Neuroinformatics

An Overview of the Human Brain Project

Stephen H. Koslow, Michael F. Huerta, Stephen H. Koslow, Michael F. Huerta

• Publisher: Psychology Press
• Year: 2013
• ISBN:
  9781134798490
• Edition: 1
• Topic: Psychology
• Subtopic: History & Theory in Psychology
• Index: Psychology

Modern neuroscience is providing profound insights into nature's most mysterious puzzle -- the human brain -- while applications of information and computer science are transforming the way people interact with each other and with the world around them. The new science of neuroinformatics, which sits at the junction, integrates knowledge and promises to catalyze progress in these dynamic and seemingly disparate areas of study. Neuroinformatics research will allow brain and behavioral scientists to make better sense and use of their data through advanced information tools and approaches. These include new ways to acquire, store, visualize, analyze, integrate, synthesize, and share data, as well as the means for electronic scientific collaboration.In this country, the principal source of support for neuroinformatics research is the Human Brain Project. The project, which is led by the National Institute of Mental Health, now supports neuroinformatics research performed by over 60 scientists. This volume presents the findings of the first group of researchers. Their efforts will begin to arm the next generation of brain and behavioral scientists with tools to attack the serious problem of information overload, and ultimately relate their findings to those obtained from different species, levels of biological organization, methods, and laboratories. And the challenges presented by the amount, diversity, and complexity of brain and behavioral data will give informatics researchers the impetus to test and expand the limits of their own science. The work described in this volume signals a change in the way scientists interact with data, instruments and each other, and points the way to a very different and richer future understanding of the human brain and mind.

1

The Human Brain Project: Past, Present, and Promise

Michael F. Huerta

Stephen H. Koslow

National Institute of Mental Health

The Human Brain Project supports research that knits together the edges of two rapidly advancing and broadly defined areas of science: neuroscience, which includes studies of brain and behavior, and informatics, which draws from fields such as information science, computer science, applied mathematics, and engineering (Huerta, Koslow, & Leshner, 1993; Koslow, 1993). The new science at this interface is referred to as neuroinformatics. Neuroinformatics research promises to significantly advance the fields contributing to this new area of inquiry, as well as to address the broad scientific issue of making optimal use and better sense of sophisticated data.

Data obtained in brain and behavioral research are very diverse. This diversity derives from the wide range of species studied, from invertebrates to humans, as well as from the spectrum of levels of biological organization studied, including molecules, cells, systems of cells, behavior, and all levels in between. Additional variety in the data pool is introduced by the interest of brain and behavioral research in understanding both normal and diseased states throughout the entire life span. Data obtained in brain and behavioral research are also vast, being generated by tens of thousands of researchers working around the world, and being reported in hundreds of journals. Finally, data obtained in brain and behavioral research are complex, being both highly dimensional and highly interconnected, with innumerable interactions among the different aspects studied. For example, findings at the molecular level may have important implications for interpretation of behavioral data.

The variety, quantity, and complexity of data from brain and behavioral research present significant problems to the scientific community. Keeping track of and integrating all of this information is beyond the scope of individual researchers, and this scope is becoming more narrow as scientific specialization increases. This, in turn, threatens the ability of scientists to make conceptual links across different areas of study. Paradoxically, such an ability is precisely the fuel that has driven much of the progress in our understanding of the brain and behavior. Thus, new approaches and tools are needed to address this issue of information overload. Informatics research can contribute to the development of solutions to this problem. Combining informatics research with brain and behavioral research, as is done in the Human Brain Project, ensures that this new line of scientific inquiry results in optimal solutions.

The neuroinformatics research supported under the Human Brain Project promises to advance both neuroscience and informatics. Neuroinformatics research will accelerate an understanding of the brain by providing the means to make better use and sense of brain data. These means and methods include novel database and querying approaches, new knowledge about data visualization and manipulation, and innovative ways to synthesize data and conduct scientific collaboration electronically. Neuroinformatics will also contribute to the development of powerful models of neural functions. For example, such models may be used to integrate data from different sources and about different aspects of neural function. Neuroinformatics research, driven by the demands made by the variety, quantity, and complexity of neuroscience data, will expand the limits of knowledge in informatics.

The Human Brain Project will alter fundamentally the ways in which newly acquired scientific data are made available to the scientific community, exchanged with collaborators, and shared and used for purposes of education and clinical activities. Distributed databases, intelligent agents, and querying tools will make it possible for scientists to once again freely relate their findings to broader scientific contexts and make conceptual links across disciplines. New ways to visualize, manipulate, analyze, and synthesize data will lead to new insights and aid in the formulation of hypotheses. Moreover, knowledge and approaches resulting from Human Brain Project research will permit the formation of electronic collaboratories based on scientific questions, rather than on the happenstance of geographic location. This will allow research teams to truly match the pace of change that characterizes contemporary science. These fundamental changes in the way brain and behavioral research is performed will likely change the paradigms of these domains; paradigm changes like these are profound, and often herald great advances in science.

The new science of neuroinformatics, supported under the Human Brain Project, will lead to solutions that are generalizable to a wide range of scientific uses, including all areas of biology. By providing new ways to interact with both data and colleagues, neuroinformatics is expected to change the way in which research is done. Moreover, the impact of this research is likely to be felt far beyond the scientific community, and has the potential to influence a wide range of information-rich endeavors.

The Past

The need for advanced information solutions for brain and behavioral science was assessed in 1989 by the Institute of Medicine of the National Academy of Sciences at the request of the National Institute of Mental Health (NIMH), the National Institute on Drug Abuse, and the National Science Foundation. The Institute of Medicine empaneled eminent experts representing the brain and behavioral sciences, as well as computer, information, and telecommunication sciences, to evaluate the desirability and plausibility of integrating informatics technologies with brain and behavioral research. This committee met and deliberated for 2 years, convening hearings, symposia, demonstrations, and task forces, and taking comments from approximately 150 other scientists. In the summer of 1991, the findings and recommendations of the Institute of Medicine were published by the National Academy Press (Martin & Pechura, 1991). The specific recommendations set out in that report are summarized as follows:

• The long-term objective of this initiative will be to develop a national and international resource of network-accessible databases containing all types of information regarding the nervous systems of humans and other species throughout their development, in both healthy and diseased states.
• The initiative will begin with peer-reviewed pilot projects carried out by consortia of research laboratories. To facilitate the development of telecommunications technology, component laboratories of a given consortium may be geographically dispersed. The pilot projects will be selected on the basis of research quality and value to the development of technology for integrating neuroscience information.
• The initiative should be international in scope.
• Public domain software useful in neuroscience research should be made available to the neuroscience community via computer networks.
• The initiative should include an advisory panel to coordinate activities and develop policy.
• The research and development carried out under this initiative should maintain a close relationship with other major research initiatives, such as the Human Genome Project and the National Research and Education Network.
• The initiative should be funded with grants, cooperative agreements, and contracts.
• The initiative should be funded by multiple sources in a coordinated fashion, with one agency or institute playing a lead role.
• The expected benefits of the initiative justify the investment of additional resources.

The NIMH has taken the lead in implementing these recommendations, many of which were incorporated in the program announcement issued in April 1993. A revised program announcement was issued in October 1995. The revised version identified specific areas of scientific opportunity important to the goals of the Human Brain Project. Each application must have an informatics research component and a brain and/or behavioral research component; areas of high priority in each of these components are given next.

Informatics Research Component

Research on Databases, Querying Approaches, and Information Retrieval. The diversity of data types in brain and behavioral research will require databases that can accommodate varied data types (e.g., textual, graphic, image, time series), querying approaches that will allow varied databases to be accessed with a single query, and retrieval of different types of data into a common information space. In addition, databases and querying and retrieval tools will need to be extensible and easily reconfigurable to adjust to the rapidly changing domain of brain and behavioral research.

Research on Data Visualization and Manipulation. Data about the brain and behavior are extremely complex and highly interconnected. This high level of complexity requires novel ways to manipulate and visualize large. interconnected data sets.

Research on Data Integration and Synthesis. As scientific specialization increases, integration and synthesis of different types of data and about different aspects of brain structure and function become increasingly difficult. Models can serve as information spaces, in which experimentally obtained data of different types and from different sources can be integrated and synthesized.

Tools for Electronic Collaboration. The ability to quickly assemble teams, independent of the geographic location, to address specific scientific questions would greatly accelerate the pace of discovery. Advanced forms of “groupware,” with tools for data acquisition, display, and manipulation, would facilitate this ability.

Research That Builds Bridges Across Existing Information Tools and Resources. The tools and approaches developed through support from the Human Brain Project will be most useful if and when they work together and can access other databases and tools, such as those associated with the Human Genome Project and the Macromolecular Structure Database. The revised program announcement emphasized that the informatics research component of each application is expected to be future-oriented and will seek to exceed the current state of the art.

Brain and/or Behavioral Research Component

Biological and Behavioral Research. This includes data and tools from biological levels of organization, such as molecules, genes, cells, and systems of cells; and from behavioral constructs, such as attention, perception, learning, memory, cognition, emotion, and language. Research that integrates across these levels and constructs is strongly encouraged.

Research That Includes Structure–Function Relationships. This is needed at all levels of organization-from cellular to behavioral. In addition to these high-priority topics, the revised program announcement also made clear that Human Brain Project research is expected to possess the following characteristics.

Generalizable. For example, algorithms for quantifying differences in three-dimensional reconstructions of data obtained from electron microscopy should generalize to volume data from confocal microscopy and magnetic resonance imaging (MRI) of whole brains.

Sophisticated Research Performed on Sophisticated Platforms. The Human Brain Project is a long-term initiative to support research and development of advanced information technologies. Computers that are sophisticated by current standards are likely to be widely available in 5 or 10 years. Today’s low-end machines are likely to be obsolete by the time the tools now being researched are made available to the scientific community at large.

Extensible and Scalable. Phase I research efforts will lead to tools and approaches intended for the scientific community at large, rather than an individual laboratory. To achieve this goal, it is important that issues of extensibility and scalability are addressed from the outset.

Designed to Assess Progress. Because research and development is ultimately intended to be of use not only to an individual laboratory, but to a wide range of laboratories, it is important that methods to assess progress toward achieving the objectives of the Human Brain Project: Phase I are addressed. This includes the development and documentation of standards by which tools will be tested for reliability and accuracy.

The Present

Just as the Human Brain Project heralds a new way to perform research, the implementation of this initiative is being done in novel ways. In accord with the scope of neuroinformatics research, the Human Brain Project is sponsored, in a coordinated fashion, by 16 federal organizations across five federal agencies: (a) the National Institutes of Health (National Institute of Mental Health, National Institute on Drug Abuse, National Institute on Aging, National Institute on Child Health and Human Development, National Institute on Deafness and Other Communication Disorders, National Library of Medicine, the National Heart, Lung, and Blood Institute, the National Institute of Dental Research, the National Institute on Alcohol Abuse and Alcoholism, the Fogarty International Center, the National Institute of Neurological Disorders and Stroke, and the National Cancer Institute), (b) the National Science Foundation, (c) the Department of Defense (Office of Naval Research), (d) the National Aeronautics and Space Administration, and (e) the Department of Energy. Representatives from all of these organizations comprise the Federal Interagency Coordinating Committee on the Human Brain Project (FICC-HBP), which coordinates, funds, and steers this effort. The National Institute of Mental Health serves as the lead organization.

The success of this multiagency strategy is reflected by the fact that the number of federal organizations sponsoring the Human Brain Project has grown from 11 to 16. The success of the Human Brain Project as a research initiative is at least partly due to the unusually high level of interaction and cooperation among several federal agencies. By utilizing the vastly different technical and administrative experiences across 16 different organizations, and by virtue of the different scientific and technical communities with which the different agencies are in contact, the Human Brain Project has attracted outstanding researchers from a variety of disciplines to address the important task at hand.

The Human Brain Project now supports over 50 neuroinformatics researchers. It is important that these researchers communicate to allow investigators to take advantage of new findings developed in others’ laboratories, and to promote cross-fertilization across research groups. Such communication also ensures that research efforts are not unnecessarily duplicated. Finally, communication within this community will encourage the sharing of resources, and will pave the way for setting up test beds for new tools and approaches.

Toward these ends, the FICC-HBP holds two meetings of Human Brain Project grantees each year. One of these, held in the spring, is focused on the close and frank communication among grantees. This meeting is held in the Washington, DC, area, allowing members of the FICC-HBP to monitor the progress and problems of the grantees’ efforts first hand. From these meetings, numerous collaborative arrangements across different groups have been initiated, and several electronic channels of communication have been set up among different grantees. These channels have subsequently been used to continue the sharing of technical information, software, and data sets.

The principal investigators on the Human Brain Project grants also attend the annual meeting of the Society for Neuroscience, which is held in the fall. This meeting allows for interaction among subsets of grantees, and also serves as a public forum at which the progress of the Human Brain Project is presented. In addition to affording the federal research managers attending the meeting an additional chance to monitor the progress of the research funded under this initiative, this allows scientists interested in, but not funded by, the Human Brain Project to keep up with the latest developments in this area, and query the researchers first hand.

To optimize the implementation of this comprehensive initiative, it is paramount to alert those in pertinent fields of the opportunities and challenges that the Human Brain Project may offer them. Toward this end, many symposia, conferences, and presentations are held and made at national and international fora to inform the communities of researchers in the fields of neuroscience, behavioral science, computer science, information science, and telecommunications.

It is important that Human Brain Project research inform, and be informed by, the global scientific community. This is important for several reasons. First, world-class research on the brain and behavior is being performed around the world, as is research on informatics and related topics. As brain and behavioral research is increasingly collaborative and global, it is paramount that neuroinformatics tools and approaches are compatible and, where possible, interoperable. This will ultimately permit scientists worldwide to store, access, utilize, and share data efficiently, and will significantly accelerate brain and behavioral research. Fulfilling this potential requires that those responsible for the research and development of neuroinformatics solutions are aware of approaches being taken by others; it also requires that coordination across different efforts take place, particularly at the international level.

The involvement of the international community is proceeding along several fronts, both at the level of Human Brain Project grantees and at the level of the federal organizations sponsoring that research. Grantees have collaborative research arrangements with scientists in several countries worldwide. With regard to activities by federal research sponsors, an international workshop on neuroinformatics research was recently held under the auspices of the United States–European Commission (US–EC) Task Force on Biotechnology Research. The report of the workshop was well received by the task force, which made several recommendations, including that a...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright
• Contents
• Foreword
• Preface
• 1. The Human Brain Project: Past, Present, and Promise
• 2. The Human Brain Project: Priority or Problem?
• 3. SenseLab: A Project in Multidisciplinary, Multilevel Sensory Integration
• 4. The GENESIS Simulator-Based Neuronal Database
• 5. Neuronal Vulnerability and Informatics in Human Disease
• 6. Goal-Directed Magnetic Resonance Brain Microimaging
• 7. Biometrics and Brain Maps: The Promise of the Morphometric Synthesis
• 8. Atlases of the Human Brain
• 9. A Structural Information Framework for Brain Mapping
• 10. Software and Methods for Quantitative Imaging in Neuroscience: The Kennedy Krieger Institute Human Brain Project
• Author Index
• Subject Index