Bruce Schatz - US grants

Professor Schatz is undertaking a one-year investigation to understand and outline the design of a computer system to support an electronic scientific community. While later proposals will be submitted to support the system, this project is to lay the necessary groundwork to enable the implementation to proceed as planned. When implemented, this system should be a new form of biological instrumentation which can effectively manipulate scientific databases. Appropriate community knowledge will be identified to be collected into a digital library and the design will incorporate the systems technology necessary to manipulate this library over nationwide networks. The community chosen is the group of scientists studying the nematode worm Caenorhabditis elegans, a major model organism in molecular biology. The "worm community" consists of some 500 members worldwide, with an unusual degree of open communication and sharing of unpublished information. The community knowledge includes formal data, such as published literature and experimental results, and informal data, such as newsletters and experimental methods. The designed system will capture a significant portion of this knowledge in electronic form and encode it into a "worm information space" which can be transparently browsed by scientists anywhere on nationwide scientific networks. Preparation of the system design requires understanding user needs and available technology. this will be accomplished by working with researchers who will be the system's initial users and who are experts on the available data and technology. Such investigation should enable the design to ensure that the system will contribute to making valuable scientific discoveries.

Neuronal pattern analysis (NPA) documents the dynamic brain processes of sensation, perception, learning and cognition by recording the electrical activity of brain neurons. Recent advances in multi-array recording technologies have greatly expanded the rate at which NPA data can be obtained, and these technologies have fostered means not previously available to study the intercorrelations of dynamic activities in neuronal networks. Computational modeling of brain dynamic activity has fostered major increment in the requirements of data processing due to the need to analyze simulated neuronal spike trains and to compare real and simulated neuronal data. These developments call for parallel development of adequate database systems for organization, rapid access, and sharing of NPA data. This project will establish a database system (DBS) for time series neurophysiological data recorded in experiments of members of the University of Illinois Beckman Institute Neuronal Pattern Analysis Group. System design and implementation will be carried out with consultation and guidance of the National center for Supercomputer Applications. This proposed system will foster community-wide sharing of times series and other forms of neural data, proved a model DBS that can generalize to other neuroscience groups, and enhance the research in the involved laboratories.

This award is for a postdoctoral associate in Experimental Science. The associate, Stella Veretnik, will be working on computational biology from an AI viewpoint.

This project constructs a digital library testbed and pursues fundamental research addressing the scalable organization of large digital collections. The testbed contains a digital collection containing journals and magazines in the engineering literature in structured SGML format plus pictorial materials obtained from commercial and professional publishers. The associated information systems initially centers about NCSA Mosaic for document display and network access of other resources. Basic research encompasses both technical and social aspects of the testbed capabilities, usage and usage patters including: sociological analysis (including ethnographic observation, surveys and other instruments); economics research over a range of issues. A general goal of the efforts is to enable the design and analysis for digital libraries infrastructure capable of scaling to very large systems.

One of the most important questions in biology is the origin of behavior: nature or nurture? This research will use genomic biology to liberate the study of behavior from the shackles of this dichotomy. The new paradigm is that the environment ("nurture"), which includes other individuals, impacts an inherited genome ("nature") by orchestrating gene expression during the lifetime of the animal. This project will analyze social behavior on an unprecedented whole-genome scale, using Apis mellifera the Western honey bee, as the model organism. Honey bees live in a complex society governed by an age-related division of labor, with each individual assuming many roles during her lifetime. Both genetic heredity and environmental conditions determine what role a bee performs, and when she performs it. The biology research will generate a unique database of gene expressions for all social behavior, recording brain gene expression for hundreds of individuals, each with a specific societal role. These microarray experiments utilize the recently sequenced genome, supported by state-of-the-art statistics. The informatics research will develop an interactive environment to analyze all information sources relevant to bee social behavior. These include genome databases from honey bee and related organisms, linked to complete scientific literature relevant to insect behavior. New text mining technology will integrate molecular description with information from physiology, behavior, neuroscience, and evolution. The BeeSpace environment will enable users to navigate a uniform space of diverse databases and literature sources for hypothesis development and testing. The software system will go beyond a searchable database, using statistical literature analyses to discover functional relationships between genes and behavior. This research will enable all scientists who study bee genes to live on the frontier of integrative biology, where biotechnology enables routine expression analysis and bioinformatics enables functional analysis unconstrained by pre-existing categories.

The broader impact of the interactive environment for functional analysis will be tested in an international community of laboratories studying honey bees and related organisms. Outreach for BeeSpace will provide integrated research and education experiences at the graduate and undergraduate levels, plus training courses and minority outreach at high school and middle school levels.