Robert Kincaid Address 519 Spindrift Way Half Moon Bay CA 94019 rhkincaid@gmail.com http://rkincaid.net Phone 650 224 1289 Education 1982 Ph.D. Theoretical Chemistry, Cornell University, Ithaca NY 1979 M.S. Theoretical Chemistry, Cornell University, Ithaca NY 1976 B.S. Chemistry, Texas Christian University, Fort Worth TX Professional Affiliations and Activities Senior Member of the Association for Computing Machinery Senior Member of IEEE & Member of IEEE Computer Society Member of International Society for Computational Biology Member of Sigma Xi Poster co-chair, 2012-2013 IEEE BioVis, Industry Liaison, 2011 IEEE BioVis Program Committee 2011-2013 IEEE InfoVis & IEEE BioVis Co-chair for Student Volunteers, 2004 IEEE Visualization Paper Reviewer for: IEEE Transactions on Visualization and Computer Graphics IEEE BioVis Symposium IEEE Visualization Conference IEEE Information Visualization Conference IEEE Symposium on Visual Analytics Science and Technology EuroVis/IEEE-VGTC Symposium on Visualization ACM Symposium on Applied Computing Proteomics, Bioinformatics, Pacific Symposium on Biocomputing Experience Agilent Laboratories May 2013 - Present Section Manager, Computational Biology and Informatics Agilent Laboratories / Molecular Technologies Lab, Santa Clara CA Leads cross-functional distributed team of computer scientists, mathematicians and computational biologist conducting research in support of data analysis of life science instrument data. Agilent Laboratories April 2000 – May 2013 Senior Research Scientist Computational Biology and Computer Science Agilent Laboratories / Molecular Technologies Lab, Santa Clara CA Main research interests are Information Visualization and Visual Analytics that support interactive and visually-oriented data mining across widely disparate data (either separately or in joint analyses; particularly how various “omics” data can be combined with other complementary measurements such as clinical attributes and phenotypes. More recently I have investigated using emerging user interface technologies in laboratory work flows such as applying augmented reality to guide manual processes, using portable devices, natural user interfaces, etc. Most of my more recent publications describe the work publically accessible, but the more interesting aspects are still company confidential. Signal Lens RFLP Decoder Signal Lens: Designed and coded a novel research prototype which provides a very compact visualization which supports ad hoc visual data mining of long electronic time series. This work was presentation at the 2010 IEEE Information Visualization Conference and received a "Paper Honorable Mention" award and was published in the IEEE Transactions on Visualization and Computer Graphics. Additionally, a brief video demo was presented by Agilent CTO Darlene Solomon at the IEEE MTT-S International Microwave Symposium in 2009 and received press coverage. This research inspired an ongoing effort within Agilent to rethink the traditional visualization paradigms of electronic test and measurement equipment using advanced concepts from the fields of Information Visualization and Visual analytics. RFLP Decoder: Designed and coded software and algorithms to support authenticating fish species; a problem important to the food industry and critical to complying with new regulations to protect endangered fish species from overfishing. This software was released commercially as a critical component of the “Agilent DNA Fish ID Solution” and published in the Journal of Visual Experiments. MassVis MassVis: Designed and coded a visual analysis research platform to support a novel proteomics workflow developed by Kurt Dejgaard at McGill University. A cleverly designed scatter plot interface provides a highly interactive information browser for discovery of putative protein complexes. Pattern similarity matching is used to match ‘‘profiles’’ of similar proteins as a predictor of membership in a protein complex. Both supervised, interactive methods are provided as well as completely unsupervised complex prediction. This work was presented at the 2009 IEEE Symposium on Visual Analytics Science and Technology. The MassVis concept has also been awarded US patent 7,930,108. Line Graph Explorer VistaChrom Line Graph Explorer: Designed visualization and supervised a summer intern to code a research prototype providing a scalable Focus+Context visualization designed specifically for large collections of line graphs. Some features from this prototype were transferred to the Agilent product “DNA Analytics”. A detailed description of the prototype was publish at the ACM Workshop on Advanced Visual Interfaces (AVI ’06, Venice Italy). Line Graph Explorer was also awarded two US patents (7,750,908 & 7,825,929). VistaChrom: Designed and wrote a visual analytics environment for analyzing microarraybased comparative genomic hybridization data (aCGH). This was transferred as part of a new microarray-based CGH platform and is now known commercially as DNA Analytics (formerly CGH Analytics). Currently over 1000 scientific papers (largely in cancer genomics) cite the CGH or DNA Analytics platforms and frequently use screen shots from the application for publication figures. A detailed discussion of the application design and methodology was published in the journal “Information Visualization”. Mass Hunter/Profiler: Designed and coded the visualization components for a new Agilent platform for analyzing proteomic and metabalomic biomarkers based using Mass Spectrometry. This software was announced and demonstrated at ASMS and released commercially in 2005. VistaClara Hewlett-Packard & Agilent Technologies June 1997 April 2000 VistaClara: Designed and coded an exploratory heat map style visualization of gene expression data that combines additional meta-data to assist in finding meaningful patterns in the data. Published in SAC 2004 Proceedings. Portions of VistaClara were incorporated into the Agilent product “Synapsia” and a refactored version of VistaClara was provided as a free plug-in to the open source network analysis platform “Cytoscape”. Technical Lead, Bioinformatics Bioscience Products/Chemical Applications Group, Santa Clara CA Responsible for the design and implementation of the data storage subsystem for a next generation Microarray system. Responsible for design and development of Microarray probe design software used internally for the design and manufacturing of DNA Microarrays. This work led to inventorship in several microarray-related patents. Successfully led a cross-functional integration effort with third party software from Rosetta Inpharmatics including design of XML schemas to enable data exchange between both systems. This work was critical to allow Agilent DNA Microarray scanners to seamlessly interoperate with Rosetta’s software. Responsible for specifying, installing and maintaining an HP NetServer running NT Server, MS SQL Server, Sybase 11 and Oracle 8. This system operated as the central data storage system for the new Micro-Array system. Engineering lead of a small team responsible for on-going software support (enhancements and bug fixes) the 241 N- And C-Terminal Protein Sequencer. Other Work Senior MS-Windows Developer. First Floor 1996 - 1997 Responsible for graphical user interfaces (design and implementation). Designed and developed a notification add-on for the SmartBookmarks/InfoPilot line which interfaces to FirstFloor ActiveX/OLE automation interfaces as well as MAPI. Developed Java applets to provide CDF navigation capabilities to Netscape Netcaster Channels. Oracle Spring 1996 Senior Software Engineer Distributed Solutions Group, Workgroup Solutions Division. Delivered ocx-based components for database import/export/load as part of a remote database administration console (Enterprise Manager). This relied on an OLE2.0 distributed computing model. Developed prototype for web software management utilizing Java with CORBA and CORBA-like ORB's. This development included rich sophisticated UI comparable to traditional standalone MFC-based applications, but was completely platform independent and accessible via Web browsers. Xerox 1985-1995 Principal Software Scientist 1995 - Implemented Windows, Macintosh and Motif-based file upload functionality to World Wide Web servers. This involved direct low-level connectivity to remote Web servers including proxy services via the Windows Sockets API, Unix sockets and MacTCP. This file upload functionality was officially adopted in HTML 3.0. This is in support of a new Web-based service that also requires a sophisticated database back-end to maintain and handle customer job requests. 1994 - Responsible for overall software architecture of a new Microsoft At Work-based multifunction fax device. Specifically responsible for implementing the low level printer driver (DMA-based) as well as a "paper user interface" (i.e. Optical Mark Recognition) based on PARC developed "DataGlyph" technology. 1993 - Responsible for developing and prototyping new product concepts based on PARC technology, as well as providing overall technical leadership to the Tools and Utilities line of business. Developed new collaborative network-based applications based on PARC research in work group collaboration. Implemented and prototyped next generation of UI products from XSoft including TabWorks (was bundled on most Compaq computers). 1991-1992 - Lead developer and team leader of Rooms for Windows, the first highly successful and visible Windows-based product from the XSoft division of Xerox. Significant contributions were made to the actual development as well as a broad range of technical program management roles. 1990-1991 - Manager of "Operating Environments and Toolkit Support" responsible for coupling Xerox proprietary environment with SunOS and X11 via interoperability tools and environments. 1988-1990 - Team leader and key contributor to the X-Environment Window project (X server provided within the ViewPoint/GlobalView environment). Personally implemented direct lowlevel modifications to Sun Microsystems' X11/NeWS server code. Significant contributor to the Companion 386 project (PC/Viewpoint interoperability via a tethered PC environment). Involved heavy use of DOS and assembler development, including DOS device driver development. 1985-1987 - Lead developer and Team Leader of a large (~15 developers) engineering group responsible for developing a C-based PC word processor (Writer II/III shipped ~1986). Good Software 1984-1985 PharmAssist 1983-1984 Contributed to development of C-based PC word processor Contributed to development of UCSD Pascal-based in-store pharmacy automation system. Publications Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Casey Grote, Veronica Lin, Linda Ding, Nicole Francisco, Kimberly Chang, Wendy Xu, Nahum Seifelassie, Robert Kincaid, Designing RealityBased Interfaces for Experiential Bio-Design, Personal and Ubiquitous Computing (Special Edition on Educational Interfaces, Software, and Technology) in press. Melanie Tory, Robert Kincaid, Comparing Physical, Overlay, and Touch Screen Parameter Controls, ACM Interactive Tabletops and Surfaces 2013 Conference (ITS), 2013 (accepted). Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Traci Haddock, Swapnil Bhatia, Douglas Densmore, Robert Kincaid, MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design, Accepted IEEE Symposium on Biological Data Visualization (BioVis), 2013 (accepted). Wendy Xu, Kimberly Chang, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit Shaer, From Wet Lab Bench to Tangible Virtual Experiment: SynFlo. ACM Internation Conference on Tangible, Embedded and Embodied Interaction (TEI’13). Sirui Liu, Kara Lu, Nahum Seifeselassie, Casey Grote, Nicole Francisco, Veronica Lin, Linda Ding, Consuelo Valdes, Robert Kincaid, and Orit Shaer, MoClo planner: supporting innovation in bio-design through multi-touch interaction. ACM international conference on Interactive tabletops and surfaces (ITS '12) 307-310. Kimberly Chang, Wendy Xu, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit Shaer, SynFlo: an interactive installation introducing synthetic biology concepts, ACM international conference on Interactive tabletops and surfaces (ITS '12) 303-306. Robert Kincaid, Tactile Guides for Touch Screen Controls (BCS HCI 2012) 339-344. Ankit Singh, Alex Endert, Lauren Bradel, Christopher Andrews, Chris North and Robert Kincaid, Using Large Displays for Live Visual History of Cyber-security Analytic Process, in International Symposium on Visualization for Cyber Security (VizSec)2011: Carnegie Mellon University. Steffen Mueller, Harini Ravi, Natalia Novoradovskaya, Robert Kincaid and Yang-Lee Chee, Enhanced fish species identification by PCR-RFLP using the 2100 Bioanalyzer system. International Food Research Journal, 2011. 18(3): p. 1154-1158. R. Kincaid, SignalLens: Focus plus Context Applied to Electronic Time Series. IEEE Transactions on Visualization and Computer Graphics, 2010. 16(6): p. 900-907. R Formosa, H Ravi, S Happe, D Huffman, N Novoradovskaya, R Kincaid and S Garrett, DNAbased Fish Species Identification Protocol. Journal of Visualized Experiments, 2010(38). R Kincaid and K Dejgaard. MassVis: Visual analysis of protein complexes using mass spectrometry. in IEEE Symposium on Visual Analytics Science and Technology. 2009. IEEE. O. Mueller, E. Chang, D. Deng, T. Franz, D. Jing, R. Kincaid, Y. Konigshofer, M. Kratzmeier, M. McNulty, H. Qian, J. Schneider, H. Schulte, U. Seedorf, X. D. Tian, M. Van Cleve, D. Yang and G. Assmann, PROCAM Study: risk prediction for myocardial infarction using microfluidic high-density lipoprotein (HDL) sub-fractionation is independent of HDL cholesterol. Clinical Chemistry and Laboratory Medicine, 2008. 46(4): p. 490-498. R. Kincaid, A. Kuchinsky and M. Creech, VistaClara: An expression browser plug-in for Cytoscape. Bioinformatics, 2008. 24(18): p. 2112-2114. A. Barsky, T. Munzner, J. Gardy and R. Kincaid, Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context. IEEE Transactions on Visualization and Computer Graphics, 2008. 14(6): p. 1253-1260. H. Lam, T. Munzner and R. Kincaid, Overview use in multiple visual information resolution interfaces. IEEE Transactions on Visualization and Computer Graphics, 2007. 13(6): p. 12781285. D. X. F. Deng, A. Tsalenko, A. Vailaya, A. Ben-Dor, R. Kundu, I. Estay, R. Tabibiazar, R. Kincaid, Z. Yakhini, L. Bruhn and T. Quertermous, Differences in vascular bed disease susceptibility reflect differences in gene expression response to atherogenic stimuli. Circulation Research, 2006. 98(2): p. 200-208. A. Vailaya, A. Kuchinsky, R. Kincaid, A. Adler, R. Tabibiazar, R. Wagner and T. Quertermous. Ontology-based statistical analysis of microarray data. in 8th Annual Bio-Ontologies Meeting. 2005. A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech and A. Adler, An architecture for biological information extraction and representation. Bioinformatics, 2005. 21(4): p. 430-438. J. Y. King, R. Ferrara, R. Tabibiazar, J. M. Spin, M. M. Chen, A. Kuchinsky, A. Vailaya, R. Kincaid, A. Tsalenko, D. X. F. Deng, A. Connolly, P. Zhang, E. Yang, C. Watt, Z. Yakhini, A. Ben-Dor, A. Adler, L. Bruhn, P. Tsao, T. Quertermous and E. A. Ashley, Pathway analysis of coronary atherosclerosis. Physiological Genomics, 2005. 23(1): p. 103-118. R Kincaid, A Ben-Dor and Z Yakhini, Exploratory visualization of array-based comparative genomic hybridization. Information Visualization, 2005. 4(3): p. 176-190. Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael Creech and Annette Adler, An architecture for biological information extraction and representation, in Proceedings of the 2004 ACM Symposium on Applied Computing, 2004, ACM: Nicosia, Cyprus. p. 103-110. R Kincaid. VistaClara: an interactive visualization for exploratory analysis of DNA microarrays. in ACM Symposium on Applied Computing. 2004. ACM. M. T. Barrett, A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry, K. Baird, P. S. Meltzer, Z. Yakhini, L. Bruhn and S. Laderman, Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proceedings of the National Academy of Sciences of the United States of America, 2004. 101(51): p. 17765-17770. G Delenstarr, H Cattell, C Chen, AN Dorsel, RH Kincaid, K Nguyen, NM Sampas, S Schidel, KW Shannon and A Tu. Estimation of the confidence limits of oligonucleotide-array-based measurements of differential expression. in SPIE. 2001. D. Huckaby, R. Pitis, R. Kincaid and C. Hamilton, Inclusion-exclusion calculation of the dipole-dipole energy of hexagonal ice and of cubic ice. The Journal of Chemical Physics, 1993. 98: p. 8105. RH Kincaid and DA Huckaby, Harmonic surface entropy of noble gas crystals: Cell cluster method. The Journal of Chemical Physics, 1983. 78: p. 2598. RH Kincaid and HA Scheraga, Revised empirical potential for conformational, intermolecular, and solvation studies. 7. Testing of parameters by application to liquid methane. The Journal of Physical Chemistry, 1982. 86(5): p. 838-841. RH Kincaid and HA Scheraga, Revised empirical potential for conformational, intermolecular, and solvation studies. 6. Testing of parameters by application to liquid ammonia. The Journal of Physical Chemistry, 1982. 86(5): p. 833-838. RH Kincaid and HA Scheraga, Acceleration of convergence in Monte Carlo simulations of aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane. Journal of Computational Chemistry, 1982. 3(4): p. 525-547. RH Kincaid and DA Huckaby, Cell cluster calculations of the surface entropy of harmonic fcc crystals. The Journal of Chemical Physics, 1982. 76: p. 3836. RL Kincaid and DA Huckaby, Two methods for calculating the effect of vacancy defects on the free energy of harmonic solids. The Journal of Chemical Physics, 1976. 65: p. 2353. Issued Patents Pat. No. 8,340,389 8,131,471 7,930,108 7,894,998 7,879,541 7,825,929 7,750,908 7,588,889 7,519,605 7,344,831 7,224,362 7,155,453 6,950,756 6,920,448 6,461,816 6,251,588 Title Cellular- or Sub-Cellular-Based Visualization Information Using Virtual Stains Methods and system for simultaneous visualization and manipulation of multiple data types Exploratory Visualization of Protein Complexes by Molecular Weight Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays Apparatus and methods of detecting features on a microarray Systems, tools and methods for focus and context viewing of large collections of graphs Focus plus context viewing and manipulation of large collections of graphs Chemical arrays and methods of using the same Systems, methods and computer readable media for performing a domain-specific metasearch, and visualizing search results therefrom Methods for controlling cross-hybridization in analysis of nucleic acid sequences Systems and methods for providing visualization and network diagrams Biotechnology information naming system Rearrangement of microarray scan images to form virtual arrays Domain specific knowledge-based metasearch system and methods of using Methods for controlling cross-hybridization in analysis of nucleic acid sequences Method for evaluating oligonucleotide probe sequences