The International Neuroinformatics Coordinating Facility

The Journal of Neuroscience, April 4, 2007 • 27(14):3613–3615 • 3613

Toolbox

Editor’s Note: Toolboxes are intended to briefly highlight a new method or a resource of general use in neuroscience or to critically analyze existing approaches or methods. For more information, see http://www.jneurosci.org/misc/itoa.shtml.

Global Neuroinformatics: The International Neuroinformatics Coordinating Facility

Jan G. Bjaalie1 and Sten Grillner1,2 1International Neuroinformatics Coordinating Facility and 2Nobel Institute for Neurophysiology, Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden

There is a growing awareness in the neu- efit from a major concerted action. For defined in the context of the INCF, is an roscience community of the need for da- this reason 12 member countries of the interdisciplinary research area combining tabases extending from genes to cognition Organization for Economic Cooperation neuroscience with information science/ and disease mechanisms. Such databases and Development have formed the Inter- technology. Neuroinformatics deals with are important for data sharing as well as national Neuroinformatics Coordinating the development of neuroscience data and for modeling and use of computational Facility (INCF), an organization that will knowledge bases together with computa- tools at different levels. The development facilitate the development of neuroinfor- tional models and analytical tools for the of this area, neuroinformatics, would ben- matics (http://www.incf.org). This effort sharing, integration, and analysis of ex- is financed by contributions from each perimental data, discovery research, and member nation (Belgium, Czech Repub- the advancement of theories of nervous Received Feb. 8, 2007; revised Feb. 20, 2007; accepted Feb. 20, 2007. lic, Finland, France, Germany, Italy, Ja- system function (Fig. 1). The ultimate J.G.B. is the Executive Director of the INCF. S.G. is the Chair of the Gov- pan, The Netherlands, Norway, Sweden, goal of the INCF is to accelerate progress erning Board of the INCF. The members of the INCF Governing Board con- in the understanding of brain function. It tribute to the development of the INCF, together with the INCF national Switzerland, and the United States), as nodes. Previous working groups of the Organization for Economic Cooper- well as from the European Commission. also may serve as a source of inspiration ation and Development (OECD) Global Science Forum (GSF) have prepared The central Secretariat of the INCF in for information sciences and develop- the background analysis that resulted in the recommendation of the OECD Stockholm will have a staff of ϳ10, in- ment of technologies using principles of Ministers of Science to establish the INCF. Chairs and cochairs of these neural processing in the brain. Under- working groups were Stephen H. Koslow (United States), Shun-ichi Amari cluding the Executive Director, Program (Japan),andStenGrillner(Europe).TheoperationsoftheINCFbuildonthe Managers, and other staff. We outline standing the brain requires integration of Understanding and Business Plan of the INCF. This article describes princi- here the objectives of the INCF and the heterogeneous and complex data col- ples only. INCF strategies and actions are subject to continuous monitoring resources that are being developed for lected at multiple levels of investigation. and approval by the INCF Governing Board. Role of the OECD: OECD is an intergovernmental organization which provides a forum for analysis, de- neuroscience. velopment, and reform of economic and social policies. The division that The mission of the INCF is to (1) co- Principal Work Program represents the basis for the establishment of the INCF is the Directorate for ordinate and foster international activities The principal work program of the INCF Science, Technology, and Industry. This Directorate provides policy advice in neuroinformatics; (2) contribute to the in areas such as biotechnology, telecommunications, and information ser- covers large areas of neuroinformatics, as vices. It includes the GSF as a venue for meetings of senior science policy development of scalable, portable, and ex- listed in Table 2. Main deliverables in- officials of OECD countries with the goal of identifying and maximizing tensible applications that can be used for clude (1) web-based portal services, fo- opportunities for international cooperation. GSF special-purpose working furthering our knowledge of the human cused on access to interoperable and inte- groupsperformtechnicalanalysesanddevelopfindingsandrecommenda- brain and its diseases; (3) contribute to the tions for actions by governments. The first such working group in the area grated databases and tools covering of neuroinformatics was established in 1996, under the forerunner of GSF, the development and maintenance of specific selected areas, (2) new approaches to use MegaScience Forum, and delivered a report in 1999 (http://www.incf.org/ database and other computational infra- of standardized terminologies and stan- med/Report_OECD_MSF_1999.pdf). At the request of the GSF, a further structures and support mechanisms; and dards for data production, and (3) novel examination was performed, leading to a second report in 2002 (http:// (4) focus on developing mechanisms for training opportunities. Some aspects of www.incf.org/med/Report_OECD_GSF_2002.pdf). The latter report was endorsed at the OECD Science and Technology Ministerial meeting in Jan- the seamless flow of information and these areas, which will be of direct rele- uary 2004. Sixteen countries, as well as the European Commission, then knowledge between academia, private en- vance for neuroscientists, are outlined elaborated the legal basis and platform for the INCF. terprises, and the publication industry. below. Correspondence should be addressed to Jan G. Bjaalie, INCF Secretariat, An extensive analysis and a series of Karolinska Institutet, Nobels va¨g 15 A, SE-171 77 Stockholm, Sweden. E- mail: [email protected]. platform documents serve as a basis for Portals to neuroinformatics resources DOI:10.1523/JNEUROSCI.0558-07.2007 the operations that are to be performed by A large number of neuroinformatics re- Copyright©2007SocietyforNeuroscience 0270-6474/07/273613-03$15.00/0 the INCF (Table 1). Neuroinformatics, as sources, ranging from data repositories to 3614 • J. Neurosci., April 4, 2007 • 27(14):3613–3615 Bjaalie and Grillner • Toolbox advanced database applications and in- Table 1. Platform documents for the INCF cluding shared tools and computational Document Description models, are currently available. A listing Understanding for the International Neuroinformatics Coordinating The legal document signed by all participants in the of many of the available resources can be Facility (http://www.incf.org/med/INCF_Understanding.pdf) INCF that sets the framework for joining the INCF found at the Neuroscience Database Business Plan for the International Neuroinformatics Coordinating The document that describes the mission and operating Gateway, hosted by The Society for Neu- Facility (http://www.incf.org/med/INCF_BusinessPlan.pdf) procedure of the INCF roscience (http://www.sfn.org/ndg). An- Program in International Neuroinformatics (http://www.incf.org/ The framework document for a future funding scheme other important and supplementary ini- med/INCF_PIN.pdf) for international neuroinformatics tiative is the Neuroscience Information Framework (http://neurogateway.org). The INCF will assist the community with the creation of an inventory of available resources, with the starting point being the activities and priorities of the INCF national nodes in each of the member countries. Furthermore, the INCF will focus on the development of portals provid- ing access to different research areas and domains, primarily to areas that are already represented by a critical mass of dis- tributed neuroinformatics resources. The motivation is not only to assist neuroscientists in finding individual resources but to facilitate rapid and smart access to relevant combinations of resources. Such integration of existing resources is demanding. It serves two primary pur- poses. The first purpose is obviously to extract the most out of the existing resources and to make the deliverables of already funded research and development as accessible and useful to the neuroscience community as possible. The sec- Figure 1. The three foci of neuroinformatics. ond purpose is to prepare the bases for future projects, in charting the present bottlenecks for integration, within the sci- cated. With new technological develop- Table 2. Principal work program for the INCF entific or technical domain or at the socio- ments and possibilities emerging in data Databases that cover basic and clinical neuroscience from logical level. After the first analysis of such production and data management, it ap- the level of the gene to behavior systems integrations, and drawing on the pears logical and necessary to gradually Infrastructure, such as portals, communication channels, initial experiences, the INCF will map the develop standards at all levels of research. database federations, and grid middleware road ahead in terms of services that will be Standardized terminologies and stan- Tools, such as simulation environments for computational developed within the scope of the INCF dards for data production will make data neuroscience, computational devices, data analysis, data work plan. Interaction with industry in less context dependent and will provide mining, data warehousing, and middleware terms of developing products is not a new opportunities for comparing and in- Construction and dissemination of models of the nervous main focus of the INCF but will be taken tegrating data from different laboratories. system and simulation of neural processes into consideration (e.g., to the extent that In developing standards, it is useful to Guidelines, standards, and ontologies sustainability of resources will benefit distinguish between exploratory and Interdisciplinary training programs Consensus on strategies and priorities and joint, possibly from introducing a commercial compo- production-oriented activity. Much of novel, funding agreements to carry out specific projects nent). The latter is also relevant to one neuroscience involves methods that are or meet specific goals goal of the INCF, the development of ca- intricate and difficult to fully standardize. General transfer of knowledge and technology pabilities for transfer of knowledge and Research itself may even lead to modifica- The INCF will facilitate and contribute to the development and access to technology. tion of standards and terminology. How- and/or dissemination of capabilities as listed. ever, large laboratories, or consortia of Standards and guidelines laboratories, may operate production- for as many domains of neuroscience as Neuroscience produces heterogeneous oriented facilities using highly standard- practical. The INCF will promote the es- datasets. The field is divided into many ized methods, including high throughput tablishment of interoperable database re- disciplines with different practices, and technologies. The INCF will interact with sources and facilitate the development of different investigators often use different such production-oriented facilities to op- standards and guidelines for data produc- terminologies. Producing data and meta- timize communication among the facili- tion, analyses, and use of terminologies. data suitable for sharing through interop- ties and between the facilities and the erable and federated database applica- larger research community. The primary Interdisciplinary training tions prepared for smart searches and goal will be to contribute to the develop- Neuroinformatics comprises many disci- analyses may therefore appear compli- ment and use of standards and guidelines plines, and development of neuroinfor- Bjaalie and Grillner • Toolbox J. Neurosci., April 4, 2007 • 27(14):3613–3615 • 3615

tem and Mouse and Rat Brain Digital At- lasing Systems have been organized. Re- ports with recommendations for action are in preparation and will be made available via the INCF website. Upcoming topics to be covered by the workshop series include Neuroanatomical Nomenclature and Taxonomy, Sustainability for Neuro- science Databases, and Portals to Neuroin- formatics Resources. Follow-up from the workshops will be taken care of by estab- lishing expert panels for the different areas covered by the workshops and by con- necting the expert panels closely to staff in the INCF Secretariat and in national nodes (Fig. 2). To the extent possible, ac- Figure 2. Overview of tasks of the Secretariat and national nodes. Decisions on the goals and actions of the Secretariat are tions of the INCF will always seek to build made by the Governing Board, with representatives from the member countries. on a careful mapping of existing resources and, when possible, to prepare for the full matics applications, whether databases, ing into account the requirements of the use of these in combination with new tools, or simulation environments, re- research community and advances in developments. quires interaction between developers neuroscience and neuroscience-related and end users. The developers may not technologies. Third, exchange schemes Future Perspectives in have experience in neuroscience, and sim- for early-career scientists need to be facil- Neuroinformatics ilarly, the end users may not have suffi- itated, offering opportunities for special- The short-term priorities of the INCF are cient experience in information sciences ized practitioners to be exposed to se- to create inventories of neuroinformatics and related disciplines. Interdisciplinary lected areas and fields that will be of resources available in the member nations training will have to assist those with a importance for their work. and to launch portals to topical, limited background in computational methods to research areas as well as to analytical tools. get a working knowledge of experimental Work Model of the INCF In a longer time perspective, the INCF will brain sciences at some level and to help A key element in the INCF operation is to prioritize actions that will lead to an im- the life scientists to become adept with re- work closely with the scientific commu- proved environment for data sharing, to quirements imposed by computational nity in adjusting and translating the work the development of larger, interoperable principles and methods. Cross- plan to practical action. To this end, INCF databases in selected areas, and to easier disciplinary training is challenging but will organize a series of topical workshops access to standardized, shared tools, as fundamental to the success of neuroinfor- that will cover not only technical issues of well as to shared environments for simu- matics and neuroscience in general. To primary importance for neuroinformat- lations and computational analysis. The raise the skills of the community of neu- ics, but also research topics coupled to da- INCF effort will progress by focusing on roinformatics researchers, several tasks tabasing of neuroscience data, tool devel- selected areas and building on success sto- must be addressed. First, there is a need to opments, or modeling of nervous system ries and experiences. It should become a develop a systematic overview of training functions. Each workshop has 10–15 in- significant achievement with neuroinfor- needs. The results of the INCF workshop vited participants, selected on the basis of matics playing the same role in the devel- series (see below) will provide important their expert skills in the particular area of opment of basic and clinical neuroscience input in this respect. Second, good prac- the workshop. To date, workshops on as bioinformatics has for genomics and tice schemes for training are needed, tak- Large-Scale Modeling of the Nervous Sys- proteomics.