David Sigfredo Angulo                                       8014 Kedvale

                                                                                                        Skokie, IL. 60076

                                                                                                           (708) 558-0206

                                                                                                           dangulo@AnguloConsulting.com

                                                                                                           http://AnguloConsulting.com

Overview:  Superlative level manager, developer, educator, and researcher that has spent a career identifying and becoming an expert in the nascent technologies that ultimately become the foremost technologies and in developing and utilizing exceptional management and communication skills.  Areas of specialization include grid, distributed, parallel, and high performance computing, biomedical informatics, object oriented technology, internet programming, test driven development, software architecture, XML, JUnit, ANT, and Agile Development.

Education

1970-1974

Attended Lake Central HS.  Graduated third in class.  SAT scores in 99+ percentile

 

1973-1974.

Attended Purdue and Valparaiso Universities while in high school.

 

1974-1975.

Attended California Institute of Technology.

 

1976-1979

1994-1998

Attended Loyola of Chicago.  Obtained MS in Computer Science.
Received the Robert B. Reisel award for outstanding academic achievement

 

2004-

Attended DePaul University as a PhD student in Computer Science

Race       Hispanic

Experience

DePaul University                               Instructor                             January 2003 to Present

Best of conference poster at SuperComputing 2004.  Leading member of team that won the SuperComputing 2002 Grand Challenge Award.  Taught undergraduate and graduate courses.  Helped investigate how best to start up a Research Institute. Chaired the Colloquium Committee. Led the process to start a Bioinformatics major.

University of Chicago         Sr. Research Systems Analyst & Graduate Instructor               July 2000 to Nov 2002
and Argonne National Labs

Developed and taught graduate level courses in XML and Web Services (new courses for the University). Lead several research projects in high performance distributed grid computing (Globus) using Java, C++, and C in heterogeneous Unix environments.  Researched adaptive techniques to maintain high performance in a changing environment (resources coming on and off line, changing load characteristics, etc.).  Elected Co-Chair of the Life Sciences Grid Research Group in the GGF.  Member of the Globus project which won the prestigious R&D 100 award. 

Loyola University                                Visiting Professor                              January 1998 to September 2001

Taught several different courses as a full time, non-tenure track faculty member.  Courses included both graduate and undergraduate OO with Java and C++, both graduate and undergraduate Visual Basic, several introductory classes with Java and Visual Basic, Web Design, and CGI/Web programming with Perl, Java Scripts, and Java Servlets.  Was the class coordinator for introductory Visual Basic.  Developed two new courses for the department (CGI/Web programming and Client/Server Web Programming).  Developed three courses for Web based remote learning (CGI/Web programming, Client/Server Web Programming, and Object Oriented Programming).

SPSS                                     Master Software Engineer                May 1993 to January 1998

Became first of the new employees to lead the company in Object Oriented Programming.  Led a team developing OLE Automation for ActiveX objects. Wrote an Object Oriented parsing system. Wrote several GUI systems.  Languages: C++, Java, VB Hardware: PC (Win 95, NT) Technologies ActiveX, COM, OLE Automation, STL, MFC, OO Design Patterns, Booch Object Design, Visual Basic OLE Scripting,

SSA                                        Sr. Software Engineer                        November 1991 to May 1993

Led team development of a client/server (PC Windows/AS-400) case tool. The code generation facility was an interpreter using PC/YACC and generated C++ code.  Led a team implementing applications using this case tool. Languages: C++ Hardware: PC (Windows, OS/2) DBMS: MS SQL, QELIB.

Datalogics                             SQA Librarian                                    October 1988 to November 1991

Identified and collected code of potential generic use, modifying code to make it generic, and documenting and advertising the resulting library. This resulted an in-house OO library. Was the resource expert for all OO technology.  Developed an in-house CASE tool for use with a relational DB.  Designed and wrote a generic text DB app. Left a year after project was canceled for downsizing. Languages: C++, C, SmallTalk, and Prolog. Hardware: VAX, PC (DOS). DBMS: Rdb, Oracle.

SIR/ISI                                  Sr. Technical staff                              December 1986 to August 1988.

Responsible for development of SIR DBMS, SIR 4GL programming language, and SIR AI products on a VAX.  Also ported product to DG machines.  Left when the firm went bankrupt. Languages: FORTRAN, DG assembler, C. Hardware: DG, VAX, PC (DOS), SUN (UNIX). DBMS: SIR, Oracle, Ingress.

Angulo Consulting             President.                                             1985 to present.

Worked for a variety of clients including tuning a McDonnell-Douglas CAD-CAM system and writing CAD-CAM macros to interface to the OS, doing cabling, financial applications. web programming, OO programming, XML, VoXML, and WML.

Orleans Co                           DP manager.                                        October 1984 to October 1985.

In charge of all communications, hardware, software development, trouble shooting, operations, and DP expenditures.  Developed specifications for a manufacturing/inventory/shipping application.  Left when the plant was closed. Languages: COBOL Hardware: DG. DBMS: INFOS, DBMS (a networked manager).

Lerner Newspapers            Programmer/Analyst.                        June 1980 to October 1984.

In charge of A/R, A/P, G/L, Circulation, and billing projects (from feasibility studies to implementation).  Helped develop a proprietary DBMS.  Wrote a communications program and a precompiler to be used with the DBMS. Languages: DG/L and DG assembler. Hardware: DG. DBMS: In-house, INFOS.

Chicago Tribune Programmer.                                       February 1979 to June 1980.

In charge of Editorial on-line system.  Wrote a CPU-to-CPU communications program. Languages: SAIL (an ALGOL derivative), Macro-10 assembly, PDP-11 assembly, 8080 assembly, and COBOL. Hardware: DEC system-10, 8080, and PDP-11.


Diversity

  • Organized and ran the diversity workshop in the NSF retreat for REU PIs in October of 2005
  • Organized and ran the Internships Workshop for Latino students at the Illinois Latino Council on Higher Education (ILaCHE) in May of 2006
  • Member of the DePaul President’s Diversity Council subcommittee on Communications  
  • Member of DePaul’s El Salvador Project. 
  • Organizing a DePaul Hispanic Faculty and Staff organization.
  • Member of Illinois Latino Council on Higher Education (ILaCHE) for 2005, 2006, and 2007.
  • Ran an NSF REU Site (Research Experience for Undergraduates) which had participation of 37% minority students.  Funded by NSF for $260,343
  • Published over a dozen papers and posters with minority and women students.
  • Mentored CTI students in the McNair Fellowship
  • Mentored three women and minority students in the DePaul URAP program.
  • Member of the CTI Diversity Committee 2006-07, 2007-08
  • Member of Hispanic and Latino Organization at the Argonne National Laboratory.

 


Publications, Talks, Grants, and Program Committees

Journal Editor

Guest Editor for the ACM Crossroads Journal Special Issue on Bioinformatics 13-1, Fall 2006

 

International Journals and Conferences: Publications and InvitedTalks

Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth Jr, David Jabon, Timothy McMurry, David Sigfredo Angulo, Stephen J. Kron, "Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry." Journal of Mass Spectrometry. Volume 42 , Issue 12 (December 2007) pp. 1076.Angulo, David and Farazdel, Abbas.  The Future of Life Sciences Applications on Grids. Global Grid Forum 17, Tokyo, Japan.  May, 2006

Kolbrun Kristjiansdottir, Donald Wolfgeher, Donald L. Helseth Jr., Nick Lucius, David Sigfredo Angulo and Stephen J. Kron. "Phosphoprotein profiling: Cell cycle regulated phosphoproteins and complexes in yeast. American Association for Cancer Research Special Conference: Advances in Proteomics in Cancer Research, Amelia Island, Florida, February 27 - March 2, 2007

Angulo, David and Farazdel, Abbas.  LS Grids.  Open Grid Forum 20, Manchester, England, July  2007

Angulo, David and Farazdel, Abbas.  LSG-RG Future Directions.  Open Grid Forum 21, Seattle, October 2007.

Angulo, David.  Pharma in LSGrid  Boston, February, 2008

Angulo, David and Farazdel, Abbas. LSG-RG Future Directions.  Global Grid Forum 10, Tokyo, Japan, February 2007

Dominic Battré, David Sigfredo Angulo, “MPI Framework for Parallel Searching in Large Biological Databases,” J. Parallel Distrib.Comput. (2006), doi: 10.1016/j.jpdc.2006.08.003

Angulo, David.  LSGrid-2007.  Third International Symposium of Life Science Grid 2006, Tokyo, Japan, November 12-13, 2006

Angulo, David Sigfredo. "The Bioinformatics Revolution," J. ACM Crossroads 13-1. Fall 2006.

Angulo, David Sigfredo. "Challenges in Systems Biology: An Interview with Dr. Lee Hood, Inventor of the DNA Sequencer," J. ACM Crossroads 13-1. Fall 2006.

Angulo, David and Farazdel, Abbas.  The Future of Life Sciences Applications on Grids.  Global Grid Forum 17, Tokyo, Japan.  May, 2006

Angulo, David and Farazdel, Abbas. LS Grids.  Global Grid Forum 18, Washington, DC, September, 2006

Angulo, David and Farazdel, Abbas.  Life Sciences Applications on Grids Global Grid Forum 11, Honolulu, Hawaii, June, 2004

Angulo, David and Farazdel, Abbas.  Healthcare and Life Sciences Applications on Grids. Global Grid Forum 12, Brussels, Belgium, September, 2004

Angulo, David and Farazdel, Abbas.  HealthGrids.  Global Grid Forum 13, Seoul, S. Korea, March, 2005

Angulo, David and Farazdel, Abbas.  Healthcare Security and Privacy. Global Grid Forum 14, Chicago, June, 2005

Angulo, David and Farazdel, Abbas.  Security and Privacy Needs of Health Grids. Global Grid Forum 15, Boston, October 2005

Angulo, David and Farazdel, Abbas.  HealthGrids Global Grid Forum 16, Athens, February2006

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Developing a Distributed and Scalable Foundation for Mass Spectrometry Data. 19th annual National Conference on Undergraduate Research. Lexington, VA April 21-23, 2005.

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor.  Mass Spectrometry in the Illinois BioGrid (Poster).  19th annual National Conference on Undergraduate Research. Lexington, VA April 21-23, 2005.

Angulo, David. Mass Spectrometry in the Illinois BioGrid (Demonstration). SC2004 Conference, Pittsburgh, PA.  Nov. 6-12, 2004.

von Laszewski, Gregor; Amin, Kaizar; Bone, Matt; Hategan, Mike; Sahasrabudhe, Pankaj; Sosonkin, Mike; Winch, Robert; Vijayakumar, Nithya; Angulo, David. Building Grid Workflows from Legacy Applications.  Proceedings of SC2004 Conference, Pittsburgh, PA.  Nov. 6-12, 2004.

·       Awarded Best of Conference Poster – 109 high quality peer-reviewed accepted posters

Angulo, David; Schilling, Alex; Drew, Kevin; Freeman, Tim.  Mass Spectra Analysis on the Illinois BioGrid.  Proceedings of NETTAB 2004 (Network Tools and Applications in Biology) Conference, Camerino, Italy.  September 5-7, 2004.

Colubri, Andrés; Raddatz, Jessica Lyn; Angulo, David.  AIfold: A Statistical Potential for Protein Folding.  Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB).  Glasgow, Scotland, UK. July 31 - August 4, 2004.

Holly Dail, Otto Sievert, Fran Berman, Henri Casanova, Asim YarKhan, Sathish Vadhiyar, Jack Dongarra, Chuang Liu, Lingyun Yang, Dave Angulo, and Ian Foster.  Scheduling in the Grid Application Development Software Project.    (Book Chapter) in Grid Resource Management: start of the Art and Future Trends.  Nabrzyski, et. al. ed.  Boston: Kluwar, 2003.

Dave Angulo. Utilizing the XML DOM in C for Grid Applications.   Invited Featured Speaker at the 2003 International WebServices/XML Conference & Expo, Toronto.

GridLab: Enabling Applications on the Grid.  Gabrielle Allen, Dave Angulo, Tom Goodale, Thilo Kielmann, André Merzky, Jarek Nabrzysky, Juliusz Pukacki, Michael Russell, Thomas Radke, Edward Seidel, John Shalf, Ian Taylor.  Grid Computing - GRID 2002, Third International Workshop, Baltimore 39-45

Toward a Framework for Preparing and Executing Adaptive Grid Programs. Ken Kennedy, Mark Mazina, John Mellor-Crummey, Keith Cooper, Linda Torczon, Fran Berman, Andrew Chien, Holly Dail, Otto Sievert, Dave Angulo, Ian Foster, Dennis Gannon, Lennart Johnsson, Carl Kesselman, Ruth Aydt, Daniel Reed, Jack Dongarra, Sathish Vadhiyar, and Rich Wolski. April 2002, Proceedings of NSF Next Generation Systems Program Workshop (International Parallel and Distributed Processing Symposium 2002), Fort Lauderdale, FL.

Design and Evaluation of a Resource Selection Framework for Grid Applications.  HPDC-11, the Symposium on High Performance Distributed Computing, July 2002, Edinburgh, Scotland

Grid Computing & Web Services: A Natural Partnership.  Invited talk at the Poznan Supercomputing Center, Poznan, Poland, February, 2002.

The Anatomy of the Grid: Enabling Scalable Virtual Organizations.  Invited talk at the 2nd US-Hungarian Grid Workshop, Budapest, Hungary, February, 2002.

Grid Computing & Web Services: OGSA for GridLab.  Invited talk at the GridLab Workshop, Poznan, Poland, February, 2002.

Adaptive Grid Computing: Detecting and Adjusting for Dynamic Grid Conditions.  Invited Demonstration and Talk given at Supercomputing 2001 conference.  November 2001.

Nomadic Grid Applications: The Cactus WORM.  Invited talk at the High Performance Distributed Computing conference and Globus Retreat, August 2001

The Cactus Worm: Experiments with Dynamic Resource Discovery and Allocation in a Grid Environment.  International Journal of High-Performance Computing Applications.  Volume 15, Number 4.  2001

 

Local Conference Publications

Puryear, Eric; Van Puymbrouck, Jennifer; Angulo, David Sigfredo; Drew, Kevin; Hollenbeck, Lee Ann; Battre, Dominic; Schilling, Alex; Jabon, David; von Laszewski, Gregor.  "Achieving I/O Improvements in a Mass Spectral Database."  ACM Crossroads Volume 13 ,  Issue 2 (December 2006) p. 11Kwak, Gil; Helseth, L. Donald Jr.; Schilling, Alex; Angulo, David Sigfredo.  Hypothetical Sequence Analyzer (Poster).  BioMedical Informatics Workshop. Chicago, IL. October 13, 2006.

Rob Vogelbacher, Benjamin Capraro, Tobin Sosnick, Shohei Koide, David Sigfredo Angulo, IBG GeneDesigner: DNA Sequence Optimization for Designed Proteins BioMedical Informatics Workshop. Chicago, IL. October 13, 2006

  • Awarded Best of Conference Bioinformatics Poster

Kwak, Gil; Helseth, L. Donald Jr.; Schilling, Alex; Angulo, David Sigfredo.  Hypothetical Sequence Analyzer (Poster). BioMedical Informatics Workshop. Chicago, IL. October 13, 2006.

Donald L. Helseth, Jr., Laurie Parker, Kolbrun Kristjánsdóttir, Kevin Drew, Don Wolfgeher, Alex Schilling and David Sigfredo Angulo.  Developing Post-Translational Modification MS Tools (Poster). Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006.

Rob Vogelbacher, Benjamin R. Carpraro, David Sigfredo Angulo, Tobin Sosnick, Shohei Koide.  IBG GeneDesigner: DNA Sequence Optimization for Designed Proteins (Poster).  Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006.

David Sigfredo Angulo, Bryan Beaumont, David Kendall, Jonathan Gemmell, Michael Boyle, Gregory Zivich, Patrick Smyth, Frantz Gabeau, Anthony Jackson.  Pelagic: A Bioinformatics Architecture in R (Poster).  Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006.

Gil D. Kwak , Larry L. Helseth Jr., Alexander B. Schilling, and David Sigfredo Angulo.  Hypothetical Sequence Analyzer (Poster). Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006.

Laurie Parker, Aaron Engel-Hall, Kevin Drew, George Steinhardt, Donald L. Helseth, Jr., David Sigfredo Angulo, Alex Schilling and Stephen J. Kron, Quantifying peptide phosphorylation using MALDI-TOF mass spectrometry, Chicago Biomedical Consortium 4th Annual Symposium, "Infrastructures for Systems Biology". Chicago, IL. September 29, 2006.

Jackson ; Angulo, David.  The Design of an Analog Computer to Simulate Protein Folding (Poster).  Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Gemmell, Jonathan; Kohn, Stephen; Angulo, David; Sosnick, Tobin; Freed, Karl; Jha, Abhishek; DeBartolo, Joseph. The Illinois Bio-Grid Protein Map (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Harman, Dennis; Angulo, David; Drew, Kevin; Schilling, Alex. A Data Model for Annotating the Peaks of Mass Spectrum Data (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Kwak, Gil; Angulo, David; Shilling, Alexander. Hypothetical Sequence Analyzer (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

·      Awarded Best of Conference Poster

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Enhancing a Mass Spectrometry I/O Framework. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Comparing Mass Spectra (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Van Puymbrouck, Jennifer; Puryear, Eric; Angulo, David; Schilling,Alex; Drew, Kevin; Jabon,David; von Laszewski, Gregor. Mass Spectrometry Database Infrastructure and Data Import Module (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

McElhaney, Renee; Angulo, David Sigfredo; Frank, Ed; Siwamutita, Paiboon; Stejerean, Cosmin. Developing MSLauncher as Analysis Tool (Poster). Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Ala Eldeen, Hussam; Angulo, David; Drew, Kevin; Battre, Dominic; Schilling, Alex; Puryear, Eric; Van Puymbrouck, Jennifer; Jabon, David; von Laszewski, Gregor. Implementing Spectral Similarity Algorithms for Protein Identification. Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Stejerean, Cosmin; Siwamutita, Paiboon; Frank, E. D.; Giometti, Carol S; Babnigg, Gyorgy; Angulo, David; Drew, Kevin; von Laszewski, Gregor. An End-to-End System for Organizing and Sharing Raw and Derived Mass Spectrometry Data. Proceedings of the 2006 DePaul CTI Research Symposium. April 2006.

Van Puymbrouck, Jennifer; Angulo, David; Drew, Kevin; Hollenbeck, Lee Ann; Battre, Dominic; Schilling, Alex; Jabon, David; von Laszewski, Gregor. A Batch Import Module for an Emprically Derived Mass Spectral Database. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Vogelbacher, Rob; Angulo, David; and Koide, Shohei. Sequence Optimization for Synthetic Genes Using a Genetic Algorithm. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Gemmell, Jonathan; Angulo, David; Sosnick, Tobin; Freed, Karl; Jha, Abhishek; Colubri, Andres; DeBartolo, Joseph; Kendall, David and von Laszewski, Gregor. Inverse Protein Folding of Ubiquitin on the Illinois Bio-Grid. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

Angulo, David . Illinois Bio-Grid Talk at the DePaul Chapter of the UPE. February, 2005.

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Mass Spectrometry in the Illinois BioGrid (Poster). Annual DePaul Science Showcase for Guidance Counselors. Chicago, IL December 10, 2004.

Gemmell, Jonathan; Angulo, David; Colubri, Andres; Sosnick, Tobin; Freed, Karl; Koide, Shohei; von Laszewski, Gregor.  Steering Monte-Carlo Protein Folding Simulations With Data From Nuclear Magnetic Resonance Experiments On The Illinois Bio-Grid.  (Poster) Proceedings of 2004 DePaul CTI Research Symposium.  November 2004.

De La Serna, Andres; von Laszewski, Gregor; Angulo, Dave; Schilling, Alex.  Illinois Bio Grid Mass Spectrum Proteomic Database. (Poster) Proceedings of 2004 DePaul CTI Research Symposium.  November 2004.

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; Von Laszewski, Gregor. Mass Spectrometry in the Illinois BioGrid. (Poster) Proceedings of 2004 DePaul Natural Sciences, Mathematics & Technology Showcase. November 2004

Angulo, David.  Graduate Research in the Illinois Bio-Grid.  Talk at the DePaul PhD Symposium.  November, 2004.

Angulo, David; Puryear, Eric.  Undergraduate Research in the Illinois Bio-Grid.  Talk at the DePaul Chapter of the ACM.  November, 2004.

Puryear, Eric; Angulo, David; Drew, Kevin; Schilling, Alex; von Laszewski, Gregor. Mass Spectrometry in the Illinois BioGrid. (Poster)  Proceedings of 2004 DePaul CTI Research Symposium. November 2004

Angulo, D. Illinois Bio-Grid. Talk given to CTI PhD Students,  October, 2004

Drew, Kevin; Angulo, David; Schilling, Alex; Freeman, Tim.  Mass Spectra Analysis on the Illinois BioGrid.  Proceedings of 2004 Midwest Software Engineering Conference, Chicago.  June 2003.

·      Awarded Best of Conference Student Poster (Kevin Drew Student)

Angulo, D. Illinois Bio-Grid. Talk given to CTI PhD Students,  October, 2003

Angulo, D. The Anatomy of the Grid and the Illinois Bio-Grid.  Talk given to CTI chapter of IEEE,  October, 2003

Angulo, D. The Illinois Bio-Grid.  Invited talk at the Bio Informatics Group (BIG), Chicago, October, 2003

Angulo, D.  Anatomy of the Grid and the Illinois Bio-Grid.  Invited talk at the Chicago Technology Park, Chicago, December, 2003.

Angulo, D. Grid Computing and the Illinois Bio-Grid.  Invited talk for the Technology Seminar Series in the Capital Computation Institute at Louisiana State University, December, 2003.

The Illinois BioGrid: A Prototype for Industry-Academe Collaboration. Adam Steele, David S. Angulo. Proceedings of 2003 Midwest Software Engineering Conference, Chicago.

An Open-Source implementation of the DOM XML Standard in C. David S. Angulo. Proceedings of 2003 Midwest Software Engineering Conference, Chicago

Computing the Smith-Waterman Algorithm on the Illinois Bio Grid (Poster). David S. Angulo, Nigel M. Parsad, Tom Goodale, Gabrielle Allen, Ed Seidel. Proceedings of 2003 Midwest Software Engineering Conference, Chicago.

Enhancing Dynamic Fluid Flow Analysis With Computational Grids (Poster). David S. Angulo, Adam Steele, Jeff Sickel. Proceedings of 2003 Midwest Software Engineering Conference, Chicago.

Intelligent Grid Migration (Poster), David S. Angulo, Scott Kuehn. Proceedings of 2003 Midwest Software Engineering Conference, Chicago.

Phylogenetics on the Illinois Bio-Grid (Poster). Adam Steele, David S. Angulo, Steve Finkelman. Proceedings of 2003 Midwest Software Engineering Conference, Chicago.

Set Extended ClassAds: Declarative Models for Performance Modeling, Resource Selection, and Mapping.  Invited talk given at the GrADS Workshop, Rice University, May, 2002.

Benefits of Cactus to GrADS.  Invited talk given at GrADS Workshop, Rice University, March, 2002.

Contracts, Resource Selection, Mapping, and Scheduling.  Invited talk at the GrADS Workshop at Rice University, July 2001

Editor and writer of the Chicago Area Digital Users Society newsletter from 1989 to 1994 (this publication won an award for outstanding quality).

Monthly article in FOCUS magazine (for Data General computers) 1987-1988.

Editor and writer of the Chicago Data General Users Group newsletter from 1980-86.

Rabbit IgG Sequencing.  Dave Angulo, Robert Good, Lee Hood.  CalTech Biology Annual Report. 1975.

 

Grants

Awarded NIH Grant as Co-Investigator for “MALDI-TOF for High Throughput Signal Transduction Inhibitor Screening”  under the NIH Roadmap for Medical Research, Grant R01 HG3864. $2.4M September 2005-August 2009.

Awarded NSF Grant as Principal Investigator for REU 353989 “REU Site for Grid Computing and Bioinformatics.”  $260,343 May 2004 – May 2007

Awarded $260,000 in computer equipment from University of Chicago, Biological Systems Division for use in projects in the Illinois Bio-Grid. November 2004

Awarded $500,000 in computer equipment from Pfizer Global Research and Development for use in projects in the Illinois Bio-Grid. June 2004

Awarded $403,100 in computer equipment from Pfizer Global Research and Development for use in projects in the Illinois Bio-Grid. April 2004

Awarded Grant from DePaul’s University Research Council Competitive Grant as Principal Investigator for “Protein Folding Problem: AI Engine”  Grant number 350629

Awarded Grant from the NCSA/Alliance as Principal Investigator for “GrADS BioInformatics” (Grant Num: ASC020033N) 2002.

Awarded Grant from the NCSA/Alliance as Principal Investigator for “Illinois Bio-Grid Workbench” (Grant Num: ASC040012) 2003 .

Conference and Journal Program Committee Memberships

Program committee co-chair Third International Symposium of Life Science Grid 2006, Tokyo, Japan, November 12-13, 2006

IEEE Transactions on NanoBioscience Program Committee, 2006.

IEEE International Conference on Computer-Based Medical Systems track on "Grids for Biomedicine and Bioinformatics” Program Committee, Salt Lake City, Utah.  June 22-23, 2006.

MSEC Program Committee, Chicago, April 29, 2006

Special Issue of Lecture Notes in Bioinformatics. Grid Computing in Life Science. Program Committee  June 2004.

EuroPar 2005, Program Committee.  Lisbon Portugal. August 30 – September 2, 2005.

International Workshop on Life Science Grid, held in conjunction with the 19th Annual Conference of JSAI. Program Commiteee.   Seoul S. Korea, May, 2005

IEEE International Conference on Computer-Based Medical Systems track on "Grids for Biomedicine and Bioinformatics.  Dublin, Ireland, June 23-24, 2005.

International Workshop on Life Science Grid, held in conjunction with the 18th Annual Conference of JSAI.  Kanazawa-city, Japan, May, 2004.

International Workshop on Grid Workflow held in conjunction with Global Grid Forum 10, Berlin, Germany.  March, 2004.

Co-Chair Life Science Grid Research Group Workshop at Global Grid Forum 7, Tokyo, Japan, January, 2003

Co-Chair Life Science Grid Research Group Workshop at Global Grid Forum 8, Seattle, Washington, June, 2003

Joint Workshop on Grid Workflow with Life Science Grid Research Group and Grid Computing Environment Systems Research Group at Global Grid Forum 9, Chicago, Illinois, October, 2003

Co-Chair Life Science Grid Research Group Workshop at Global Grid Forum 10, Berlin, Germany, March, 2004

Co-Chair Life Science Grid Research Group Workshop on Life Sciences Applications on Grid at Global Grid Forum 11, Honolulu, Hawaii, June, 2004

Co-Chair Life Science Grid Research Group Special Workshop on Healthcare and Life Sciences Applications on Grids at Global Grid Forum 12, Brussels, Belgium, September, 2004

Co-Chair Life Science Grid Research Group Special Workshop on HealthGrids at Global Grid Forum 13, Seoul, S. Korea, March, 2005

Co-Chair Life Science Grid Research Group Special Workshop on Healthcare Security and Privacy at Global Grid Forum 14, Chicago, June, 2005

Co-Chair Life Science Grid Research Group Special Workshop on Security and Privacy Needs of Health Grid at Global Grid Forum 15, Boston, October 2005

Co-Chair Life Science Grid Research Group meeting on HealthGrids at Global Grid Forum 16, Athens, February 2006

Co-Chair Life Science Grid Research Group meeting on The Future of Life Sciences Applications on Grids at Global Grid Forum 17, Tokyo, May 2006

 

Other External Service

NSF Review Panel, December 2007.

NSF Review Panel, November 2006.

NSF Review Panel, June 2006

NSF Review Panel, November, 2005

NSF Review Panel, April, 2005

Board of Directosr, Illinois Medical District BiTMap program. 2005-present.

Board of Directors, Bio Synthesis Center (BioSyncC) at the Field Museum of Natural History in Chicago, a project in the Encyclopedia of Life, 2007-present.

 

DePaul University CTI Committee Membership

Member of CS Program Committee.  2002-03, 2003-04.

Member of DS Program Committee.  2002-03, 2003-04, 2004-05, 2005-06.

Member of SE Program Committee.  2002-03, 2003-04, 2004-05, 2005-06, 2006-07, 2007-08

Member of ECT Program Committee.  2002-03, 2003-4.

Member of the Research Environment/Scholarship Committee. 2003-04, 2005-06 2006-07, 2007-08.

Chair of the Research Environment/Scholarship Committee. 2006-07, 2007-08.

Member of PhD Committee.  2005-06, 2006-07, 2007-08

Chair of the PhD Committee’s Subcommittee on Competitive Funding 2005-06, 2006-07, 2007-08

Chair of the Colloquium Committee.  2003-04.

Member of the Colloquium Committee 2003-04, 2004-05

Chair of the Bioinformatics Program Workgroup 2004-05, 2005-06, 2006-07, 2007-08.

 


BioInformatics

2007-present

Member of the Board of Directors of the Field Museum of Chicago’s Biodiversity Synthesis Center (BioSyncC), a subproject of the multi-institutional Encyclopedia of Life project.

2007

Co-Chair Life Science Grid Research Group meeting on “Storage Grids in Healthcare,” at Open Grid Forum 20, Manchester, UK, May, 2007

2007

Co-Chair Life Science Grid Research Group meeting on “LSG-RG Future Directions,” at Global Grid Forum 19, Chapel Hill, North Carolina, January, 2007

2006-present

Member of the Board of Directors for the Illinois Medical District’s Bioinformatics Training Program (BiTMaP)

2006

Guest Editor for the ACM Crossroads Journal Special Issue on Bioinformatics 13-1

2006

Program committee co-chair Third International Symposium of Life Science Grid 2006, Tokyo, Japan, November 12-13, 2006

2006

IEEE Transactions on NanoBioscience Program Committee, 2006

2006

IEEE International Conference on Computer-Based Medical Systems track on "Grids for Biomedicine and Bioinformatics” Program Committee, Salt Lake City, Utah.  June 22-23, 2006.

2006

Awarded University Research Assistant Program Grant at DePaul for “An Empirically Derived Tandem Mass Spectral Database  in the Illinois Bio-Grid” 

2006

Biomedical Informatics Workshop Program Committee, Chicago, October, 2006.

2006

Co-Chair Life Science Grid Research Group meeting on The Future of Life Sciences Applications on Grids at Global Grid Forum 17, Tokyo, May 2006

2006

Awarded University Research Assistant Program Grant at DePaul for “An Empirically Derived Tandem Mass Spectral Database  in the Illinois Bio-Grid”

2006

Awarded Best of Conference Poster  for  poster by Kwak, Gil; Angulo, David; Shilling, Alexander. Hypothetical Sequence Analyzer (Poster). Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006.

2006

Awarded Best of Conference Bioinformatics Poster for poster by Rob Vogelbacher, Benjamin Capraro, Tobin Sosnick, Shohei Koide, David Sigfredo Angulo, IBG GeneDesigner: DNA Sequence Optimization for Designed Proteins (Poster).  BioMedical Informatics Workshop. Chicago, IL. October 13, 2006

2006

Co-Chair Life Science Grid Research Group meeting on LS Grids, at Global Grid Forum 18, Washington DC, September, 2006

2006

8 publications in international journals and conferences

2006

20 publications in local conferences

2005

Awarded NIH Grant as Co-Investigator for “MALDI-TOF for High Throughput Signal Transduction Inhibitor Screening”  under the NIH Roadmap for Medical Research, Grant R01 HG3864. $2.4M

2004

Awarded University Research Assistant Program Grant at DePaul for “Illinois Bio-Grid” 

2004

Awarded NSF Grant as Principal Investigator for “REU Site for Grid Computing and Bioinformatics.”  Grant number REU 353989  $260,343

2003

Awarded University Research Council Competitive Grant at DePaul for “Protein Folding Problem – AI Engine”  Grant number 350629

2002

Leading member of a team that won two of the three Grand Challenge Problem awards at Super Computing 2002.  My portion involved implementing a BioInformatics program (Smith-Waterman) on the Grid.  It ran on a set of 7000 processors in 14 countries in 5 continents.

2002-present

Chair of the Global Grid Forum Research Group on Life Sciences (BioInformatics)

2002-present

Directed students in a research project to enhance a Mass Spec application by making the code use parallel and Grid/Distributed Computing technologies. This application was written in C and Globus.

2002-present

Directed students in a research project to enhance the FastA algorithm by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C+and Globus.

2002-present

Directed students in a research project to enhance the Smith-Waterman algorithm by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C and Globus.

2002-present

Directed students in a research project to enhance the BLAST algorithm by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C and Globus.

2003-present

Directed students in a research project to enhance the Metropolis Coupled Monte Carlo Markov Chain algorithm (used for phylogenetic tree creation) by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C and Globus. This application is utilized in the funded project NSF 0228675, ATOL: Early Bird: A Collaborative Project to Resolve the Deep Nodes of Avian Phylogeny, P.I.: Shannon Hackett.

2003-present

Directed students in a research project to enhance the successful implementations of software to simulate lipid bilayers and biological membranes using both the Configurational Bias Monte Carlo Method (CBMC) and Molecular Dynamics (MD). The simulations provide a wealth of detailed information about the atomic level properties of water and lipid molecules which can be compared with experiment, and can be used to help to construct better theoretical models. Current simulations being done involve the properties of cholesterol in lipid membranes. Cholesterol is known to be an essential component of mammalian cell membranes but its exact role is not well understood. We are using a novel simulation technique which combines traditional Molecular Dynamics under conditions of constant temperature and pressure, and Configurational Bias Monte Carlo. The combined simulation methods provide more efficient sampling of the huge number of configurations of the lipid-cholesterol system. Previous simulations have been run at up to 1600 lipid or cholesterol molecules, and 52,000 water molecules. The size of the simulation cell is about the same size as observed nano-domains, or "rafts" which play important functional roles in membranes. We are increasing these simulations by an order of magnitude in the physical dimensions and 2 to 3 orders of magnitude in time by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C and Globus.  This application is utilized in the funded project NIH 7R01GM054651-04, Simulations of Cholesterol in Lipid Bilayers, P.I.: H. Larry Scott

2003-present

Directed students in a research project to Grid software that aids in the development of a complete physical map of the region of the human genome that shows linkage to Bipolar disorder (BP) and to close all existing gaps in the published Human Genome Project and Celera maps. Following that, a complete molecular characterization of the region is to be made, which will serve as a framework for identification of a susceptibility variant for BP.  Thus, the project will create a high density SNP map specific for the region in question, supported by software.  The software aids in making annotations for the sequences, which is utilitarian for other projects.  Expanding the nature of the software for utilitarian purposes for other projects as a web service leads to a vast increase in the demand on the computational resources.  Therefore, we have implemented this software on the shared resources of the Illinois Bio-Grid using the IBG Workbench software tools.  This application is utilized in the funded project NIH 5R01 MH065560-01, Fine Genomic Mapping of 13q32 in Bipolar Disorder, P.I.: Elliot Gershon

2002

Awarded Grant from the NCSA/Alliance as Principal Investigator for GrADS BioInformatics (Grant Num: ASC020033N)

2002

Partner in the Chicago Supercomputer Center as Director of Programming.  Directed application development in a Mass Spectometry for Vector Supercomputer project.

1975

Performed a research project sequencing rabbit Immunoglobulin-G under renowned professor Leroy Hood at the California Institute of Technology. Dr. Hood is now the President and Director of the Institute for Systems Biology.  I was an undergraduate at the time.  See publications.

1976-1979

Majored in Biology (and Physics with Math minor) at Loyola University of Chicago

 


Grid and Distributed Computing Technology

2004

Best of Conference poster at SuperComputing 2004 (top conference in field – 109 high quality accepted posters)

2003

Awarded University Research Council Competitive Grant at DePaul for “Protein Folding Problem – AI Engine”  Grant number 350629

2002

Leading member of a team that won two of the three Grand Challenge Problem awards at Super Computing 2002.  My portion involved implementing a BioInformatics program (Smith-Waterman) on the Grid.  It ran on a set of 7000 processors in 14 countries in 5 continents.

2002-present

Chair of the Global Grid Forum Research Group on Life Sciences (BioInformatics)

2002

Member of the Globus team, which won the R&D 100 award.

2002-present

Directed students in a research project to enhance a Mass Spec application by making the code use parallel and Grid/Distributed Computing technologies.  This application was written in C++ and Globus.

2002-present

Directed students in a research project to enhance the FastA algorithm by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C++ and Globus.

2002-present

Directed students in a research project to enhance the Smith-Waterman algorithm by implementing it in code using parallel and Grid/Distributed Computing technologies. This application was written in C++ and Globus.

2002-present

Directed students in a research project to enhance the BLAST algorithm by implementing it in code using parallel and Grid/Distributed Computing technologies.  This application was written in C++ and Globus.

2000-present

Performed research (coding) in dynamic adaptation to Grid environments.  These applications needed to monitor dynamic performance of the application and compare this to expected values for performance. The applications further needed to detect variances in the monitored performance from the expected value and, upon substantial degradation, locate new resources where the application is expected to perform better and migrate the application to those resources.  This work led to several publications (see publications section). This application was written in C, C++, and Globus, and was based on the Cactus application framework.

2001-2002

Worked with Ph.D. students in developing the Set Extended ClassAds language.  This declarative language allows specification of compute resources to a broker.  The language also allows the writer to specify a performance model, which is used to predict performance on the selected compute resources.  (see publications section).  This application was written in C++ and Globus.

2000-2002

Worked with the leaders in Grid Technology on the GrADS project to create an architecture to perform resource location and selection, application staging and launching, contract monitoring, dynamic adaption to changing Grid environments, etc.  This work led to several publications.  See http://hipersoft.cs.rice.edu/grads/.  This application was written in C, C++, and Globus.  My work was based on the Cactus application framework.

2002

Directed students in developing C language additions to the gSOAP package, which is a C version of a SOAP engine.  The additions included making a GSI transport layer (GSI is a Grid Security package from the Globus Toolkit) and adding support for document/literal encoding (in addition to the already existing SOAP-section 5 encoding).  This was used as an inter-processor communications protocol for Grid distributed applications.

2002

Performed research and directed students in a project to develop the Globus Toolkit OGSA architecture in the C language.  This was used as an inter-processor communications protocol for Grid distributed applications.

2002

Managed a project to develop the Globus Toolkit on the Windows platform.

1998 - present

Performed research in several areas pertaining to distributed computing utilizing OO techniques (primarily in Java and C).  These research projects concern dynamic load balancing in a cooperative environment between the client application and the resource allocation libraries.  The environment must be cooperative because in a non-cooperative environment, the client knows nothing (and should know nothing) about the nodes available nor the relative processing power of those nodes.  Similarly, the load balancer knows nothing about the ideal ways of distributing the application.  In a cooperative environment, the client supplies information about the process to be distributed to help the load balancer make more efficient uses of the resources.

 


Management

2003-present

Managed a team of students that varied from 6 to 25 in number and sometimes included other faculty.  Also managed a $350,000 NSF grant and a $2.5 million NIH grant.  This team wrote bioinformatics software for high performance distributed grid computing

 

2001-2002

Led a research team involving 9 universities and 14 programmers in adaptive techniques used in high performance distributed grid computing

 

2001-2002

Managed a $1 million contract with MicroSoft in the Globus Project to port the Globus Toolkit to Windows

 

2002

Managed a 4 person team that developed a C version of a Grid Service Architecture used in creating Grid Service Clients and Servers.  A Grid Service is a Web Service using SOAP, WSDL, WSIL, etc. to work with Grid Technologies – a form of Distributed Computing.

 

2001-2002

Managed a 2 person team that developed a Portal to control High Performance Cactus Numerical Simulation applications.

 

2001-2002

Managed a 3 person team that managed two high performance multiprocessor Linux servers and one high performance multiprocessor Sun server with Solaris.

 

1997-2002

Managed a 25 person volunteer team managing a Unix Internet server for Chicago Mensa and Mensa International

 

1994-1998.

Directed several teams at SPSS in object oriented programming and OLE Automation of ActiveX COM objects.  The teams had from 3-6 members.

 

1990

 

At Datalogics, occasionally performed as a team leader with a staff of one to two programmers.  Used TIMELINE and did frequent project time estimates.

 

1986

 

Managed several projects as a consultant, which had a staff of two programmers.

 

1984-1985.

At the Orleans Company, managed the entire data processing staff, which consisted of a programmer and an operator.  Was in charge of all hiring decisions.

 

1980-1988

 

Directed the Chicago Data General Users Group as a member of the executive board and one year as president.  This is a professional organization with about 100 member companies.

 

1986-1988

 

Directed the North American Data General Users Group as a member of the executive board (as national secretary).  This is a professional organization with about 2000 member companies and a budget of about $750,000 a year.

1989-1991

 

Directed the Chicago Area Digital Users Society as a member of the executive board.  This is a professional organization with about 400 member companies.

1991-2000

 

Chapter Director of the Loyola chapter of Sigma Pi.  Average membership of 40.

1993

 

Ran the Illinois Regional Sigma Pi leadership school.

 

 

 


SGML/HTML/XML/Text Systems

 

2002

Directed students in developing a C version of DOM parser.

2002

Directed students in developing additions to the gSOAP package, which is a C version of a SOAP engine.  The additions included making a GSI transport layer (GSI is a Grid Security package from the Globus Toolkit) and adding support for document/literal encoding (in addition to the already existing SOAP-section 5 encoding).

2002

Directed students in developing architectures to enable client applications to utilize SOAP, WSDL, and WSIL in C.

2002

Directed students in developing a WSDL to SOAP generator engine..  This was written in Java, but the code generated was C.  Generated both client stubs and server skeletons.

2002

Gave several professional and educational tutorials on XML technologies, such as XPATH, XML-Schema, XML-Namespace, SOAP, WSDL, and WSIL.

2001, 2002

Developed and taught a new course at the University of Chicago in XML.  Taught SAX, DOM, XPATH, DTDs, Schemas, Namespaces, XSLT and more.

2001

Wrote a wrapper around a Resource Selector library to enable utilization as an internet service.  This wrapper was written in SOAP and included C++ as well as JavaScript (on web pages) clients.

1988-1991

Developed an in-house CASE tool for use with a relational DB.  This tool was a generic text DB application that would store text objects based on their SGML markup.  It worked generically by parsing the DTD and creating a database from the elements defined in the DTD.

1998-2001

Developed and Taught several Web programming courses at Loyola University of Chicago.  Also taught introductory Web page development.  The Web programming courses included teaching HTML, CGI, HTTP, Perl, JSP, and Java Servlets.

1997-2002

Manager of a 25 person volunteer team managing a Unix Internet server for Chicago Mensa and Mensa International

1995-2001

Webmaster for Chicago Area Mnsa.  Designed and wrote the webpage with forms and Java applications. http://chicago.us.mensa.org

1999, 2000, 2001, 2002

Awarded best local American Mensa Webpage

1997, 1998, 1999, 2000, 2001

Nominated for the best local American Mensa Webpage.

1995-1998

Webmaster for Sigma Pi Fraternity, International.  Designed and wrote the webpage with forms and Java applications. http://www.sigmapi.org

1994-2001

Chair of the Sigma Pi Fraternity Technology committee. Duties included writing and implementing usenet policies, writing and implementing policies for chapter webpages, implementing several e-mail list servers, implementing usage of e-mail for the headquarters, implementing chapter reporting via html forms, and implementing a multi-purpose e-mail list on the web page with a Java application.

1997-2002

Chair of the Chicago Area Mensa Cyberspace committee.  Duties included overseeing Web page development, installing a server with BSDi Unix with ongoing system administration, installing several e-mail list servers, writing a Java application for the Web page that displays current and past month activities, coordinating Java Web page applications for newsletter publishing and for event registration, and setting up local and public usenet newsgroups for access via browsers.


Internet

2003-present

Developed (and/or managed development of) scores of different web programming systems, including Web Services (SOAP, WSDL, & Apache Axis), JSP, Servlets, Struts, CGI, and others.

2002

Developed (along with students) a C version of a Grid Service (Web Service for a Grid form of Distributed Computing) as part of the Globus Project.  This used SOAP, WSDL, and WSIL and the Apache Axis Server.

2002

Developed and taught a new course at the University of Chicago in Web Services.  Taught XML Schema, SOAP, WSDL, WSIL, UDDI, Java programming of Web Services using Tomcat.

2001, 2002

Developed and taught a new course at the University of Chicago in XML.  Taught SAX, DOM, XPATH, DTDs, Schemas, and XSLT

2001

Wrote a wrapper around a Resource Selector library to enable utilization as an internet service.  This wrapper was written in SOAP and included C++ as well as JavaScript (on web pages) clients.

2000

Wrote the worlds first XML based web server serving conference schedules in three media: WAP phone, web pages, and Voice VoXML.

1999-present

Developed and taught several Internet Programming courses.  Content included HTML, HTTP, CGI, Perl, Java Servlets, RMI, Internet Security, JSP, and XML.

1999

Wrote several CGI and Java Servlet programs for various web sites, including Sigma Pi Fraternity, International, Chicago Mensa, and various clients.

1997-2002

Managed a 25 person volunteer team managing a Unix Internet server for Chicago Mensa and Mensa International

1999, 2000, 2001, 2002

Awarded best local American Mensa Webpage

1997, 1998

Nominated for the best local American Mensa Webpage.

1995-2001

Webmaster for Chicago Area Mensa.  Designed and wrote the webpage with forms and Java applets. http://chicago.us.mensa.org

1995-1998

Webmaster for Sigma Pi Fraternity, International.  Designed and wrote the webpage with forms and Java applications. http://www.sigmapi.org

1994-2002

Chair of the Sigma Pi Fraternity Technology committee. Duties included writing and implementing usenet policies, writing and implementing policies for chapter webpages, implementing several e-mail list servers, implementing usage of e-mail for the headquarters, implementing chapter reporting via html forms, and implementing a multi-purpose e-mail list on the web page with a Java application.

1997-2002

Chair of the Chicago Area Mensa Cyberspace committee.  Duties included overseeing Web page development, installing a server with BSDi Unix with ongoing system administration, installing several e-mail list servers, writing a Java application for the Web page that displays current and past month activities, coordinating Java Web page applications for newsletter publishing and for event registration, and setting up local and public usenet newsgroups for access via browsers.

1997-1998

Developing a national membership database in Java for American Mensa.

1997

Developed OLE Automation for COM ActiveX objects in C++ at SPSS. These objects were spreadsheet like objects for a statistical software package.  The objects allowed dimensions to be pivoted for interactive research on data dependencies.  The Automation interface allowed full searching capabilities on the multidimensional structure as well as a display enhancement interface.

These ActiveX objects won the Smithsonian Institution Permanent Research Collection of Information Technology award in 1997.

1999-2001

Developed and Taught several Web programming courses at Loyola University of Chicago.  Content included coding CGI in Perl, hand coding the HTTP protocol in Java, coding Servlets in Java, coding JSP, coding Java Applets, etc.

 


Pedagogy

Developed and taught the following graduate courses at University of Chicago as a part-time instructor in 2002

·         CSPP 53030 Web Services

This course included topics in XML Schema, WSDL, SOAP, WSIL, UDDI, and writing webservices in Java for Tomcat

Developed and taught the following graduate courses at University of Chicago as a part-time instructor in 2001 and 2002

·         CSPP 545 (later 53025) Electronic Data and Document Exchange (XML)

This course included topics in XML, DTD, XML Schema, XPATH, XSLT, SAX, DOM, and more

Developed and taught the following graduate courses at University of Chicago as a part-time instructor in spring and summer 2002

·         CSPP 59410 Independent Grid Programming

This course guided students in a research programming project in Grids (distributed computing), Web Services, Grid Services, XML, BioInformatics, Virtual Reality, and more.

Developed and taught the following new course for undergraduate study over the web in conjunction with eCollege (distance learning) for Loyola University of Chicago under an appointment as a Visiting Instructor in 2000 and 2001

·         CS 225 Introduction to Web and CGI Programming using JavaScript and Perl

·         CS 227 Client/Server Web Programming using Java servlets

Developed and taught the following new course for undergraduate study for Loyola University of Chicago under an appointment as a Visiting Instructor in 2000 and 2001

·         CS 227 Client/Server Web Programming using Java servlets

Developed and taught the following new course for undergraduate study for Loyola University of Chicago under an appointment as a Visiting Instructor in 1998-2001

·         CS 225 Introduction to Web and CGI Programming using JavaScript and Perl

Taught the following graduate courses at Loyola University of Chicago under an appointment as a Visiting Instructor in 1999 and 2000

·         CS 473 Object Oriented Programming in C++ and Java
This course included topics in serialization, design patterns, and concurrency

Taught the following undergraduate courses at Loyola University of Chicago under an appointment as a Visiting Instructor in 1999 and 2000

·         CS 271 Data Structures using Java

·         CS 272 Object Oriented Programming in C++ and Java

·         CS 374 Operating Systems

Taught the following graduate course at Loyola University of Chicago under an appointment as a Visiting Instructor in 1998 and 1999

·         CS 473 Object Oriented Programming in C++ and Java
This course included topics in serialization, design patterns, and concurrency

Taught the following undergraduate courses at Loyola University of Chicago under an appointment as a Visiting Instructor in 1998 and 1999

·         CS 170 Introduction to Programming using Java (majors)

·         CS 271 Data Structures using Java

·         CS 272 Object Oriented Programming in C++ and Java

Taught the following graduate courses at Loyola University of Chicago as a part-time instructor in 1998:

·         CS 488 Visual Basic Seminar

Was the class coordinator for CS 125 (Introduction to Programming using Visual Basic) at Loyola University of Chicago in 1998

Taught the following undergraduate courses at Loyola University of Chicago as a part-time instructor in 1998:

·         CS 125 Introduction to Programming using Visual Basic (non-majors)

·         CS 120 Introduction to Computer Applications

·         CS 101 Introduction to the WWW

Performed on-the-job training of other computer professionals in Object Oriented (C++) programming in 1993, 1994, 1995, and 1996

 


Object Oriented Technology

 

Software Architecture, Test Driven Development, JUnit, Eclipse,

1998 - present

Performed research in several areas pertaining to distributed computing.  Utilized OO techniques (primarily in Java).  These research projects concern dynamic load balancing in a cooperative environment between the client application and the resource allocation libraries.  The environment must be cooperative because in a non-cooperative environment, the client knows nothing (and should know nothing) about the nodes available nor the relative processing power of those nodes.  Similarly, the load balancer knows nothing about the ideal ways of distributing the application.  In a cooperative environment, the client supplies information about the process to be distributed to help the load balancer make more efficient uses of the resources.

1998 - 2000

Taught C++ and Java, in several undergraduate and graduate OO courses at Loyola University of Chicago.

1994 - 1998.

Worked in C++ at SPSS as one of 3 very senior programmers with the title Master Software Engineer.  Taught other programmers theory and practice of object oriented programming and analysis.

1991 – 1994.

Worked in C++ at SSA as the local expert in Object Oriented Technology (at that time, a nascent technology).  Taught other programmers theory and practice of object oriented programming and analysis.

1989 - 1991.

Worked in C++ at Datalogics and became the local expert.  At this time, Object Oriented Technology was largely unknown in industry.  Taught other programmers theory and practice of object oriented programming and analysis.  Wrote a generic class library and incorporated some public domain libraries into it.  Wrote a class documenter, which allowed documentation to be written in the code (in the header file) and would extract it from there and write a manual and on-line help text.  Wrote a system to allow word indexing of a textual database.  Helped design and write a document database with two views: structural elements (in SGML) and composed pagination.

1990.

 

Worked in SmallTalk at Datalogics and wrote a small prototype system in order to evaluate the potentials of SmallTalk.

1991.

 

Worked in Objective C for a research project as part of my Master's Degree curriculum.  This project is event driven and interacts with the NeXT machine's DSP in real time.

1991.

 

Wrote a generic set of classes in C++ under Microsoft Windows to implement a genetic algorithm and an A* algorithm.  This will be used as a pedagogical paradigm of object oriented programming use in AI in a paper that I will try to get published.

1991-1993

 

Designed, wrote, and implemented a set of base classes in C++ at SSA that were used with generated code for a client/server CASE tool.  Also wrote the prototype code that the code generator would generate. The essence of these classes was based on the Codd/Date E-R model.  Classes existed for Entities, Relationships, Windows, Databases, Elements, and other general categories.  Also assisted our first client in designing and implementing the first set of applications (GL) developed by this CASE tool. (the application to be sold as part of BPCS). Taught other programmers theory and practice of object oriented programming and analysis.

 

 


Event Driven Software and GUI

Fall 1990.

 

Worked in SmallTalk under OS/2 at Datalogics and wrote a small prototype text database.  The user is shown a list of SGML elements in one pane and chooses one.  This updates the next pane with the contents of that element.

 

Summer-Fall 1991.

 

Worked in Objective C for a research project as part of my Master's Degree curriculum.  The GUI interface was to simulate a graphic equalizer and record equalization settings used by sound experts.  The sound expert was to change the value of a slider as though it was a band on an equalizer and the program interacted with the NeXT DSP in real time to perform the given equalization.

 

1989-1990.

 

Wrote a major generic text database system in C++ and RDB at Datalogics.  This system, while not truly event driven, was created with classes that would perform the action as though it were selected as an event.

 

Spring, 1991.

 

Wrote a paper and gave a talk as part of the requirements for a course at Loyola's Graduate School which described tools and programming techniques for programming in Windows.  The professor stated that this was the best paper in the class.

 

1991-present.

 

Currently writing a generic genetic algorithm and a generic A* algorithm as a research project as part of my Master's Degree curriculum.  These systems are written in Borland C++ under DOS Windows.

 

Fall 1991.

 

Took the Microsoft Windows Technical Workshop.

 

 

1991-1993

 

Designed, wrote, and implemented a set of base classes in C++ at SSA to be used with the generated code for a client/server CASE tool and the prototype code that the code generator would generate.  The base classes worked with the generated code to form Windows applications to run on the PC (the server portion of the applications was created elsewhere).  The Windows base classes and generated classes used the Borland C++ environment with Applications Frameworks.  Borland's base classes were encapsulated with configurable base classes to lend a degree of compiler/base class independence.  Since the project was started in 1991, it was not known how Microsoft would develop their OOP development environment so no provision to bypass Borland's DDVT methodology was taken.  Also assisted our first client in designing and implementing the first set of applications (GL) developed by this CASE tool. (the application to be sold as part of BPCS)

 

 


AI

Spring 2006 - ?

Directed a graduate student performing research in datamining of protein structure data

Fall 1998 to present

Performed research in several areas pertaining to distributed computing utilizing OO techniques (primarily in Java).  These research projects concern dynamic load balancing in a cooperative environment between the client application and the resource allocation libraries.  This can be considered AI because one of the client applications that are involved in the study to participate in a distributed environment pertains to a search space that is searched using a heuristic mini-max search in a two-person zero-sum game.  The alpha-beta search algorithm enhancement is particularly challenging in a distributed environment.

Summer-Winter 1991.

 

Wrote a generic set of classes in C++ under Microsoft Windows to implement a genetic algorithm and an A* algorithm.  It was intended for use as a pedagogical paradigm of object oriented programming use in AI (object-oriented programming was quite new at the time).

 

Summer 1991.

 

Used Franz Lisp extensively in a graduate class at Loyola as part of my Master's Degree curriculum.

 

1989 to 1991

 

Enhanced and maintained a system written in PROLOG that took a simple BNF language as input and gave as output a System Requirements Document text file, a System Design Document text file, a SQL schema, and a set of C and C++ modules to work with the data (including storing and retrieving the data from a choice of several different database managers and a screen).

 

1990

 

Designed and wrote a system in PROLOG on the PC under DOS that worked with an SGML DTD.  It took the DTD and listed all potential tags in context along with all formatting issues that each tag could affect so that a document could be drawn up describing what each tag in context would do.

 

1996

Took a graduate course at Loyola in Neural Nets as part of my Master's Degree curriculum

 


Hardware

IBM  PC (MS-DOS, OS/2, XENIX, Windows, MINIX, Win 95, Win 98, Win NT, Win 2000, WIN XP FreeBSD, Linux RedHat, Linux SUSE, BSDi, Linux Debian)

18 years 1988-present

 

Sun (Solaris)

5 years 2001-present

 

SG2

5 years 2001-present

 

VAX

 

5 years

 

NeXT

0.5 years

DG (RDOS, AOS, and AOS/VS)

8 years

 

8080

 

3 years

 

DECsystem-10

 

2 years

 

PDP-11 (RSTX and UNIX)

 

3 years

 

Univac-1100

 

1 years

 

Commodore 128

 

6 years

 

TI99

 

3 years

 

SUN (UNIX)

 

1 years (circa 1988)

 

3B5 (UNIX)

 

2 years (circa 1988)

 

3B15 (UNIX)

 

2 years (circa 1990)

 

IBM RS6000

 

0.5 years (circa 1993)

 

 


Languages

XML

10 years 1988-1991 (SGML) and 1999-present

Java

11 years 1995-present

C++

 

18 years 1988-present

 

C

 

20 years 1986-present

C#

4 years 2002-present

Perl

3 years 1998-2001

Visual Basic

4 years 1995-1999

80x46 Assembler

 

2 years

 

SmallTalk

 

0.5 years

 

Objective C

0.5 years

 

PROLOG

 

2 years

 

DG/L

 

6 years

 

ALGOL

 

5 years

 

DG assembler

 

4 years

 

FORTRAN

 

8 years

 

PDP-11 assembler

 

3 years

 

COBOL

 

4 years

 

LISP (FRANZ)

 

1 year

 

8080 assembler

 

3 years

 

DECsystem 10/20 assembler (MACRO)

 

2 years

 

BASIC

 

4 years (also see Visual Basic)

 

SAIL (an ALGOL derivative)

 

2 years

 

IITRAN

 

1 year

 

PL/C

 

1 year

 

PL/1

 

1 year

 

Pascal

 

4 years

 

 

 


Databases

MS SQL Server

 

Used this LAN based version of a relational database manager at SSA to use in the internals of generated applications using our case tool.

 

 

QELIB (DBASE)

Used this PC relational database manager at SSA to use in the internals of generated applications using our case tool.

 

RDB - VAX

 

Used this VAX/VMS relational database manager at Datalogics to build a major generic text database system in C++.  Also developed an in-house CASE tool that generated C++ classes using embedded SQL.  Also developed a generic toolset of classes in C++ to do word context searching.

 

Oracle

 

Used this relational database manager at Datalogics to build systems both on the VAX and on the PC under DOS.  This work was mainly embedded SQL but some work with FORMS was done.

 

SIR

 

Converted this relational database manager to run on DG under AOS/VS (from VAX). Also helped debug the core product under VAX.  Began designing a screen oriented forms definition with intelligent user guidance (worked on this design until the company went bankrupt).

 

Codasyl - Lerner

 

Helped design and implement this Codasyl based database manager to run on DG RDOS machines.  The Codasyl functionality was implemented for an ALGOL based language (DG/L).  Also implemented an entire accounts receivable and general ledger system using this DBMS.

 

DBMS - DG

 

Used this relational database manager at the Orleans Company to develop many new small support programs for an inventory / manufacturing / orders system.  Developed mainly in SQL.

 

Sybase

 

Used this relational database manager at many client sites while consulting and at SIR to analyze the competition's product.

 

 

Informix

 

Used this relational database manager at many client sites while consulting and at SIR to analyze the competition's product.

 

DM

 

Used this (pseudo) relational database manager at Datalogics to maintain a textual database system.  Worked mainly in C calling database routines directly.

 

INFOS

 

Used this ISAM database manager at a number of client sites while consulting. Worked in C, COBOL, and FORTRAN calling database routines directly.

 

 

ISAM

 

Used this DECsystem-10 ISAM database manager at the Chicago Tribune to maintain an inventory / depreciation system in COBOL.

 

 


Communications

1980

 

Wrote a system at the Chicago Tribune to send files over an asynchronous line between two TOPS-10 machines.  At that time, DEC didn't have a working system to do this.  All hand shaking protocols and communication packets were designed and implemented (in a client / server configuration).

 

1982

 

Designed and wrote a system at Lerner to send files and perform functions on the file system (list directories, delete files, etc.) over a synchronous IPC (inter-processor communications) line between an S-130 running RDOS and an S-230 running AOS.  At that time, Data General didn't have a working system to do this.  All hand shaking protocols and communication packets were designed and implemented.

 

1985

 

Performed the communications hardware setup when a system was physically moved to a new site.  This included installation and testing of muxes and a wide area network.

 

 

1991

 

Designed and wrote a system at Datalogics to manage graphic files for a VAX cluster in an Oracle database.  This was written in C++ and worked in a client / server mode keeping separate threads for each connected user.  It utilized DECnet software.

 

1994

 

Took a minor role in helping debug client/server communications for applications generated by our case tool.  This required using NSD and CPIC.

 

 


Hardware Management

2003-Present

Managed and taught teams of students (up to 25 in number) using and managing my own 20 node Torque/DCC/Maui cluster and 20 node SunFire and machines from other institutions in the Illinois Bio-Grid.

2001-2002

Managed a 3 person team that managed two high performance multiprocessor Linux servers and one high performance multiprocessor Sun server with Solaris.

 

1997-2002

Manager of a 25 person volunteer team managing a Unix Internet server for Chicago Mensa and Mensa International.

 

1984-1985

Was in charge of entire DP site.  Performed some cable laying, connector wiring, and end-to-end testing.  Ran diagnostic functions on an MV-4000 (Data General) CPU. In charge of all procurement.

 

1985-1987

In various consulting contracts, installed cabling and end-to-end connections for new installations.

1985

Performed the communications hardware setup when a system was physically moved to a new site.  This included installation and testing of MUXes and a wide area network.

 

1978

While attending college, built my own micro-computer system based on an S-100 bus and an 8080-A microprocessor.  Wrote a monitor for this system as well as an 8080 assembler.

 

1997-present

Sysadmin of the internet server that supports Chicago Mensa, American Mensa, and Mensa International.  The system runs under BSDi

 

 


CASE tools programming

1982-1983

Wrote a generic screen-oriented database maintenance system in DG/L (a C-like language).  The programmer used this system by creating a forms definition file which specified field locations on the screen, prompt strings, which database field the screen field was connected to (along with computations and validations), and access options (read, write, etc.).

 

1986 to 1988

Designed a screen based forms definition package.  A programmer would use the system via a set of predefined keys which would designate certain screen portions as prompt fields, input fields, output fields, calculation routines, etc.  The system worked in conjunction with a pre-defined SQL schema, which allowed for easy access to database field names.

 

1989 to 1991

Enhanced and maintained a system written in PROLOG that took a simple language as input and gave as output a System Requirements Document text file, a System Design Document text file, a SQL schema, and a set of C and C++ modules to work with the data (including storing and retrieving the data from a choice of several different database managers and a screen).

 

1990

Designed and wrote a system in PROLOG on the PC under DOS that worked with an SGML DTD.  It took the DTD and listed all potential tags in context along with all formatting issues that each tag could affect so that a document could be drawn up describing what each tag in context would do.

 

1991-1993

Helped design and took a lead in writing a CASE tool for client/server applications.  The server was an AS/400 and the client was a PC under Windows.  The definition facility ran on a PC under OS/2.  The code generation facility was implemented as an interpreter using PC/YACC.  The generated code was C++ for Windows.  Also, helped a different team implement the first set of applications (GL to be sold on the open market) using this case tool.

 

 


Compilers

1978

While attending college, built my own micro-computer system based on an S-100 bus and an 8080-A microprocessor.  Wrote a monitor for this system as well as an 8080 assembler.

 

1982-1984

Wrote a pre-processor for DG/L (a block-oriented ALGOL based language) at Lerner to allow for a named database field variable interface to be created and used like modern C like structures.  By the generic way this system was designed, it could also be used as a preprocessor macro generator.

 

1987

Wrote a cross assembler for the 8086 in C on a VAX.

1990-1991

Enhanced and maintained a CASE tool in PROLOG that would generate documents, SQL schema, and C++ modules.  Used Turbo-PROLOG's toolbox to create and parse a BNF language.

 

1993

Wrote an object oriented equivalent of YACC and developed a cross code generator/compiler for the PC to generate IBM RS6000 RISC assembly code.  This was a combined personal project and projects for two different graduate courses.

 

1991-1993

Helped write a case tool code generator as an interpreter running under OS/2 and developed in PC/YACC and C.  The output of the interpreter was C++ code for the PC for Windows.

 

 


Other

Member of the Board of Directors of the Illinois Medical District’s BiTMap program 2005 to present.

Chair of the Global Grid Forum Research Group on Life Sciences (BioInformatics) 2002 to present (http://www.cs.uchicago.edu/~dangulo/LSG and http://www.gridforum.org)

Chair of the DePaul University School of CTI Bioinformatics Workgroup, 2004-05, 2005-06.

Chair of the DePaul University School of CTI Colloquium Committee, 2003-04.

Founder of the Illinois Bio-Grid 2003 to present

Chicago Mensa Cyberspace Chair 1997 to 2002.

Member of American Mensa Cyberspace Committee 1998 to 2002.

Member of Mensa International Cyberspace Committee 1998 to 2002.

Member of American Mensa and Mensa of Illinois from 1993 to 2004.

Founder and leader of the Sigma Pi alumni club at Loyola.

Chicago Mensa Webmaster 1995 to 2001.

Sigma Pi International Webmaster 1995 to 1999.

Sigma Pi International Technology Chairman 1994 to 2000.

Chapter Director of Sigma Pi chapter at Loyola from 1991 to 2000.

Sigma Pi Illinois Regional Leadership Coordinator 1993

Executive Board member of the Chicago Area Digital Users Society from 1989 to 1991.

Secretary of the North American Data General Users Group 1986 to 1988 (about 3000 member companies, budget of $750,000 per year).

Secretary of the Chicago Area Data General Users Group 1987 to 1989.

President of the Chicago Area Data General Users Group 1986.

Secretary of the Chicago Area Data General Users Group from 1980 to 1985.

Awards

Best of Conference Poster (my student lead author) at MSEC/CTIRS 2006

Best of Conference Poster at Super Computing 2004 (top conference in field).

Best of Conference Student Poster (my student lead author) at MSEC 2004

Leading member of group that won two of three Grand Challenge awards at Super Computing 2002. (extremely prestigious)

Loyola University Robert B. Reisel award for outstanding academic achievement, 1998.

R&D 100 Award from R&D Magazine (Globus Toolkit 2.0) 2002 (extremely prestigious).

Smithsonian Institution Permanent Research Collection of Information Technology award winner (Pivot Tables SPSS) 1997 (extremely prestigious).

Awarded American Mensa Chairman's Award (its highest award) 1999

Awarded Chicago Mensa Service Award (its highest award) 1999

Winner Indiana Science Fair 1974 - entered in International Science Fair

NMSQT national semi-finalist (award for high SAT score 99+ percentile) 1973

Loyola University Chess Champion 1977

Lake Central High School Chess Champion 1974

Best American Mensa Web Page 2002

Best American Mensa Web Page 2001

Best American Mensa Web Page 2000

Best American Mensa Web Page 1999

Nominated for best American Mensa Web Page 1998

Nominated for best American Mensa Web Page 1997