WOJCIECH KASPRZAK                                                   December 6, 2001
 

BORN:  May 19, 1964                                              (301) 846 5537  (W)
HOME:  8008 Sunnybrook Ct.                                       (301) 695 7774  (H)
       Frederick, MD 21701                                      kasprzak@ncifcrf.gov
  

EDUCATION      Master of Science degree in Computer Science (GPA 3.9)
               Johns Hopkins University, 
               Whiting School of Engineering, Baltimore, MD 21218. 

               Bachelor of Science degree in Electrical Engineering  
               University of Maryland at College Park, College Park, MD 20742.

PROFESSIONAL   Science Applications International Corporation                  Frederick, MD
EXPERIENCE     Intramural Research Support Program (IRSP)
               and National Cancer Institute's Advanced Biomedical Computing Center (ABCC)

               Scientific Applications Analyst 

                 Supporting the Laboratory of Experimental and Computational Biology 
               by working on the development of an integrated client-server, message 
               passing, RNA structure analysis workbench called STRUCTURELAB, which 
               utilizes the heterogeneous LAN environment including SGI ,SUN, and 
               Compaq/DEC Alpha workstations and servers, as well as mainframes, such 
               as multiprocessor CRAYs, SGI ONYX, (Unix, Ultrix, Unicos), a MasPar MP-2 
               massively parallel SIMD computer, and the now phased-out Vax mainframes
               (VMS).

                 Working on a STRUCTURELAB Web server using a generic (platform-
               independent) Internet interface to be available to the scientific 
               community at large.
                 Developing new methodology for RNA secondary structure data 
               visualization, phylogenetic analysis, and common structural motif 
               elucidation.
                 Exploring use of an object-oriented database system as part of the 
               system.
 
                 Analyzing user needs for new tools and desired interfaces, 
               interacting with other automation professionals to best incorporate 
               existing software into the system, and programming the solutions.
               Serving expanding user base and maintaining and debugging the system 
               on a variety of platforms at the ABCC (SGI, SUN, and Compaq/DEC Alpha).
               Constantly expanding and adjusting the system configuration to the 
               changing ABCC hardware and available remote applications.

                 Assisting in research projects with local and remote collaborators.
                 Preparing system demos, presentations, and co-authoring publications
               describing STRUCTURELAB, and research utilizing its tools.
               (see Bibliography below)
               (with IRSP since March 1997 to present)
               (with ABCC from August 1996 to March 1997) 

               Science Applications International Corporation               Frederick, MD   
               National Cancer Institute's Biomedical Supercomputing Center (now ABCC)
               Jr. Scientific Applications Analyst.
                 
                 Worked on restructuring the RNA analysis workbench for use on 
               any internally redefinable LAN and invocation from a World Wide Web 
               front page under Unix OS environment.
                 Worked on design, implementation, and performance optimization 
               of new STRUCTURELAB modules, and developing the system's Graphical 
               User Interface.
                 Assisted users of STRUCTURELAB and expanding the system to meet 
               their needs.  Assisted in research collaborations.  Prepared 
               system demos and presentations. 
                  Responsible for installing, upgrading, and tuning the Allegro 
               Common Lisp development environment.  Maintained the RNA research 
               software system versions on SUN Sparc and SGI platforms.
               (August 1992 - August 1996) 

               DynCorp/Program Resources Inc.                               Frederick, MD  
               National Cancer Institute's Biomedical Supercomputing Center (FBSC)
               Research Associate.
                 
                 Worked on an inter-system (UNIX-UNIX, UNIX-VMS) communications 
               software module for the SUN/UNIX-based RNA structure analysis 
               software utilizing  heterogeneous computing environment of the FBSC 
               network of machines and the NIH's computing center in Bethesda, MD. 
               (DCRT).  Development done in the Common Lisp environment (Lucid and 
               Allegro CL).  (August 1990 - August 1992)

               Program Resources Inc.                                       Frederick, MD.   
               National Cancer Institute's Biomedical Supercomputing Center 
               Laboratory Assistant. 
               
                 Developed inter-computer communications system consisting of 
               a device driver module and the user interface for a PDP11/44 
               mainframe and two COMTAL image processors (in Fortran).
                 Provided assistance to COMTAL users.  Installed and debugged 
               Ethernet software on the PDP-11 node.  Maintained, and upgraded 
               the RSX operating system on the PDP-11.
               (1987 - 1989, summer full-time, part-time during the school year.)

  SKILLS       Platforms: (SUN, SGI, Compaq/DEC workstations, CRAY supercomputers,  
               SGI ONYX MIMD platforms, CONVEX mini-supercomputer, MasPar SIMD 
               massively parallel machine, VAX mainframes, PDP11 mainframe, PCs)  
               Operating Systems: (UNIX, PC Linux, Win95/NT, PC Linux, VMS, DOS, RSX)
               Programming Languages: (Lisp and its development environment, C++, 
               C, Fortran, BASIC, PASCAL, Unix shell scripts, awk, HTML, Java (limited))  
               Scientific Software: (GCG package, Genetic Algorithm for RNA secondary
               structure prediction, MFOLD/RNAstructure RNA/DNA secondary structure 
               prediction packages, MPSRCH - Massively Parallel Sequence 
               search on MasPar, RNA_2D3D and RasMol visualization software, Rnamot), 
               Word Processors: (GNU Emacs, MS Word, WordPerfect, Latex)
               Databases: (SQL, Sybase, dBASEIV, AllegroStore Object-Oriented Database 
               System)

  PERSONAL     Born May 19, 1964.  U.S. citizen. 
  
  REFERENCES   Available upon request
 
_______________________________________________________________________________________

  PUBLICATIONS:

   1) Atha, D.H., Kasprzak, W., O'Connell, C.D., and Shapiro, B.A.: Prediction of DNA 
      single strand conformational polymorphism (SSCP): Analysis by capillary 
      electrophoresis and computerized DNA Modeling. Nucleic Acids Research, 
      29(22):4643-4653, 2001.

   2) Bruce A. Shapiro, D. Bengali, W. Kasprzak, J-C. Wu, RNA Folding Pathway
      Functional Intermediates: Their Prediction and Analysis, Journal of Molecular
      Biology, 312:27-44, 2001.

   3) Bruce A. Shapiro, D. Bengali, W. Kasprzak, J-C. Wu, Computational Insights
      into RNA Folding Pathways: Getting from Here to There, In Proceedings of the
      Atlantic Symposium on Computational Biology, Genome Information Systems
      and Technology, (March 2001), ACM, Inc.,10-13

   4) Co-authored a book chapter:
      Bruce A. Shapiro, W. Kasprzak, J-C. Wu, K. Currey, RNA Structure-analysis:
      A Multifaceted Approach, In "Pattern Discovery in Biomolecular Data," edited by 
      Jason T. L. Wang, Bruce A. Shapiro, and Dennis Shasha, Oxford University Press, 
      183-215, 1999
   
   5) Wojciech Kasprzak and Bruce A. Shapiro, Stem Trace: An Interactive Visual Tool 
      for Comparative RNA Structure Analysis, Bioinformatics, 15/1:16-31, 1999.

   6) Bruce A. Shapiro and Wojciech Kasprzak, STRUCTURELAB: A heterogeneous bioinformatics
      system for RNA structure analysis, Journal of Molecular Graphics, 14:194-205, 1996. 

   7) Bruce A. Shapiro, J. Chen, T. Busse, J. Navetta, W. Kasprzak, J. Maizel, Optimization and
      performance analysis of a massively parallel dynamic programming algorithm for RNA
      secondary structure prediction, The International Journal of Supercomputer Applications,
      9(1):29-39, 1995. 

   8) Bruce A. Shapiro and Wojciech Kasprzak, Structurelab: A heterogeneous computer system
      for the analysis of RNA structures, In Proceedings of the Association of Lisp 
      Users Meeting and Workshop, Boston, MA. August, 1995. 
      (Paper on the software implementation issues presented at the conference.) 

-------------------------------------------------------------------------------------------

CONFERENCES AND TUTORIALS:

   Lisp Users and Vendors Conferences 
 *  LUV '91 Gaithersburg, MD.
 *  LUV '93 Boston, MA.
        CLOS I & CLOS II  (Common Lisp Object System - OO lisp)
        CLIM I            (Common Lisp Interface Manager - OO GUI)
        Code optimization
 *  LUV '94 Berkeley, CA. 
        Advanced CLOS
        Performing Lisp (code optimization)
        DB: Relational DB interface, OODB
 *  LUV '95 Boston, MA.  Presented paper on the RNA Analysis software.
        Emacs Lisp (emacs editor & Lisp interface)
        Lisp Optimization
        CLIM

 *  TOOLS USA '96 (Technology of Object-Oriented Languages and Systems),
    Santa Barbara, CA.
        OO Technology for Scientific Computing
        OO Distributed Computing
        Testing OO Software (The Firesmith Method)
   
 *  SPRING RESEARCH FESTIVAL '97 - contributed to a poster presentation.

 *  BIOINFORMATICS '97 - San Diego, California., Sept. 1997.
        Presented poster featuring work done with Dr. Bruce Shapiro;
        " Stem Trace: An Interactive Visual Tool for Comparative RNA Structure Analysis"
  
 *  RNA '98 - The Third Annual Meeting of the RNA Society. Madison, WI., May 1998.

 *  SPRING RESEARCH FESTIVAL '99 - contributed to a poster presentation. 

 *  NARI '2K (Novel Approaches in RNA Informatics), 
    Montreal, Quebec, Canada, May 18-19, 2000
       Presented a poster: 
       "Stem Trace: A GUI-based Tool for an Exploratory RNA Structure Analysis."
       Prepared a demo CD of the STRUCTURELAB, featuring various uses of the Stem Trace
       tool, installed and demonstrated the system at the conference 
       (on an SGI work station).

 *  The Sixth Johns Hopkins Folding Meeting, Berkeley Springs, W.V., March 17-20, 2001

 *  KDD-2001: Seventh ACM SIGKDD International Conference on Knowledge Discocery and
    Data Mining; San Francisco, CA., August 26-29, 2001.  

-----------------------------------------------------------------------------------------