Associate Director, Medical Informatics Department
School of Medicine, Stony Brook University
Stony Brook, New York 11794-8330
1-631-619-0888 (voice)

Education

 1991 - M.S. in Computer & Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY
1990 - B.S. in Computer & Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY
Experience  
9/2006 - Present Associate Director, Department of Medical Informatics, Stony Brook Univeristy
8/2006 - 1999 Director of Information Technology, Dept. of Pharmacological Sciences, Stony Brook University
1999 - 7/2006 Supervising Program Analyst, Stony Brook University – Office of Scientific Affairs
1993 - 1998 Senior Program Analyst, Stony Brook University – Dept. of Pharmacological Sciences
Current Projects Nexus - Collaborative 3D RDF visualization and editing system using WebGL, OpenSimulator, and Second Life
Encore - Drupal 7.X module providing interface between Drupal and Wowza Streaming Server (new)
Past Projects Monolith - Collaborative Molecular Visualization for OpenSimulator and Second Life

Speaking Events

October 25, 2010 - Internet Librarian 2010 - "RDF Search Alchemy - Drinking the Semantic Koolaid" - protoype search for joined PubMed 2010 RDF conversion with Health Science Center Library's MARC Catalog RDF conversion.

March 24, 2009 - ISTE Speaker Series event: Monolith: Rapid Molecular Visualization for Second Life

Conferences

 

 

 

 

 

 

2011 - 2nd Annual VIVO Conference (Poster presentation)
2011 - Gordon Research Conference - Visualization in Science and Education (Poster Presentation)
2011 - VIVO Implementation Conference
2011 - NIH Workshop on Value Added Services for VIVO (March 25-26)
2011 - Conference on Semantics in Healthcare and Life Sciences (CSHALS 2011) (Poster Presentation)
2010 - Association of American Colleges (AAMC) - Washington, DC
2010 - American Chemical Society (ACS) CINF - RDF Boston, MA
2010 - Conference on Semantics in Healthcare and Life Sciences (CSHALS 2010)
2009 - Association of American Colleges (AAMC) - Boston, MA
2009 – Network-Based Information Systems (NBIS) 2009 Indianna University - Purdue University
2009 - 2009 Fourth International Conference on Digital Information Management (ICDIM) University of Michigan Ann Arbor, MI, USA
2009 – Northeastern Group on Educational Affairs (NEGEA), Hershey, PA
2009 – Virtual Worlds Conference (Enage Expo) , New York, New York
2008 – Association of American Colleges (AAMC) - San Antonio, Texas
2008 – Northeastern Group on Educational Affairs (NEGEA), Burlington, Vermont

 

Professional Activities

 

 

 

 

2005 - present - Chair & Chief Network Engineer – Academic, Research, and Computing and Networking (ARCAN) group
2008 - present Senate sub-committee for computing and communications
2007 - Senate sub-committee for computing and communications (ex-officio)
2006 - Senate sub-committee for computing and communications (ex-officio)
2005 - Senate sub-committee for computing and communications (ex-officio)
2000 - Search committee for UNIX administrator for HSC Library
2000 - Search committee for UNIX administrator for Medical Informatics
1999 - Search committee for Web support person in Medical Informatics
1999 - Electronic Communications Committee
1999 - Search committee for Director of UHMC Networking
1998 - Pharmacological Sciences 25-year anniversary organizational committee
1998 - Structural Biology Institute (SBI) organizational committee
1998 - Search committee for two programming positions in Medical Informatics
1998 - Mock-review committee for BNL PDB Databank
1996 - Search committee for UNIX administrator in Medical Informatics
1996 - Search committee for web master in Medical Informatics
1995 - Search committee for programming position in Medical Informatics
1994 - Site visit at UCSF computer graphics lab
Publications Siddhartha Basu, Erich Bremer, Chun Zhou, and Daniel F. Bogenhagen - MiGenes: a searchable interspecies database of mitochondrial proteins curated using Gene Ontology annotation, Bioinformatics (2005)

Acknowledgements

 

 

 Dmitry O. Zharkov, Gali Golan, Rotem Gilboa, Andrea S. Fernandes, Sue Ellen Gerchman, Jadwiga H. Kycia, Robert A. Rieger, Arthur P. Grollman, and Gil Shoham"Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate" EMBO J. 2002 February 15; 21(4): 789-800. (acknowledged for work on Molecular Modeling)

Zharkov, D.O. & Grollman, A.P.  MutY DNA glycosylase:  base release and intermediate complex formation.  Biochemistry 37 12384-12394 Adipogenesis (1998). (acknowledged for work on Molecular Modeling)
Computing Skills
 Semantic Web: Resource Description Framework (RDF), RDFS, OWL, SPARQL, Virtuoso, Jena, VIVO

 Databases: MySQL, MS-SQL 2008/2000, 7.0, 6.5, PostGRES SQL, Oracle 8iR3, Oracle 10g, TerraData
  Web Protocols: HTML5 (WebSockets, Webworkers, Canvas2D), WebGL
   Web Software: Jetty, Tomcat, Apache HTTP, Microsoft IIS, DSpace, Alfresco, SugarCRM
  Networking: NFS/NIS, SMTP, LDAP, H.323, SIP, TCP/IP, IPX/SPX, HTTP, SSH, WebDAV, Windows Update Server, Norton Anti-virus Server
  Networking Hardware: Cisco Catalyst 6513, 45XX, 35XX switches, Cisco Firewall FSM, ISS Proventia G1200, Nortel 450T, 350T, IBM/ISS RealSecure, various protocol analyzers
  Video Teleconferencing: Tandberg/Cisco Codian 4250, Tandberg/Cisco C90, C60, Tandberg/Cisco Content Management System, Tandberg/Cisco Management System
  Internet:  Darwin Streaming Server, Shoutcast, Drupal 5-7, Second Life, Mambo/Joomla Content Management Systems 1.X, Norton Security for SMTP, CommuniGate Mail/Calendaring 4.X-5.X, Sun IMS 3.X-5.X, Sun Calendaring, Mecury Mail, Sendmail, Oracle Collaboration Suite, MS VPN
  Languages:  Java/JDBC/CORBA, Javascript, C#, Prolog, C/C++, Perl, Second Life LSL, CGI, C Shell Scripting, Netbeans, Eclipse, Borland Delphi 1 to 2006, JBuilder 1.0-2006, LISP, Object Pascal, DAP-FORTRAN, FORTRAN, MS-Visual Basic, dBase, Assembly
  Operating Systems: Windows 7/2008/2003/XP/2000/NT/ME/98/95/3.1X, RHEL 3.0-5.X, CentOS, Unbuntu, MacOSX, iPhone, Redhat Linux 6.x-9.x, Redhat Fedora, Novell Netware 3.x, AIX, SCO UNIX, MS-DOS, VAX/VMS, MTS, OS/2, IRIX, Solaris