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. -----------------------------------------------------------------------------------------