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

2004-2008

Attended DePaul University, exited as ABD for a PhD in Computer Science

2009

Converted a large enterprise web site to get it running on a new system. This project was written in Python, Javascript, CSS, and Flash, and was in such a mess, that the consultant hired to do the work gave up and subcontracted with me to do the work. There w\ere over 10,000 lines of code.

2009

Wrote an internal, web based, database system for management of inventory from scratch. The system was developed in Ruby on Rails, and included Javascript and mysql. About 5000 lines of code.

2010

Wrote a medium sized (2500 lines of code) web based system to upload files for use with a custom bioinformatics program (protein folding and docking). Technologies used: PHP, CSS, Linux shell scripting.

2002-2009

Designed, architected, and wrote a huge (~250,000 lines of code) system to analyze huge datasets with complex novel algorithms. Utilized Data Mining techniques and novel distributed database algorithms to extract information from a terabyte sized dataset. The overall system utilized both a Java based GUI desktop application, and web based, Java Struts modules. The system also contained modules in C++ to manage the distributed database. Some of the web based modules used cloud computing and Software as a Service technologies with scalable modules to support massively compute parallel processing on a massively data parallel dataset. Advanced statistical algorithms were invented and implemented for the Data Mining. Managed a team of 30 developers and a $2.5 million budget for this complex proteomic analytical system.

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. Implemented a BioInformatics program (Smith-Waterman) on the Grid. It ran on a set of 7000 processors in 14 countries in 5 continents.

2002-2009

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.

2002-2006

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.

2002-2003

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.

2002-2003

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

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.

2000-2005

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 - 2008

Performed research (coding) 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.

2003-2008

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.

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.

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.

Software Architecture, Test Driven Development, JUnit, Eclipse,

1998 - 2008

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.

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)

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

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, Linux Ubuntu, Linux CentOS)

22 years 1988-present

Sun (Solaris)

9 years 2001-present

SG2

5 years 2001-2006

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)

XML

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

Java

15 years 1995-present

C++

22 years 1988-present

C

24 years 1986-present

C#

8 years 2002-present

Perl

12 years 1998-present

PHP

10 years 2000-present

Ruby on Rails

1 year 2009-present

Python

3 years 2008-present

HTML

15 years 1995-present

CSS

6 years 2004-present

Ajax

3 years 2007-present

XHTML

9 years 2001-present

SQL

27 years 1883-present

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

mysql

Have used this SQL database for nearly a decade on scores of different projects, too many to list or recall

postgres

Have used this SQL database for nearly a decade on scores of different projects, too many to list or recall

SQL

Have used this language on many different database platforms for decades

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.

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.

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.

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.

2003-Present

Managed and taught teams of students (up to 30 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.

1997-2002

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

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.

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.

2007-2009

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

2006-2008

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

Over 35 publications in international journals and conferences

2003-2009

Over 50 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.

2002-2009

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

2002-2008

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

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.

2002-2003

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.

2002-2003

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.

2003-2006

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.

2003-1008

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

2003-1008

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