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Global coordination in neuroinformatics

The International Neuroinformatics Coordinating Facility (INCF) is an organization that coordinates and fosters international activities in neuroinformatics. Their mission is to contribute to the development and maintenance of database and computational infrastructure for neuroscience research, and to enable access to freely accessible data and analysis resources for the international research community. INCF works at the intersection of many disciplines, including medicine, biology, computer science, and physics, to develop advanced tools and approaches for understanding the brain.

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Global coordination in neuroinformatics

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  1. Global coordination in neuroinformatics Jan G. Bjaalie INCF Secretariat Karolinska Institutet Stockholm

  2. Belgium Czech Republic Finland France Germany Italy Japan Netherlands Norway Poland Sweden Switzerland United Kingdom United States

  3. INCF Structure of the INCF Definition of INCF Neuroinformatics Mission Motivation Action

  4. International Neuroinformatics Coordinating Facility Structure

  5. International Neuroinformatics Coordinating Facility Structure

  6. International Neuroinformatics Coordinating Facility Structure

  7. International Neuroinformatics Coordinating Facility Structure

  8. International Neuroinformatics Coordinating Facility KI: building and administrative services KTH: HPC Structure

  9. 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

  10. INCF Neuroinformatics: At the intersection between many disciplines: • medicine • biology • behavioural sciences • physics • computer science • mathematics • engineering Databases Tools Models Definition

  11. 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

  12. 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

  13. 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

  14. Action

  15. 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

  16. 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

  17. 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

  18. 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

  19. Neuroimage db integration Large-scale modeling Digital atlasing Nomenclature Portal Standards Training Action

  20. Action

  21. Members recruited from Workshops, and other 1 Program Officer 10-15 invited participants 1 reporter Action

  22. 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

  23. 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

  24. 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

  25. INCF Neuroinformatics Portal • Platform for providing research oriented services to the neuroscience community world-wide • Domain oriented services • Basic services Action

  26. 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

  27. 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

  28. 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

  29. INCF Neuroinformatics Portal Basic services Software center Action

  30. 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

  31. INCF Software Center

  32. INCF Software Center Use Case: Who (actor)... does what (interaction) with the system... for what purpose (goal)

  33. 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

  34. INCF Secretariat

  35. International Neuroinformatics Coordinating Facility

  36. www.incf.org INCF Congress Stockholm, September 7-9, 2008 www.neuroinformatics2008.org

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