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

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

International Neuroinformatics Coordinating Facility Structure

International Neuroinformatics Coordinating Facility Structure

International Neuroinformatics Coordinating Facility Structure

International Neuroinformatics Coordinating Facility Structure

International Neuroinformatics Coordinating Facility 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 ToolsModels INCF Neuroinformatics: Definition

At the intersection between many disciplines: medicine biology behavioural sciences physics computer science mathematics engineering INCF Neuroinformatics: Databases ToolsModels 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 Forum OECD Global Science Forum INCF Neuroinformatics: Databases ToolsModels 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 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

Principal Work Program Action 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

Principal Work Program Action Informatics applied to neuroscience ACTIVITY AREAS: Large-scale modeling Digital atlasing Neuroimage database integration Neuroanatomical nomenclature Neuroscience contributions to informatics Training for neuroinformatics

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

WORKSHOPACTIVITY Large-scale modeling1. 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 atlasing1. 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 Nomenclature1. 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 terminologies 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 From topical analyses to 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 Large-scale modeling Digital atlasing Neuroimage db integration Nomenclature 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 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 INCF Neuroinformatics Portal

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.

Action INCF Neuroinformatics Portal 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 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

INCF Software Center

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

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 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

INCF Secretariat

International Neuroinformatics Coordinating Facility

INCF Congress Stockholm, September 7-9,