Timothy Daly

146 Century Farm Road

Clinton, PA 15026





Work Experience


Carnegie-Mellon University:  Pittsburgh, PA (May 2013 – Present)


     Visiting Scholar (GHC 7227)

          Research on proving the Axiom Computer Algebra System correct

          Proving Axiom Sane: The 30 Year Horizion


     Scone Knowledge Representation Project (Lisp)

          Research, design, and implement an Artificial Intelligence system

         for Robot-Human cooperation on a tire changing task.
        TIRES: Robot-Human Cooperation (AI Research)


     Exfiltration Prevention Project (VHDL/Verilog)

         Design and implement FPGA Security devices to detect and

         prevent exfiltration of Confidential documents


Literate Software:  Pittsburgh, PA (November 2012 – April 2013)


     Implementation of BioInformatics algorithms


Cigital:  Pittsburgh, PA (May 2012 – November 2012)

    Top Secret Security Clearance

    Cigital is the leader in Software Security Consulting


           Taught Attack and Defense course for U.S. Air Force


           Taught HP Fortify, AppScan and AppDetective courses


           Security Code Review for SWIFT Financial (C++)


           Detailed security review, both hardware and software, for

           a hardware security module (HSM) chip, including a review

           of Cryptographic, SSL and TLS, and Public Key Infrastructure

           implementation issues.


Literate Software:  Pittsburgh, PA (February 2011 – May 2012)

  Consulting contracts:


           Develop a management plan for conversion of online course

           material to mobile devices (iPad/Objective C), (Android/Java)


           Develop a multi-touch vision tracking system (C++)


           Design parallel DNA sequence alignment using GreenArrays

           hardware chips (Forth, C)


           Design literate software extraction program (Lisp)


Carnegie Mellon University:  Pittsburgh, PA (July 2005-February 2011)

   The Carnegie Mellon Software Engineering Institute (SEI) is a federally funded
  research and development center.  The SEI staff has advanced software engineering    
  principles and practices in software engineering, computer security, and process


 Computer Forensics – Member of team developing “cutting edge” tools to

            to enable government and law enforcement agencies to recognize and combat

            emerging cyber threats..


 Concordia – (Independent Research Project) Concordia is an architecture for the  
           parallel generalization of patterns, finding their invariant structure, and using
           those patterns to predicate associations.


            XNET CERT “train as you fight” Exercise Network is a cyber-security platform

          for doing “live fire” exercises to replicate real-world cyber attack, defend, and

            respond missions. Main focus involves writing dynamic IPTable module to

            route remote users to back end server farms. https://www.vte.cert.org/vteweb/

Function Extraction (FX)  is a disruptive new technology that will substantially improve the economics of software development and increase the dependability of software systems.  Function Extraction applies mathematical foundations to automate calculation of the behavior of software, the objective being to replace slow and fallible manual methods of code reading and inspection with fast and correct computation of behavior.  Main focus of involves the definition of semantics for Intel instruction set. http://functionextraction.info/fxlong.wmv


 Network Situational Awareness (NetSA) iSiLK Configuration Editor  The CERT/NetSA has developed and maintains a suite of open source tools for monitoring large-scale networks using flow data. The System for Internet Level Knowledge (SiLK) is an efficient network flow collection and storage infrastructure that will accept flow data from a variety of sensors. SiLK also provides a suite of efficient command-line tools for analysis. iSiLK is a graphical front-end for the SiLK tools, designed to work with an existing installation of the SiLK analysis suite. Contribution to iSiLK was the Configuration Editor written in Python. http://thewebmaestra.com/isilk.html

Member of Board of Directors of the Association of Lisp Users http://lisp.org/alu/home

CAISS Institute City College of New York:
New York, NY (Sept 2002-May 2005)

       Research professor leading three open source projects: Axiom, Magnus, and Doyen.
      Managed 7 students.

       Worked with ACM and ISSAC.
      Research work in Literate Programming.


       Lead developer on Magnus, an infinite group theory package
      Exploratory Infinite Group Theory (Gilbert Baumslag, Marianna Papaleo, Xiawei
      Xu, Marcos Zyman, Peggy Dean)

       ~150k lines of source code



        Lead developer on Doyen, a liveCD science platform.

        Doyen - Science Platform (Wilken Rivera, Jose Alfredo Perez)



        Indefinite Grant (Bill Sit, Gilbert Baumslag, Sean Cleary, Douglas Troeger)

        Research in Symbolic Indefinites

        NSF Principle Investigator


        ITR Grant Proposal Axiom (Jan 2003) and  (Jan 2004)


        Conference Chair “The Future of Scientific Computation” (CCNY 2004)

        FEDORA - RedHat Active Developer        


WorldCom: Rye, NY (Oct 2000-July 2002)

       Team Lead to install monitoring system for all data center switching within
      WORLDCOM (93 Worldwide) . SNMP monitoring for failure alerts and billing.
      Wrote a Java/XML program to audit actual equipment vs monitoring database.


       Managed a lab of networking equipment and racks of Linux and Sun servers to test
      management software and network configurations for Worldcom data centers.


        Wrote performance and stress testing software for high-end backbone routers and

  Cold Spring Harbor Labs: Long Island, NY (Oct 2000-April 2001)

       Consulting work for Stein Labs developing a program to enable Biochemistry
      researchers to search and annotate DNA patterns.

                  Contract work on web-enabling SNP searches in DNA sequences

Westport, CT (Feb 2000-Oct 2000)

       Developed a converged user interface for 4 internal systems that are used to deploy
      web based measurement and marketing programs (a Facade pattern). Written in
      Java and Perl. Developed a Makefile hierarchy to coordinate multiple developers.


   UUNet: Katonah, NY (Dec 1998-Feb 2000)

         Responsible for designing programs to monitor the status of servers and databases
        on the UUNET global hosting network (~3500 nodes).


        Wrote a multithreaded, distributed monitoring program in Java that used the Model-
        View-Controller pattern. It shows the status of hosts and databases, displays a
        "trouble board" of failing systems, and  interfaces to a Remedy trouble-ticket


         Specified and created a networking lab to test Gigabit switching networks from
        various vendors for deployment in UUNET centers.


   Approach: Valhalla, NY (Dec 1996-Dec 1998)

        Technology demonstration for Comcast. Wrote a statistics program demonstrating
       the use of Java (J++) and DCOM. The statistics were shown on a web page

         using an applet.


         Business case detailing a plan to build up its EDI consulting.  Created

         Java classes that implement the segments and constructed the

         BAPLIE (shipping) and JAPRES (job application) message sets.


         Product to handle all aspects of paying commissions to sales people at Comcast.
        This was an 18 month, 10 person effort. As one of the primary developers on the

         project, the efforts included:

           - A proof-of-concept in Java. The proof of concept used both Access and a SQL
            6.5 Server database using ODBC.

          - Wrote  SQL and Stored Procedures to access and validate data.

          -  The central payment system in C++ and Visual Basic.

          -  Responsible for 3 major DLLs of the final system to handle the business rules
            and commission payment computations.

          -  Wrote OLE Automation objects in C++ to interface a commercial rule engine to
             the final system. The engine was run out of process using MTS and DCOM
             components. All testing was done in Java.

           - Wrote a debugging COM component that send TCP/IP (UDP) packets to a Java
            debugging package I wrote. The system was constructed to run on Windows NT.


         Co-lead for development of  an ECommerce guide for use in pre-sale client


        Systems Analysis for requirements gathering and use-case design for streaming
       video presentations.

        Development of a reuseable 3-tier architecture using CORBA and Java, interfacing
       with COM components. And UML patterns to automate the construction of large
       portions of the architecture for client applications.



International Business Machines Corporation:  Yorktown Heights, NY (1978-1996) Thomas J. Watson Research Center

       Natural Language Understanding  – Developed CHART parser and knowledge
      representation program (KREP-based) to read mail, extract sentences involving
      priority phrases, scheduling phrases, and meeting phrases to sort, prioritize, and
      schedule calendar events.


       Rewriteable Paper (1995) – Independent research project to invent, patent, and

       develop rewriteable paper based on organic materials.


       Axiom Symbolic Computation System (1995) – Research and development of  
      commercial product in computer algebra. Primary task was the development of
      system interpreter internals, written in Lisp. Develop algebra for Denavit-Hartenberg


       ECLPS (1989) – Development of commercial rule-based programming language for
      Expert Systems. Common Lisp, based on OPS5 from CMU.


       FAME (1989) – Wrote KROPS, the implementation language for FAME (Financial
      and Marketing Expert) based on OPS5 for rules and KREP for knowledge


       BOXER (1986) – Research in Robot Planning. Invented and developed a system to
      reason about solid models and generate robot motion to perform automatic assembly

       as a “design-to-build” system.


       AML (1984) – Co-author of AML Robot Language, an IBM commercial
      real-time robot control. Received Patent for Slip Sensor (#4,605,354)


        VM/370 Systems Programmer (1981) – Mainframe operating system performance
       and tuning. Co-authored subsystem to manage free storage, shipped as part of high
       performance upgrade to VM/370.


        ARCHIVE (1979) - Designed and developed an online archival storage and retrieval
       system using a hierarchy of disk and tape backups.


Unimation: Danbury  Ct (May 1976-July 1978)

  VAL Co-developed Real Time commercial robot programming language.



Open Source Work  (1997-present)


          Axiom – Computer Algebra system, originally written at IBM Research and

                          sold as commercial competitor to Mathematica and Maple. Open

                          sourced in 2001. Lead developer (http://axiom-developer.org) Active.


          Magnus – Infinite Group Theory Computer Algebra system, originally written

                            at City College of New York CAISS Institute. Lead developer.

                            (http://sourceforge.net/projects/magnus) Active.


          Doyen – Scientific Platform on Live CD. Used by Sage, Axiom, and Magnus.

                         Lead developer. (http://daly.axiom-developer.org/doyen) Active.


         PingerProtocol-agile real-time monitoring of internet backbone routers and

                          data center server racks. Used for trouble detection at Worldcom.

                          Lead developer. (1997, project defunct)


Teaching Experience


          City College of New York, New York, NY                

             Open Source Programming (Fall 2004)


         Vassar College, NY Poughkeepsie, NY

             Compilers (Spring 1990)

             Programming Languages (Fall 1990)


          William Patterson University, Wayne, NJ

             Data Structures (Fall 1981)      



 Polytechnic Institute of New York:  Brooklyn, NY (September 1997) Ph.D program  (thesis incomplete) Topic: “Provisos -- Conditional Computational Algebra”


 Fairleigh Dickinson University:  Teaneck, NJ (May 1980) M.S. Computer Science.  


 Montclair State College:  Montclair, NJ (June 1975) B.A. Mathematics, minor Computer Science.  


Related Courseware


           Operating Systems, Systems Programming, Reliable Software, Switching Theory,
          Dynamic Simulation, Automata Theory, Formal Languages, Numerical Analysis,
          Compiler Design Image Analysis, Pattern Recognition, Learning Machines



Computer Languages


            JAVA, C++, C, LISP, ECLPS, OPS5, AML, VAL, PASCAL, PL/I,


            MASM, BOOT, A# (Computer Algebra Languages), UNIX shells,

            MACRO(DEC assembly lang.), BAL(IBM assembly lang.)

            HASL(Intel 8080 assembly lang.)




Daly, T., Proving Axiom Sane: The 30 Year Horizon

International Congress on Mathematical Software, Notre Dame, August 2018


Daly, Timothy Axiom: Literate Programming in the Large Carnegie Mellon University, January 2013


Daly, Timothy; Roostapour, Laleh; Fahlman, Scott Planning Challenges in a Cooperative Tire Changing Task Carnegie Mellon University, January 2013


Daly, Timothy Clojure in Small Pieces Nov. 2013


Daly, Tim Publishing Computational Mathematics Notices of the American Mathematicsl Society, Vol 59, No. 2, Feb 2012 pp 320-321


Daly, Timothy Intel Instruction Semantics Generator SEI/CERT Research Report, March 2012


Daly, Timothy; Linger, Rick; Prowell, Stacy; Burns, Luanne Concordia: Google for Malware Journal of Information Systems and e-Business Management (accepted for publication)


Linger, Richard;, Sayer, Kirk; Daly, Tim; Pleskoch, Mark Function Extraction Technology: Computing Behavior of Malware Proceedings of Hawaii International Conference on System Sciences, Kuaui, Hawaii, January 2011


Linger, Richard; Daly, Tim; Pleszkoch, Mark Computation of Software Behavior: 2010 Development and Application of Semantic Reduction Theorems for Behavior Analysis SEI/CERT TEchnical Report CMU/SEI-2011-TR-009, ESC-TR-2011-009, Feb 2011, Carnegie Mellon Unversity


Daly, Timothy; Linger, Rick Test and Evaluation: Robot Forward Kinematics CERT IRAD Report, Feb 2010


Pleskoch, Mark; Daly, Timothy; Cohen, Cory Automatic Generation of Hidden Markov Models for the Detection of Polymorphic and Metamorphic Malware SEI/SERT IR&D Project Briefing, Oct. 2010


Daly, Timothy; Burns, Luanne Concordia: A Google for Malware 6th Annual Cyber Security and Information Intelligence Rsearch Workshop, Oak Ridge National Labs, April 21-23, 2010


Daly, Timothy; Burns, Luanne Concurrent Architecture for Automated Malware Classification Proceeding of Hawaii International Conference on System Sciences, Kuaui, Hawaii, January 2010


Sayer, K. Pleszkoch, M., Daly, T., Linger, R., Prowell, S. Function Extraction for Malicious Code Analysis CERT 2009 Research Report (R. Linger, Ed) Software Engineering Institute, Carnegie Mellon University, Pittsburgh PA, 2010


Pleszkoch, Mark; Daly, Tim; Linger, Rick; Sayre, Kirk Notes on Function Extraction Technology Research Report, Software Engineering Institute, Carnegie Mellon University, Pittsburgh PA, 2010


Linger, R.., Daly, T., Advanced Technology for Test and Evaluation of Embedded Systems CERT 2009 Research Report (R. Linger, Ed) Software Engineering Institute, Carnegie Mellon University, Pittsburgh PA, 2010


Linger, Rick; Mark Pleszkoch; Kirk Sayre; Timothy Daly Computing the Behavior of Malware SEI/CERT Research Report, 2010


Burns, Luanne; Daly, Timothy, FXplorer: Exploration of Software Behavior: A New Approach to Code Understanding and Verification, Function Extraction for Computation of Software Behavior. Proceedings of Hawaii International Conference on System Sciences, Kona, Hawaii, January, 2009.


Daly, T. CONCORDIA: Cognitive Cord Architecture SEI/CERT Carnegie Mellon University, 2008 (video) (slides)


Daly, Timothy, Axiom Information Sources Axiom Project Documentation Nov. 2008 (video)


Burns, Luanne; Daly, Timothy; FXplorer: Exploration of Software Behavior A New Approach to Code Understanding and Verification, Function Extraction for Computation of Software Behavior. SEI/CERT Research Report, 2009


Bartholomew, Redge; Burns, Luanne; Daly, Tim; Linger, Rick; Prowell, Stacy Function Extraction: Automated Behavior Computation for Aerospace Software Verification and Certification, American Institute of Aeronautics and Astronautics, Sonoma, CA 2007.


Linger, R., Burns, L, Daly, T., Pleszkoch, M., Prowell, S., Sayre, K., Walton, G, Function Extraction Invention Disclosure, 2007.


Daly, Timothy Functional Extraction of Virtual Machine Viruses, SEI/CERT Research Report, Nov. 2007


Daly, Timothy; Ferullo, Daniel; Prowell, Stacy The Instruction Semantics Generation for GCC Register Transfer Language, SEI/CERT Research Report, Sept. 2007


Daly, Timothy Deriving Memory Shape, SEI/CERT Research Report, Aug. 2007


Daly, Timothy The vi program, SEI/CERT Research Report, June. 2007


Baumslag, Gilbert; Daly, Timothy Magman Login Simulator, Center for Algorithms and Interactive Scientific Software (CAISS), City College of New York, June 2007


Daly, Timothy; Pleszkoch, Mark The Program-Data Separation Issue, SEI/CERT Research Report, May. 2007


Daly, Timothy Incremental FX Test Cases, SEI/CERT Research Report, Jan. 2007


Daly, Timothy System Interrupt Discovery Subsystem (SIDS), SEI/CERT Research Report, Jan. 2007


Mili, A., Daly, T., Pleszkoch, M, Prowell, Stacy, A Semantic Regognizer for computer Loop Behavior, Proceedings of Hawaii International Conference on System Sciences, Kona, Hawaii, January, 2007.


Linger, Richard; Burns, Luanne; Daly, Timothy; Pleszkoch, Mark; Prowell, Stacy; Sayre, Kirk; Walton, Gwendolyn Function Extraction Technology: Toward Next Generation Software Engineering SEI/CERT FX Video


Linger, R., Daly, T., Pleszkoch, M., Prowell, S., and Walton, G. Function Extraction (FX) Technology: Automated Calculation of Program Behavior for Software Assurance Proceedings of NSA High Confidence Software and Systems Conference, Ft. Meade, MD, 2006


Daly, T. Axiom: The 30 Year Horizon. A Tutorial Dec 2005 288 pages Lulu.com

ISBN 141166597X


Daly, Timothy Axiom -- Thirty Years of Lisp, Invited Lecture, NYC Lisp Users Group, NY, May 2005


Daly, Timothy Axiom -- The Thirty Year Horizon, Lecture, Axiom Conference, April 2005


Daly, Timothy Open Source Philosopy ECPI College of Technology, May 2004


Baumslag, Gilbert; Buchberger, Bruno; Daly, Timothy The Andrews-Curtis Conjecture Center for Algorithms and Interactive Scientific Software, CAISS Research working report, March 2005, City College of New York


Daly, Timothy; Baumslag, Gilbert; Sit, William; Cleary, Sean; Troeger, Douglas Indefinite Problems Center for Algorithms and Interactive Scientific Software, CAISS Research working report, March 2005, City College of New York


Daly, Timothy The Structure of Magnus Center for Algorithms and Interactive Scientific Software (CAISS), CAISS Research working report, March 2005, City College of New York


Baumslag, Gilbert; Daly, Timothy Magnus: A System for Infinite Group Theory Computation Center for Algorithms and Interactive Scientific Software (CAISS), City College of New York


Daly, Timothy Computational Mathematics and Literate Programming Invited Lecture, Mathematics Dept., University of Pisa, Dec. 2003


Daly, Timothy Axiom Invited Lecture, Libre Software Meeting. Metz, France, July, 2003


Daly, Timothy Literate Programming Invited Lecture, Libre Software Meeting. Metz, France, July, 2003


Daly Timothy; Perez, Jose Alfredo; Rivera, Wilken Doyen: A Live CD Platform for Mathematics Center for Algorithms and Interactive Scientific Software (CAISS), City College of New York


Daly, T. Axiom Computer Algebra System ACM SIGSAM Bulletin, Vol 36. No. 1, March 2002 Workshop on Open Source Computer Algebra, Lyon France (Invited Paper)


Daly, Timothy Axiom Invited Lecture, Free Software Conference, Lyon, France, May, 2002


Daly, Tim Pinger: A Worldcom SNMP Network Monitor Worldcom Internal Project


Daly, T., Provisos: A Programming Extension for Conditional Computational

Algebra (Ph.D. Thesis, incomplete) 1995


Daly, T., Susan: Adding Meaning to Desktop Folders, IBM Internal publication

May, 1992


Jenks, et.al., Axiom: The Scientific Computation System Springer-Verlag, NY

ISBN 0-387-97855-0 May, 1992


Daly, T., Axiom Library Compiler Book Chapter 21, NAG LLC, England, May 92

Daly, T., Kastner, J.; Mays, E
. Integrating rules and inheritance networks in a knowledge-based financial marketing consultation system, Volume 3, Issue , 5-8 Jan 1988 Page(s):496 - 500 HICSS 1988


Daly, T., Verification and Validation of Rule Based Programs, ASME June 1989


Daly, T., Integrating Rules and Inheritance Networks IBM RC 13144, Sept 1987


Schor, Marshall; Daly, Timothy; Lee, Ho Soo; Tibbetts, Beth

Advances in RETE Pattern Matching

Proc. of AAAI, AAAI-86 August 1986 pp226-232 0-934613-13-3


Schor, Marshall; Daly, Timothy; Lee, Ho Soo; Tibbetts, Beth

YES/OPS Extensions to OPS5: Language and Environment

Technical Report RC-11900 IBM T.J. Watson Research Center

Yorktown Heights, NY 10598, 1986


Daly, T., Boxer – A Design-to-Build System IBM RC 11096

Yorktown Heights, NY 10598, 1986


Daly, T., Boxer – A Design-to-Build System

invited presentation at MIT Robot Symposium (June 1985)


Bozman. G., Buco, W., Daly, T., Tetzlaff, W. Analysis of free storage algorithms-Revisited. IBM Systems Journal 1. 23, 1 (Feb. 1984). 44-64

Baxter, Keith; Daly, Timothy
A Hobbyist Robot Arm

Byte Magazine Vol. 4 No. 2 pp 84-88  (Feb. 1979)