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CPATH: CDP: Integrating Biology and Computing: Empowering Future Computer Professionals
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Workshop on Integrating Biology and Computing
(Sponsored in part by a grant from the National Science Foundation 0829607)
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Date : 5th April 2010
Venue : IST 333, Penn State University, University Park Campus
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SCHEDULE
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7 : 30 - 8 : 00 A.M
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Breakfast
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8 : 15 - 8 : 45 A.M
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Interaction between Biology and Computing
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Joan Peckham, NSF Program Director
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9 : 15 - 10 : 00 A.M
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Invited Talk 1 : Anton Nekrutenko, Penn State Chair : Reka Albert,Penn State
Biography : Dr. Nekrutenko is an Associate Professor of Biochemistry and Molecular Biology at Penn State University. His research focuses on a variety of problems that can be formulated and solved within the framework of comparative genomics.
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“Integrating tools with data and ensuring reproducibility of research in life sciences”
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10 : 15 - 11 : 00 A.M
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Invited Talk 2 : Krishnendu Chakrabarty, Duke University Chair: Yuan Xie
Prof. Chakrabarty is a recipient of the 1999 National Science Foundation Early Faculty (CAREER) Award, the 2001 Office of Naval Research Young Investigator Award, the Mercator Professor awardfrom Deutsche Forschungsgemeinschaft, Germany, for 2000-2002, and best paper awards at the 2001 IEEE Design Automation and Test in Europe (DATE) Conference, the 2005 IEEE International Conference on Computer Design, and the 2007 IEEE International Conference on VLSI Design. He is a recipient of Duke University's 2008 Dean's Award for Excellence in Mentoring. Prof. Chakrabarty is currently serving as an ACM Distinguished Speaker.
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“Biochemistry on a Chip for Clinical Diagnostics: The Interplay Between Bio-molecular Recognition, Optimization Algorithms, and Computer-Aided Design.”
The speaker will describe how Computer Engineering concepts of optimization and automated design are revolutionizing laboratory procedures in molecular biology. Several droplet-based microfluidic biochip prototypes for clinical diagnostics have been designed using synthesis methods adopted from electronic chip design, and commercial screening products (chips + instrument) are expected to be announced later this year. Graph theory concepts, wire-routing routing algorithms from VLSI design, and combinatorial optimization methods have been used for designing droplet routing pathways and parallelizing fluidic operations in these chips. The speaker will also outline a Biochips Engineering course at Duke University that integrates basic concepts in molecular biology with chip design, optimization algorithms, and microfluidics.
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12 : 00 - 1 : 00 P.M
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Lunch Focus Talk : Kerry Bernstein Chair: Suman Datta, Penn State
(Invited Talk 3)
Biography : Mr. Bernstein received the B.S degree in electrical engineering degree from Washington University in St.Louis, and retired from IBM after 30 years of distinguished service since 1978. He holds 40 US Patents, and is a co-author of 3 college textbooks and multiple papers on high speed CMOS. His interests are in the areas of high performance circuit technology, delay variability, and CMOS radiation response. He is a senior member of IEEE, and is on the staff of “Research Update in Neuroscience” at Marine Biological Laboratories, Woods Hole, MA. He is a recognized leader in the field of applying emerging technologies to designing computing systems.
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“Interfacing Electronics with Live Cells”
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1 : 00 - 1 : 45 P.M
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Invited Talk 4 : Laurent Itti, Departments of Computer Science, Psychology and Neuroscience Graduate Program University of Southern California
Chair: Bob Collins, Penn State
Biography : Dr. Laurent Itti received his M.S. in Electrical Engineering with a specialization in Image Processing from the Ecole Nationale Superieure des Telecommunications, Paris, France, in 1994. He received his Ph.D. in Computation and Neural Systems from the California Institute of Technology, Pasadena, California, in 2000. He has since then been an Assistant (2000-2006) and Associate (2006-present) professor of Computer Science and voting faculty member of the cross-disciplinary Neuroscience Graduate Program at the University of Southern California (USC), Los Angeles, California. Dr. Itti has authored over 100 peer-reviewed publications in journals, books, and top-ranked conferences. Dr. Itti teaches Artificial Intelligence, Brain Theory and Neural Networks, Introduction to Robotics, Visual Processing, Neuroscience Core Course, Neural Basis for Visually Guided Behavior, and Computational Architectures in Biological Vision. Dr. Itti's laboratory comprises 15 students, postdocs and engineers, and is recipient of grants by the National Science Foundation, DARPA, the National Geospatial-Intelligence Agency, the Human Frontier Science Program (HFSP), the Office of Naval Research, the Army Research Office, and the National Institutes of Health. Dr. Itti has been distinguished through a number of awards, including the 2008 Okawa Foundation Research Award, being one of the 16 nationally selected speakers at the 2007 National Academy of Engineering's Frontiers of Engineering Symposium, and serving on Program Committees for several conferences by IEEE.
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“Modeling bottom-up and top-down visual attention in humans and monkeys”
Visual processing of complex natural environments requires animals to combine, in a highly dynamic and adaptive manner, sensory signals that originate from the environment (bottom-up) with behavioral goals and priorities dictated by the task at hand (top-down). Together, bottom-up and top-down influences combine to serve the many tasks which require that we direct attention to the most ''relevant'' entities in our visual environment. While much progress has been made in investigating experimentally how humans and other primates may operate such goal-based attentional selection, very little is understood of the general mathematical principles and neuro-computational architectures that subserve the observed behavior. I will describe recent computational work which attacks the problem of developing models of visual attentional selection that are more flexible and can be strongly modulated by the task at hand. I will back the proposed architectures up by comparing their predictions to behavioral recordings from humans and monkeys. I will show examples of applications of these models to real-world vision challenges, using complex stimuli from television programs, modern immersive video games, and outdoor localization of autonomous robots.
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1 : 45 - 2 : 30 P.M
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Invited Talk 5 :
Mariusz Lubomirski, Johnson and Johnson East Coast Research Center.
Biography: Dr. Lubomirski Graduated with BSc degree in Electronic, Computer and Systems Engineering from Loughborough University UK in 1987. He obtained PhD degree in Mathematical Statistics from University of Birmingham UK in 1991. He went on to work for variety of industries to include mining, steel and aerospace. In 2000 he joined biotech sector working for forensic DNA and then NIH. Since 2005 he supports drug discovery efforts at Johnson and Johnson East Coast Research Center.
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“Mathematical Modeling and Analysis of Brain PET Images”
Positron Emission Tomography (PET) is well established imaging technique enabling investigation of functional processes in the body. When used to image brain it yields much needed information about progression of disease, drug efficacy and understanding of drug acting mechanisms. Critical elements of the analysis of PET data involve mathematical, statistical, signal processing, software and GUI development techniques. This presentation will give example of the use of these techniques for the determination of drug dose response within brain.
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2 : 45 - 3 : 30 P.M
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Invited Talk 6 :
Anne Milasincic Andrews Professor of Psychiatry, University of California, Los Angeles
Chair: Darryl Farber, Penn State
Biography: Andrews is a Professor of Psychiatry and Biobehavioral Sciences at UCLA. She received her B.S. in Science from the Pennsylvania State University and her Ph.D. in Chemistry from the American University. She also attended the George Washington University, Sino-Soviet Institute for Russian Area Studies. Andrews was a U.S. Department of Education Fellow and an NIH Predoctoral Intramural Research Training Award (IRTA) Fellow in the Laboratory of Clinical Science at the National Institute of Mental Health (NIMH), where she carried out her doctoral research under the direction of Dr. Dennis Murphy. Andrews continued as a Postdoctoral IRTA Fellow and a Senior Staff Fellow at NIMH. In 1998, she joined the faculty at the Pennsylvania State University in the Departments of Chemistry and Veterinary and Biomedical Sciences and was affiliated with the Huck Institutes Neuroscience and Molecular Toxicology Programs. Andrews is a member of the American Chemical Society, Society for Neuroscience, Society for Electroanalytical Chemistry, and the Serotonin Club. She has served on multiple review panels for the National Institute of Mental Health and the National Institute on Neurological Disorders and Stroke.
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“Bioinspired Computing -- A Two-Way Highway”
I would cover our development of Matlab and Labview routines to visualize and analyze the kinetics of biomolecular recognition and transport of neurotransmitters and to deconvolve and process complex data from in vivo neurotransmitter signaling. I would also hit the highlights of what I covered in our course about deriving inspiration for novel computing paradigms inspired by information processing in the brain.
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3 : 30 - 4: 30 P.M
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Panel 2: "Challenges in interdisciplinary innovations in Undergraduate Curriculum"
Chair: Tom Richard, Penn State
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Panelists : Greg Link, U. of York
Benjamin Bishop, U. of Scranton
William Hancock, Penn State
Sam Thangaiah, Slippery Rock
Tom Litzinger, Penn State
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