Erich Bremer - Curriculum Vitae

Director for Cyberinfrastructure, Health Sciences Division of Applied Informatics
School of Medicine, Stony Brook University
Stony Brook, New York 11794-8330


1991 - M.Sc. in Computer & Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY
1990 - B.S. in Computer & Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY
9/2013 - present Director for Cyberinfrastructure, Health Sciences Division of Applied Informatics, Stony Brook University
responsible for over-seeing Health Sciences Research and Academic systems and network infrastructure, data and computational infrastructure, and web infrastructure and technological direction for and it's related web sites.
9/2013 - present Stony Brook University Libraries, Interim Director for Information Technologies
9/2006 - 9/2013 Associate Director, Department of Medical Informatics, Stony Brook University
1999 - 8/2006 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 – Department of Pharmacological Sciences
Current Projects Haylyn - Collaborative 3D RDF visualization and editing system using WebGL, OpenSimulator
Encore - Drupal 8.X module providing interface between Drupal and Wowza Streaming Server (in-development)
WebID4VIVO - Adds W3C WebID provisioning and authentication to VIVO.
Past Projects Monolith - Collaborative Molecular Visualization for OpenSimulator and Second Life

Speaking Events

2013 - CEWIT - Identity and Authentication using Semantic Web Technologies (WebID4VIVO)
October 25, 2010 - Internet Librarian 2010 - "RDF Search Alchemy - Drinking the Semantic Koolaid" - protoype search for PubMed 2010 RDF conversion linked with Stony Brook University Health Science Center Library's MARC Catalog RDF conversion.
March 24, 2009 - ISTE Speaker Series event: Monolith: Rapid Molecular Visualization for Second Life








2013 - CEWIT - Big Data Architecture and Analytics (track co-chair)
2014 - Conference on Semantics in Healthcare and Life Sciences (CSHALS 2014)
2013 - Conference on Semantics in Healthcare and Life Sciences (CSHALS 2013)
2013 - Coalition for Network Information (CNIFall 2013 (Washington, DC - December 9-10, 2013)
2013 - Coalition for Network Information (CNISpring 2013 (San Antonio, TX - April 4-5, 2013)
2012 - Conference on Semantics in Healthcare and Life Sciences (CSHALS 2012) 
2012 - Coalition for Network Information (CNIFall 2012 (Washington, DC - December 10-11, 2012)
2011 - 2nd Annual VIVO Conference (Poster presentation)
2011 - Gordon Research Conference - Visualization in Science and Education (Poster Presentation)
2011 - VIVO Implementation Conference (June 23-24)
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 - Fourth International Conference on Digital Information Management (ICDIM) University of Michigan Ann Arbor, MI
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





2013 - present - World Wide Web Consortium (W3C) Advisory Committee representative for Stony Brook University
2013 - present - American Association for American Colleges, Group on Information Resources (AAMC GIR), Stony Brook University representative
2011 - present - WebID Community Group, contributing to WebID specifications
2012 - present - Coalition for Network Information (CNI), Stony Brook University representative
2014 - present - Stony Brook Semanic Web Meetup, Organizer
2005 - present - Chair & Chief Network Engineer – Academic, Research, and Computing and Networking (ARCAN) group
2008 - present Senate sub-committee for computing and communications
2005-2007 - 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

Professional Affiliations 2007-Present - Institute of Electrical and Electronics Engineers (IEEE)
2013-Present - Association for the Advancement of Artificial Intelligence (AAAI)
2012-Present - International Society for Computational Biology (ISCB
Grant Work

2006-Present - New York State Department of Health (NYSDOH) on-going work being performed under a memorandum of understanding between State University of New York (SUNY) and the NYSDOH

2012 - CTSAconnect Consortium -an 18-month contract from Booz Allen Hamilton and the National Center for Advancing Translational Sciences, worked as part of Stony Brook University Team.  Contributed to CTSA ShareCenter project.

2011 - VIVO Mini-Grant: Integrating the UMLS Ontology into VIVO for Linking Biomedical Scientists, awarded from the NIH VIVO consortium.  team member

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) pubmedid: 16388773




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, Jena, VIVO
NoSQL / Triple-stores: Virtuoso, Jena TDB, Jena SDB, Sesame
SQL Databases: MySQL, MS-SQL 2008/2000, 7.0, 6.5, PostGRES SQL, Oracle 8iR3, Oracle 10g, TerraData
  Web Specifications: 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 5-8, Joomla 1.X, Norton Security for SMTP, CommuniGate Mail/Calendaring 4.X-6.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, SL-LSL, CGI, C Shell Scripting, LISP, Object Pascal, DAP-FORTRAN, FORTRAN, MS-Visual Basic, dBase, Assembly
IDE: Netbeans, Eclipse, Borland Delphi 1 to 2006, JBuilder 1.0-2006

  Operating Systems: Windows 8/7/2008/2003/XP/2000/NT/ME/98/95/3.1X, RHEL 3.0-6.X, CentOS, Unbuntu, MacOSX, iPhone, Android, Redhat Fedora, Novell Netware 3.x, AIX, SCO UNIX, MS-DOS, VAX/VMS, MTS, OS/2, IRIX, Solaris