Seminar Series past events

Michael Becich, M.D., Ph.D.
Chairman of the Department of Biomedical Informatics, Professor of Biomedical Informatics, Pathology, and Information Sciences and Telecommunications, University of Pittsburgh.

Biomedical Informatics and Translation Research, Center for Clinical and Translational Informatics at the University of Pittsburgh Medical School
The University of Pittsburgh (along with UC Davis) was recently awarded a Clinical and Translational Science Award (CTSA - see http://ctsaweb.org/.The presentation will focus on the plans for biomedical informatics support of clinical and translational research at the University of Pittsburgh. A profile of current tools and infrastructure in place will be presented along with the challenges facing our CTSA implementation. 

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Thomas M Jones, M.D.
Chief Medical Officer, Tolven

An Open Source Approach to Health Care IT; Disruptive technology in action
In The Innovator’s Dilemma, Clayton Christensen reviews the significant differences between large companies that continue to rely on sustaining technologies that enhance current trends in an industry continue revenue generation and small companies that create disruptive technologies that herald the future. While he has cogent advice for large firms that, through technology watch groups, monitor and occasionally create disruptive technologies, he expresses more confidence in the finding that small companies will continue to provide the kernels for disruptive technologies. In the monograph “Open Source Software: a Primer for Health Care Leaders”, Goulde and Brown say that “The (health care IT) industry must rethink the way it develops patient-information software to reduce costs and increase flexibility, examine the way it distributes software to providers, and look at ways to add value to commonly used software rather than producing competing, functionally equivalent applications.” Goulde and Brown go on to say that health care IT is beginning to adopt the disruptive technology of open source software to address the challenges of: sharing patient information beyond the walls of individual institutions creating regional health information networks that allow duly authorized providers to securely and easily exchange clinical information expanding the use of electronic health records Tolven is an organization dedicated to the creation of disruptive, open source technology for health care information systems. Our company is one of the first open source organizations to focus solely on the delivery of healthcare and life science information technology solutions. Currently, Tolven has created an open source, standards based interoperability platform for health care, as well as patient/consumer and clinician solutions (i.e., an EHR configured for practicing clinicians – the eCHR - and a “companion” EHR configured for patients – the ePHR). The solutions created by Tolven are designed to support collaboration among patients/consumers, physicians and other care providers.

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Vimla L. Patel, Ph.D., D.Sc., F.R.S.C.
Professor & Interim Chair, Dept. of Biomedical Informatics Director, Center for Decision Making and Cognition
Ira A. Fulton School of Engineering, Arizona State University
Professor of Basic Medical Sciences
Director, Medical Education Research
The University of Arizona College of Medicine-Phoenix

Cognition and Biomedical Informatics: Relationship between Knowing, Thinking, and Doing
Technological development often outstrips its productive use in a community of practitioners. Enhanced functionality and efficiency afforded by new machinery needs to be balanced with concerns for usability, learnability, and adaptability to the needs of the setting. As information becomes more readily accessible in the near future, will the need to engage in effortful learning be diminished? If answers to questions can be obtained much more easily through new information resources, will it be as important to have knowledge in one's head? Research in cognitive science at the interface of Biomedical Informatics addresses some of these lurking questions.  

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Cecil Lynch, M.D., M.S.
Chief Knowledge Engineer, Ontoreason, Informatics Consultant, CDC

An Ontological Approach to BioSense Message Analysis for National Syndromic Surveillance
The CDC has embarked on a massive effort to centralize a feed of anonymized HL7 messages for the purpose of enhancing surveillance for agents of bioterrorism and for syndromic surveillance of routine public health pathogens. This leads to new challenges for processing the millions of messages received each day to glean clinical, laboratory, pharmacy and radiology findings of interest and pertinence, and route these to the appropriate analyst for further evaluation in a timely way. I will present an ontological, services based method that allows direct message processing, classification, runtime analysis and visualization of extracted knowledge that can aid the human analyst to meet the mission of timely and accurate evaluation of messages to promote situational awareness. 

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Welcome
Claire Pomeroy, M.D., M.B.A.
Vice Chancellor, Human Health Sciences
Dean, School of Medicine,UCDHS

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Overview, Objectives and Future of IT in the UC System
Peter Yellowlees, M.B.B.S., M.D.
Professor of Psychiatry and Director of Academic Information Systems, UC Davis

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Health Informatics: US and International Experiences
Don E. Detmer, M.D.
President and CEO, American Medical Informatics Association

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eHealth in California
Barbara Johnston, M.S.N.
Executive Director, California Telemedicine and eHealth Center

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Telemedicine and Distance Learning in the UC System
Thomas Nesbitt, M.D., M.P.H.
Executive Associate Dean for Administration and Clinical Outreach, UC Davis School of Medicine
Director, Center for Health & Technology

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Getting More eScience Mileage from Cyberinfrastructure
Bertram Ludaescher, Ph.D.
Associate Professor, Computer Science, UC Davis

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California EDRS: Anatomy of a Large-Scale Public Health Information System
Michael Hogarth, M.D.
Associate Professor, Department of Pathology and Laboratory Medicine, Department of Internal Medicine, UC Davis Health System

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Kevin Dawson, M.D., Ph.D.
Director, Informatics (Knock-Out Mouse Project, UC Davis)
Senior Informatics Scientist (NCMHD Center of Excellence in NutritionalGenomics)

OMICS -Genomic, Proteomic, Metabolomic Data in Tomorrow's Health Care: Information-Driven Decision-Making and Personalized Medicine
In the next 10 years, the availability of patient genotype information will transform health care. The cost of a whole genome scan is expected to drop below a thousand dollars per person. Practically all persons in the industrialized world will be genotyped. This will open the door for a more refined approach to estimate the individual’s risk to a disease or the predicted response to therapeutic choices. Multigenic, complex diseases, e.g., type II diabetes mellitus, hypertension, obesity will be managed using patient-specific information rather than one-fits-all diagnostics and trial-and-error-based therapeutic decision algorithms. Pharmacogenomics will become a reality. In addition to genotype information, the use of gene expression, proteomic, metabolomic, and epigenetic profiles will add to the complexity of healthcare. Current OMICS technologies, the data they generate, and the methods used for data analysis will be discussed. 

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Chris Brandt, D.V.M., M.S.
Instructional Media Development Specialist, Veterinary Medicine Teaching Hospital, UCDavis

VCARS -The Veterinary Computerized Anesthetic Record System
VCARS - The Veterinary Computerized Anesthetic Record SystemVCARS was designed to capture pre-anesthetic and peri-anesthetic record information using Tablet PCs, wireless networking, and a database driven, internet based, Flash application. Surgical case information including patient demographics and procedures is imported from the VMTH hospital information system or entered manually. Anesthetists then use web-based system document their pre-anestheticfindings and develop their anesthetic plan which includes drugs, equipment,and special procedures. Once the patient is anesthetized, a wireless,ruggedized Tablet PC is used to record vitals (blood pressure, heart and respiration rate), drug administration, fluid therapy, anesthetic gas settings, laboratory results, patient location, and other events.Supervising anesthesiologists are able to view multiple cases from a central location.  

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Charles P. Friedman, Ph.D.
Associate Director for Research Informatics and Information Technology, National Heart, Lung, and Blood Institute, NIH

"Breakthrough" Informatics: Prospects for a Paradigm Shift in Biomedicine
The presentation will begin by suggesting a "fundamental theorem" that unifies the field of informatics across biological research, clinical research, health care, and education. The fundamental theorem directs us to think about informatics as a field in pursuit of making people better at what they do, by forming synergistic partnerships between persons and information technology. The value of the fundamental theorem, to clarify thinking about this rapidly evolving and easily misunderstood field, will be illustrated with several examples. The notion of the fundamental theorem will then be extended. I will define "incremental" informatics--which includes much of the progress in informatics to date--as work that seeks to enhance practice-as-usual in a field, without altering in significant ways how work is done. In incremental informatics, it usually is not clear whether the person-technology partnership is making matters better or worse. I will then introduce a new concept of "breakthrough" informatics where the person-technology partnership engenders revolutionary change in how work is done, largely by making possible things that were not possible before, and where it is often visible to the naked eye that the effect of the partnership is transforming or paradigm shifting. I will contrast examples of incremental and breakthrough informatics as they apply to basic and clinical research, health care, and the education of health professionals. I will recommend that, in these times of scarce resources, we set our sights exclusively on informatics with breakthrough potential.  

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Linette Scott, M.D., M.P.H.
California Department of Health Services

GIS for Public Health: Experiences in the California Department of Health Services
Geographic Information Systems (GIS) is an advanced tool which facilitates data interpretation and representation geographically and can be a sophisticated decision support tool for resource management. This presentation will provide a brief history of GIS, a description of current uses of GIS in public health, and a description of current uses and plans for GIS in the California Department of Health Services.  

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Peter Yellowlees M.B.B.S., M.D.
Professor of Psychiatry and Director of Academic Information Systems, UC Davis Health System

Virtual Reality, Pedagogy, Simulations and Online Education - the future is nearly here
This presentation will focus on online educational approaches and collaborative learning environments which incorporate a number of exciting technological innovations from the fields of virtual reality and simulation. The pedagogy of adult learning will be explored and mapped to the many and varied new educational tools that are now becoming available via the internet and which will gradually change the way that teachers and students interact and work together to attain their objectives in the distributed and open classrooms of the future. A number of practical demonstrations of online learning environments will be incorporated into the presentation. 

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Christopher Longhurst, M.D., M.S.
Clinical Assistant Professor, Department of Pediatrics, Stanford School of Medicine

Physician Lead, Clinical Informatics, Lucile Packard Children's Hospital

High Reliability in Pediatric Healthcare: The Symbiosis of Clinicians and IT
Recent research suggests that the nature of medical errors in children's healthcare differs substantially from adults. This talk will focus on how information technology can facilitate highly reliable pediatric healthcare. Using the current EMR implementation at Lucile Packard Children's Hospital at Stanford University as a launching pad, we will discuss issues such as online clinical documentation and the brewing national controversy over CPOE in the ICU setting. 

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Joachim Diederich, Ph.D. 
Chair, Department of Computer Science American University of Sharjah Sharjah, UAE

Machine Learning methods for the detection of schizophrenic language behavior
Artificial intelligence techniques and in particular machine learning are applied to a text classification task to determine mental health problems. Inputs are transcribed speech samples from a “structured-narrative task” and outputs are psychiatric categories such as schizophrenia. In a preliminary trial, subjects from three groups generated speech samples: those with clinically diagnosed schizophrenia (31 patients), clinically diagnosed mania (16 patients) and controls (9 subjects). Even though the structured narrative task resulted in the use of a limited vocabulary by all subjects (only a total of 1100 different words were used), a classification performance approaching 80% accuracy was achieved for the schizophrenia vs. control task. Classification results at this level indicate that the method is suitable for diagnostic or screening purposes. It is expected that results improve further in experiments utilizing free-speech samples. 

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Joan Ash, Ph.D., M.L.S., M.B.A.
Associate Professor, Department of Medical Informatics and Clinical Epidemiology Associate Professor, Libraries Oregon Health and Science University

The Upsides and Downsides of Computerized Provider Order Entry Systems in Hospitals While the benefits of computerized physician/provider order entry (CPOE) have been well described, the hazards have not been the subject of research until quite recently. Joan Ash will discuss the results of her research team's studies over the past six years on success factors for implementing CPOE and on overcoming the unintended consequences of CPOE.  

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Matt Bishop, Ph.D.
Professor, Department of Computer Science, UC Davis

Basic Information Security
This talk presents a brief survey of computer security. We discuss what computer security is, what it is supposed to provide, and various issues that constrain how security can be provided. Various principles of secure design are described. We will also show the Clinical Information Systems Security model, a model reflecting medical practices in Britain.  

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Michael Hogarth, M.D.
Associate Professor, Department of Pathology and Laboratory Medicine, Department of Internal Medicine, UC Davis Health System

CA-EDRS: Building and Deploying a Mission Critical System for California
California currently processes over 250,000 new death certificates per year (1 in 10 deaths in the U.S.). CA-EDRS is California’s system for electronic death certificate registration and provides the ability for coroners, funeral directors, doctors, and hospitals to submit electronic death certificates for registration 24 hours a day. The CA-EDRS system was built by UC Davis and deployed on January 1st 2005. CA-EDRS system development required the use of software engineering and informatics strategies that allowed rapid iteration without compromising quality. The challenges and ‘lessons learned’ in the development of the CA-EDRS system are described. Concepts and principles relevant to the development of large-scale, mission-critical public health informatics software systems are also presented. 

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Dale Alverson, M.D. 
Professor of Pediatrics and Regents Professor, Medical Director, Center for Telehealth and Cybermedicine Research Health Sciences Center University of New Mexico

Distributed Immersive Virtual Reality Simulation for Education, Training and Performance Assessment
Simulations are being used in education and training to enhance understanding, improve performance, and assess competence. Validated virtual reality (VR) simulations provide a means of making experiential learning reproducible and reusable. Advanced communication networks, such as Internet2 Access Grid, allow dissemination of these simulations and collaborative learning independent of distance. Our ongoing experiences led to an inter-institutional, interdisciplinary collaboration to further develop and evaluate an integrated, fully immersive, interactive VR system designed for medical education and training. This environment employs simulations that are visually three dimensional and are driven dynamically by a rules-based artificial intelligence engine within FLATLAND ™ (a virtual environments development software tool) and associated commodity hardware. These efforts have, in turn, led to iterations of the system to improve practical applications to meet specific user requirements; cutting across the integration of computing, networking, human-computer interfaces, learning, and knowledge acquisition. VR simulation creates a safe environment to make mistakes and could allow rapid deployment for just-in-time training, education on demand, or performance assessment. *Co-authors: Thomas P. Caudell, Stanley M. Saiki Jr, Andrei Sherstyuk, Kathleen Kihmm, Mark Bowyer, Alan Liu, Gilbert Muniz, Timothy E. Goldsmith, Susan M. Stevens, Robert Coulter, Frank Gilfeather.

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Bertram Ludaescher, Ph.D. 
Associate Professor - Department of Computer Science, UC Davis

Managing Scientific Data: From Data Integration to Scientific Workflow
Many scientific disciplines and computational sciences require effective and efficient ways to manage scientific data. An obvious technical challenge in several of these disciplines is the massive volume of data (sometimes now reaching Terabyte and Petabyte proportions). A maybe less obvious challenge lies in the (semantic) complexity and heterogeneous nature of scientific data. In this talk, I will give an overview of the challenges and approaches towards a solution for managing and integrating complex, heterogeneous scientific data. In a nutshell, ontologies and logic-based knowledge representation techniques can help in capturing scientific vocabulary and "domain knowledge", thereby facilitating data integration. Furthermore, tasks such as data access, integration, analysis, and visualization can be "glued" together by capturing them as individual processes of a larger scientific workflow. In this way, scientific workflows facilitate the (semi-)automation and reproducibility of scientific data management, analysis, and knowledge discovery. Examples from bioinformatics, ecoinformatics, and geoinformatics, motivated by various ongoing projects, are used to illustrate scientific data integration and workflow issues and techniques.

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William Hersh, M.D. 
Professor and Chair of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Image Retrieval in Biomedicine
Despite the growth in on-line biomedical information and search engines to find it, there are still significant challenges in retrieving information, especially for content that is not purely textual. This well-known leader in information retrieval will describe the current state of the art, what has been learned from research, and projects addressing the retrieval of more complex information types such as images and educational objects.

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Johnathon A. Showstack, M.P.H., Ph.D.
Professor of Medicine and Health Policy Academic Information Technology Coordinator, Office of the Executive Vice Chancellor Associate Director, Institute for Health Policy Studies University of California, San Francisco

IT in Academic Health Centers
The adoption and development of information systems and technologies at academic health centers (AHCs) has been substantially slower than in other major industries. The reasons for the lag in adoption of these technologies, the current state of information systems, and possible future developments at AHCs will be explored. The social, economic, clinical, and technological forces affecting the use of information systems in AHCs will be discussed in the context of AHCs as complex social and economic organizations.

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Cecil Lynch, M.D., M.S.
Assistant Adjunct Professor and Chair of Medical Informatics, Chief Public Health Informatics Enterprise Architect for CA DHS

Artificial Intelligence in Public Health Applications
Public health surveillance has typically been done with pen and paper but the CDC Public Health Information Network has started to transform the national public health surveillance infrastructure to an electronic based set of systems. Many of these systems have simply transformed the paper form to a screen representation with little else to distinguish the computer method of data collection from the paper based method. This lecture will entail an overview of how California is departing from this paradigm by using a highly structured and flexible knowledge source with built in rules in combination with a backward and forward chaining rule engine to drive it's statewide morbidity reporting application. We will discuss the advantages of abstraction of vocabulary and rules from the application and discuss issues of maintenance and authoring of an ontological knowledge model.

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Wasyl Malyi, Ph.D.
Director & Chief Informatic Scientist, Bioinformatics Shared Resource Core, NIH NCMHD Center of Excellence in Nutritional Genomics, UC Davis

Biocomputation: New Paradigms & Technologies
As Systems Biology becomes more and more of a unifying force in the arenas of Genomics, Proteomics, Metabolomics, Nutrigenomics, and the other ‘omics’ sciences, most currently existing biocomputational platforms will be overwhelmed by the informatic tasks soon to be demanded by researchers. Within the next several years, we predict that increasing numbers of experiments will produce databases consisting of hundreds to thousands of measurements on tens of thousands to hundreds of thousands of entities such as genes, proteins and small molecules. For example, a nutrigenomics crossover intervention study could easily involve 200 subjects, each sampled 100 to 200 times over six months – with each sample analyzed for genomic and proteomic expression and metabolomic profiling of over 200,000 entities, producing about eight billion individual measurements for the entire experiment. Significant improvements in computational infrastructures will be needed to analyze, visualize, and discover new knowledge about these entities and their complex interactions in living organisms. These computational challenges will rival those found today in nuclear weapons simulations, climate modeling , weather prediction, astrophysics, and hydrodynamics. In this presentation, I will discuss the nature of the hardware and software components of biocomputational infrastructures that will enable researchers to achieve these goals.

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Mark A. Musen, M.D., Ph.D.
Professor of Medicine (Medical Informatics) and Computer Science, Head - Stanford Medical Informatics, Stanford University

Building Ontologies from the Ground Up
Building ontologies that capture the concepts and relationships in different areas of human activity no longer is exclusively the province of philosophers or even that of computer scientists. Professionals of all kinds increasingly recognize the importance of creating explicit, formal models of the activities and objects with which they deal in their work and of the data that drive their decision making. Nowhere has the development of ontologies become more important than in biomedicine, where there are burgeoning grassroots efforts to codify human knowledge fur purposes of document retrieval, data analysis, and decision support. These pragmatic efforts, such as the initiative to develop the Gene Ontology, are enormously important. They do not always adhere to standard conventions for domain modeling or knowledge representation, however. There are obvious growing pains as workers most concerned about content knowledge learn to formalize that knowledge in a way that can facilitate automated information management and decision making. Professional societies, government agencies, and educational institutions can be enormously beneficial in providing resources to bolster these activities and to ensure that resulting ontologies are sound and maximally reusable. The advent of "the information society" requires the codification and dissemination of human knowledge in electronic form. Particularly in biomedicine, the people who work closest to that knowledge are already taking major strides to build the necessary ontologies and knowledge resources.

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Glenna Gobar, D.V.M., M.P.V.M., M.S.
Adjunct Assistant Professor, School of Medicine,  Co-Investigator/Co-Director of the California Electronic Death Registration System (CA-EDRS)

What do funeral directors, coroners, local health departments, and the office of vital records expect or want from CA-EDRS?
The speaker will discuss the process of involving end users from "conceptual ware" to "soft ware". This process begins with requirement gathering, progresses to design, development, testing, and does not end with deployment of a software application. This is only the beginning of rollout...

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