriented services- Basic services
INCF Neuroinformatics Portal
Action
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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
INCF Neuroinformatics Portal
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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
INCF Neuroinformatics Portal
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Action
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.
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Action
INCF Neuroinformatics Portal
Basic services
Software center
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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
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INCF Software Center
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Use Case:
Who (actor)...does what (interaction) with the system...for what purpose (goal)
INCF Software Center
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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
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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
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Expenses Budget 2008
52 %
2 %
26 %
20 %0 %
Staff Expenses
Running Expenses
Program Expenses
Professional Services
Secretariat Facilities
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International Neuroinformatics Coordinating Facility
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www.incf.org
INCF CongressStockholm, September 7-9, 2008
www.neuroinformatics2008.org