WOJCIECH KASPRZAK August 27, 2003 BORN: May 19, 1964 (301) 846 5537 (W) HOME: 8008 Sunnybrook Ct. (301) 695 7774 (H) Frederick, MD 21701 kasprzak@ncifcrf.gov EDUCATION 1989 Bachelor of Science degree in Electrical Engineering University of Maryland at College Park, College Park, MD 20742. 1994 Master of Science degree in Computer Science The Johns Hopkins University, Whiting School of Engineering, Baltimore, MD 21218. Additional Courses: 1991 Hood College, Frederick, MD Systems Analysis 1991 FAES Graduate School, NIH Programming in C Language Bethesda, MD Concepts in Object-Oriented Programming 1994 The Johns Hopkins University, Design and Analysis of Algorithms Baltimore, MD PROFESSIONAL Science Applications International Corporation Frederick, MD EXPERIENCE Basic Research Program (BRP) previously with National Cancer Institute's Advanced Biomedical Computing Center (ABCC) (Scientific Applications) Analyst, Programmer Supporting the Laboratory of Experimental and Computational Biology (NCI, LECB). Assisting in research projects with local and remote collaborators. Preparing system demos, presentations, and co-authoring publications and posters describing STRUCTURELAB and research projects utilizing its tools. (see Bibliography below) Working on an integrated RNA structure analysis workbench called STRUCTURELAB; a message passing, client-server architecture, taking advantage of the heterogeneous LAN environment, including SGI, SUN, Alpha (Unix), and PC/Linux workstations and servers, as well as mainframe machines, such as multiprocessor CRAYs and SGI Origins. (Included MasPar MP-2 massively parallel SIMD computer and VAX mainframes (VMS OS), which have been phased out of use.) Constantly expanding and adjusting the system configuration to the changing ABCC hardware and available remote applications. Working on a STRUCTURELAB Web server using a generic (platform- independent) Internet interface to be available to the scientific community at large (a minor Java-based project). Exploring use of an object-oriented database system as part of the system. Developing new methodology for RNA secondary structure data visualization, phylogenetic analysis, and common structural motif elucidation. 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 user base and maintaining and debugging the system on a variety of platforms at the ABCC (SGI, SUN, Alpha, and PC/Linux). Training students in use of the system and supervising their work on research projects. (with SAIC,BRP since March 1997 to present) (with National Cancer Institute's Advanced Biomedical Computing Center (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 re-definable 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. 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 (now ABCC) 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, Alpha workstations, PCs, CRAY supercomputers, SGI MIMD platforms, CONVEX mini-supercomputer, MasPar SIMD massively parallel machine, VAX mainframes, PDP11 mainframe Operating Systems: UNIX, Linux, Win9x and newer, Win NT, DOS, VMS, 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, Clustalw sequence alignment, RNAmot sequence and structure alignment, RNA_2D3D, RasMol and Midas visualization software Word Processors: GNU Emacs, MS Word, WordPerfect, Latex Databases: SQL (Sybase, dBASEIV), AllegroStore - an object-oriented database system PERSONAL Born May 19, 1964. U.S. citizen. REFERENCES Available upon request _______________________________________________________________________________________ AWARDS: 1) First Place Poster prize. SAIC's Basic Research Program (BRP) Retreat 2003, St. Michaels, MD., May 11-13, 2003. Kasprzak, W., and Shapiro, B.A.: "Alternate Conformations of the HIV-1 Dimer Initiation Site Explored by the Massively Parallel Genetic Algorithm and the Structurelab Computer Workbench." 2) SAIC's Science Achievement Award, December 2000. _______________________________________________________________________________________ PUBLICATIONS: 1) Book chapter: Shapiro, B.A., Bengali D., Kasprzak W.: and Wu, J-C.: Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm. In "Computational Biology and Genome Informatics," edited by Jason T.L. Wang, Cathy H. Wu, and Paul P. Wang, New Jersey, World Scientific Publishing Co., 2003, pp. 1-33. 2) Kasprzak, W. and Shapiro B.A.: Structural Dependencies of the HIV-1 Dimer Initiation Site as Determined by the Massively Parallel Genetic Algorithm. The Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences - METMBS '02, Las Vegas, June 2002, Vol. 1, pp. 48-54. 3) 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. 4) Shapiro, B.A., Bengali, D., Kasprzak, W., and Wu, J-C.: RNA Folding Pathway Functional Intermediates: Their Prediction and Analysis, Journal of Molecular Biology, 312:27-44, 2001. 5) Shapiro, B.A., Bengali, D., Kasprzak, w., and Wu, J-C.: 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 6) Book chapter: Shapiro, B.A., Kasprzak, W., Wu, J-C., and Currey, K.: RNA Structure-analysis: A Multifaceted Approach. In "Pattern Discovery in Biomolecular Data," edited by Wang J.T.L., Shapiro B.A., and Shasha D., Oxford University Press, 1999, pp. 183-215. 7) Kasprzak, W. and Shapiro, B.A.: Stem Trace: An Interactive Visual Tool for Comparative RNA Structure Analysis, Bioinformatics, 15/1:16-31, 1999. 8) Shapiro, B.A., and Kasprzak, W.: STRUCTURELAB: A heterogeneous bioinformatics system for RNA structure analysis, Journal of Molecular Graphics, 14:194-205, 1996. 9) Shapiro, B.A., Chen, J-H., Busse, T., Navetta, J., Kasprzak, W., and Maizel, J.V.: 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. 10) Shapiro, B.A., and Kasprzak, W.: 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.) _______________________________________________________________________________________ ATTENDED CONFERENCES [TUTORIALS] AND PRESENTED POSTERS: * Assisted student Steven Cole in GA runs, analysis, and preparation of a poster for the NIH's Summer Research Program: "Changes in the Predicted Secondary Structure of Interleukin-2 mRNA Associated with Its' CD28-Mediated Stabilization" * SAIC's Basic Research Program (BRP) Retreat 2003, St. Michaels, MD., May 11-13, 2003. Presented a poster awarded the First Place Poster prize: Kasprzak, W., and Shapiro, B.A.: "Alternate Conformations of the HIV-1 Dimer Initiation site Explored by the Massively Parallel Genetic Algorithm and the Structurelab Computer Workbench." * Bioinformatics, Biostatistics, and Computational Biology Faculty meeting, Gaithersburg, MD., November 6, 2002. Presented poster: Kasprzak, W., and Shapiro, B.A. in collaboration with Atha, D.H., and O'Connell, C.D.: "Computer Prediction of Single-Stranded DNA Secondary Structures Constrained by Capillary Electrophoresis Results." Contributed to the second poster: Shapiro, B.A., Kasprzak, W., and Li, W.: "Macro and Micro Structural Analysis of Nucleic Acids." * International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences - METMBS '02, Las Vegas, NV., June 2002. Co-authored, with Dr. B. Shapiro, a paper on HIV-1 Dimer Initiation Site structures (see bibliography for a full reference). * KDD-2001: Seventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining; San Francisco, CA., August 26-29, 2001. * The Sixth Johns Hopkins Folding Meeting, Berkeley Springs, W.V., March 17-20, 2001 * Novel Approaches in RNA Informatics (NARI 2000), Montreal, Quebec, Canada, May 18-19, 2000 Presented a poster: Kasprzak, W., and Shapiro, B.A.: "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 available SGI workstation. * SPRING RESEARCH FESTIVAL '99 - contributed to a poster presentation. * RNA '98 - The Third Annual Meeting of the RNA Society. Madison, WI., May 1998. Participated in Dr. Bruce Shapiro's presentation by giving a live demo of Structurelab tools available at the time. * 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" * SPRING RESEARCH FESTIVAL '97 - contributed to a poster presentation. * 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) ] * Lisp Users and Vendors Conference (LUV '95) Boston, MA. Presented a paper on the RNA Analysis software (see bibliography for a full reference). [ Emacs Lisp (emacs editor & Lisp interface) ] [ Lisp Optimization ] [ CLIM (Common Lisp Interface Manager - OO GUI) ] * LUV '94 Berkeley, CA. [ Advanced CLOS ] [ Performing Lisp (code optimization) ] [ DB: Relational DB interface, OODB ] * 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 '91 Gaithersburg, MD. _________________________________________________________________________________________