§       4+ years of experience in Bioinformatics and 5+ years of experience as a software engineering.

§       Second place worldwide in the IEEE CSIDC - design and implementation of a Bluetooth based computer system (Washington DC, 2002).

§       Object-oriented analysis and design; extensive working knowledge of multi-language N-tier applications with an emphasis on Service Oriented Architecture (SOA), design patterns and frameworks (UML, RUP, Hibernate, JSF, EJB, Spring, SOAP Axis, Java Beans, and POJO).

§       Software architecture/technical leadership proven in all aspects of System Development Life Cycle.

§       Hands-on designing of Bioinformatics web portals with back-end high throughput pipeline.

§       Significant experience in designing and implementing mobile solutions for cell phones and PDA?s.

§       Programming Languages: C, C++, Java, Perl, C#, PHP, Flash, SQL PL/SQL, Assembler, Basic.

§       Web Development: Web 2.0 expertise in HTML/JavaScript/CSS, AJAX (DWR, CGI::Ajax, Prototype), JavaServer Faces, JSP, Java WebStart/Swing/Applets, SOAP, WSDL.

§       System Administration: CVS, Apache, Tomcat, UNIX, Windows, Linux (Debian, RedHat), Solaris.

§       Database Design and Maintenance: Oracle (8, 9,10g), MySQL, PostgreSQL, MS SQL Server.

§       Broad range of commercial applications and tools, including: MS Office, Eclipse, JDeveloper, Visual Studio .NET, SunOneStudio, Rational Suite, Enterprise Architect, numerous other tools and libraries.

§       Bioinformatics tools (BLAST, BLAT, Fasta, Phrap/Phrep/Consed).

§       Excellent written, verbal, and presentation skills.

Lawrence Livermore National Laboratory                                                          California, USA
Technical Lead/Software Design Engineer at Joint Genome Institute (JGI)       5/2005 ? present

As technical lead I designed, developed, and maintained systems for high throughput genome annotation and DNA sequencing project management (team of 4 developers). Gathered requirements, supported and collaborated with scientists from within the organization and external clients. Used Service Oriented Architecture (SOA) to integrate systems and technologies at JGI.

§       Designed (50%), implemented, and deployed, 6 production releases of the Global Project Tracking System (GPTS). The system manages research and development projects at JGI and allows coordination of data processing and resource flow.

§       Maintained, developed, and supported eukaryotic annotation and web portal - Genome Portal.

§       Designed and developed Comparative Genomics Portal for Plants as 3-tier application. Integrated JavaServer Faces web portal with Spring/Hibernate middle layer and Mysql 5 back-end database. The system used existing Sun Grid Engine (SGE) to perform computer intensive analysis.

§       Designed and implemented (100%) the Genome Editor web module - thanks to this community genome annotation tool, 20+ organisms databases were curate remotely (online) and even more waits in the pipeline to be processed. Developed the module applying Web 2.0/AJAX approach - used combination of JavaScript, CSS, C++, Perl and SQL.

§       Designed for GPTS 3-tier architecture with Oracle database in the back-end, Tomcat application server and two types of clients (Java Swing, and web - JavaServer Faces (JSF)).

§       Designed and implemented (95%) J2EE middle layer as set of SOAP web services and Java Hibernate framework to facilitate persistent object databases. Moreover, using SOAP over https (with SSL certificates) protocol provided a secure platform to integrate the GPTS with internal Java Swing and Web based clients and with external systems at the JGI.

§       Designed (20%) and implemented (50%) Java Swing client which provides a user with Excel like UI and allows for collaborative modification (thru the middle layer) of virtual spreadsheets. Deployed the client as a Java WebStart application. Thus, the solution combined with the https protocol allowed a user the launch securely standalone Java application from the JGI web page.

§       Designed (50%) and implemented (30%) GPTS Web client - The component provides login page and variety of web reports from the GPTS database. JavaServer Faces framework and Exadel Eclipse plug-in were used to increase productivity and decrease maintenance costs.

§       Designed (100%), implemented (100%), and deployed (100%) 4 production versions of the Groups Rights Users Management (Grum) JavaServer Faces Web application with Hibernate database layer and integrated it with other systems using SOAP/https. The system provides management of user and group authentication for web-based applications. Designed Oracle database schema in a 3rd normalized form. Developed GRUM/SOAP clients using Java, Perl, C++ and Python.

§       Managed the CVS repository and deployment strategy for GRUM GPTS and Genome Portal.

§       Developed JUnit testing framework for SOAP web services and Java Swing application.

§       Provided Java, SOAP, Eclipse, and other training and support to the JGI developers.

§       Contributed to annotation of: Aspergillus niger, Phaeodactylum tricornutum, Nectria haematococca, P. stipitis, Mycosphaerella graminicola, Xenopus tropicalis, Aspergillus niger, Branchiostoma floridae, Physcomitrella patens, Chlamydomonas and support of the Genome Annotation Group.

Lawrence Livermore National Laboratory                                                          California, USA
Software Design Engineer at Protein Structure Prediction Center                     5/2004 - 5/2005

Designed, developed, and maintained system for Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. This system is an extended facility for collection, evaluation, and publication of protein structure prediction.

§       Designed and implemented CASP6 web portal and visualization in Perl (CGI, DBI, JavaScript/CCS and Eclipse). Integrated the Portal with the pipeline and provided data mining features.

§       Devised caching mechanism on both client and server site that boosted portal performance.

§       Developed high throughput protein structure comparison pipeline (24 nodes) and designed back-end PostgreSQL database for 60,000+ protein structure models.

§       Designed and developed data mining tools, with advanced web interface for results analysis.

§       Developed protein structure comparison algorithms and modules for prediction analysis in C/C++.

§       Automated data exchange between the system and BLAST, PDB, SCOPE portals in order to find the best homologous protein structure.

§       The system was followed by the publication in scientific journal, Protein Science, and is still in use.

§       Supported and collaborated with scientists to provide the means of objective evaluation of protein structure prediction methods.

Poznan Supercomputing and Networking Center                                              Poznan, Poland
Software Design Engineer                                                                                  9/2002 - 04/2004

Worked in a team of 4+4 developers to develop Whole Genome DNA assembler and integrated it with Bioinformatics infrastructure using Sun Grid Engine (SGE), distributed workflow system (Globus), and J2EE visualization module. Collaborated with scientists on SARS-CoV virus assembly and analysis.

§       Developed Whole Genome DNA assembler ASM (C++/MPI) and deployed it in the grid (SGE). Full lifecycle software development from user requirements to deployment and support.

§       Developed search engine in Perl to query external sources (EMBL & NCBI databases).

§       Analyzed and created shotgun data from the Human Genome Project and SARS-CoV.

§       Improved the DNA assembly finishing interface (Java Applet) and integrated it with ASM.

§       Benchmarks of DNA assembly applications (Phrap, Phred, Consed package, CASP3, FAKII) - results published in a scientific journal Acta Biochimica Polonica.

ComArch global provider of IT Business Solutions                                             Poznan, Poland
Software Design Engineer                                                                                  11/2003 - 3/2004

Developed logistic web portal, EANIC, a catalogue of products and establishments with ASP/C# front-end, PL/SQL middle layer and Oracle database. Worked on EANIC in a group of 9 developers to implement user requirements and complete documentation.

§       Developed several web user modules in C#/ASP and integrated with Visual Studio .NET automated documentation generator (NDoc - XML based generator).

§       Designed and developed database layer of the application in C# and several packages of stored procedures PL/SQL in Oracle Database using Visual Studio .NET.

§       Collaborated with system designers in the design and development phase (UML, Oracle designer).

MobileBox Mobile Computing Systems                                                              Poznan, Poland
Software Design Engineer / Mobile applications designer                                 4/2003 - 10/2003

Designed and developed several GSM cellular phone and PDA (PockedPC) clients, which used common server site J2EE framework. Lead development of J2ME applications at MobileBox. Collaborated with client representatives and sales department over system specification and client?s requirements.

§       Designed and implemented eLka - driving license instructor application. Developed eLka both as PocketPC (MS eMbedded VC++) application and J2ME application.

§       Designed and developed J2ME application, ReadTec, which provides home convectors and energy meters management in major water and power provider in Poznan.

§       Designed and implemented a Java object oriented database deployed and used in cellular phone.

§       Integrated both eLka and ReadTec with back-end J2EE middle layer.

Media Port                                                                                                          Poznan, Poland
Software Design Engineer                                                                                  5/2001 - 1/2003

Developed several small and medium size projects including web banners (Java applets), games, and web applications. Involved in full software life cycle and provided expertise to other development teams.

§       Developed package of 20 computer games (Flash as ActiveX controls placed within MFC application).

§       Developed several web applications including postcard portal using PHP and PostgreSQL.

§       M.Sc. in Design and Maintenance of Information Systems, Poznan University of Technology (Poland 2004) - Thesis area "Data formats in DNA sequences processing used to automatic comparing of efficiency of Bioportals"

§       B.Sc. in Computer Science,  Poznan University of Technology (Poland 2002) Thesis area "Design and implementation of CarTooth Project - Car Payment System"

§       Computer Systems and Digital Machines Poznan High School of Electronics (Poland 1999) Computer Systems and Digital Machines Thesis area "Low level programming of step engines"

§       Computational Biology, Stanford University, USA

§       Web Services and Service-oriented Architecture, LLNL classes

§       DNA Microarrays: Experimental Design, Data Analysis and Gene Regulation, ASM2007 workshop

§       Erasmus Scholarship Universitat Siegen, Germany Research area "Assembly applications used in SARS virus assembling"

Second place in the IEEE - CSIDC                                                                      Washington, DC
Computer Society 3rd Annual International Design Competition                       06/2002

§       Full project report is published on the IEEE web page and it describes innovative embedded system for a wireless payment in the public and commercial parking lots. Several modules were designed and implemented. Three of them became a core of the system: an administration center with user friendly interface (Visual Studio .NET and MS SQL Server); a parking meter device with Bluetooth and Ethernet communication and an external device - CarTooth with 8051 processor, acceleration meter and Bluetooth communication. Full report -

§       A modified eXtreme Programing, Visual Studio .NET, MS eMbedded Visual C++, Pocket PC

Organization of CASP6                                                                                       Gaeta, Italy
Critical Assessment of Techniques for Protein Structure Prediction                   2004/2005

YACC/LEX, Bluetooth technology, Pattern design

1.       A. Kryshtafovych, M. Milostan, L. Szajkowski, P. Daniluk, J. Moult, and K. Fidelis "Protein Structure Prediction Center; DataManagement System for CASP6 Experiment" Proteins Science 10.1002/prot.20718

2.       P. Daniluk, L. Szajkowski, A. Kryshtafovych, and K. Fidelis "Identifying model-target similarity using local descriptors of protein structure." Sixth Meeting on the Critical Assessment of Protein Structure Prediction, Gaeta, Italy, December, 2004, p.162-163.

3.       J. Blazewicz, M. Figlerowicz, P. Formanowicz, M. Kasprzak, B. Nowierski, R. Styszynski, L. Szajkowski, P. Widera, M. Wiktorczyk "Assembling SARS-CoV genome new method based on graph theoretic approach" Acta Biochimica Polonica 51, No.4, 2004.

4.       J. Blazewicz, M. Figlerowicz, P. Jackowiak, D. Janny, D. Jarczynski, M. Kasprzak, M. Nalewaj, B. Nowierski, R. Styszynski, L. Szajkowski, P. Widera "Parallel DNA Sequence Assembly" Proc. ENC 2004, IEEE Computer Press, Alamitos, CA, 2004, pp. 378-382

5.       Identifying model-target similarity using local descriptors of protein structure. Daniluk, P., Szajkowski, L., Kryshtafovych, A., and Fidelis, K. Sixth Meeting on the Critical Assessment of Protein Structure Prediction, Gaeta, Italy, December, 2004, p.162-163 6.

6.       M. Kowalski, B. Nowierski, M. Rein, L. Szajkowski, J. Kniat "CarTooth Project - Car Payment System" Poznan University of Technology,  Poznan, Poland, July, 2002 IEEE Application Id: 53SHTX

7.       L. Szajkowski, A. Padki, P. Pace, Kristen M. Taylor, L. A Hornick, G. M. Werner, D. M. Platt " The multi-laboratory project management - The Global Project Tracking System" DOE InterLab 2006 conference, October 2006

8.       I. V. Grigoriev, A. Aerts, A. Kuo, R. Otillar, A. Salamov, A. Terry, K. Zhou, K. F., J. Jhavery, W. Huang, L. Szajkowski, G. Werner "Automated Genome Annotation and Analysis of Eukaryotes" 17th International Conference on Genome Informatics, December 18-20, 2006, Yokohama Pacifico, Japan

9.       L. Szajkowski, J. Blazewicz, E. Pesch, "Data formats in DNA sequences processing used to automatic comparing of efficiency of Bioportals" Poznan University of Technology,  Poznan, Poland, July, 2004

10.   Blazewicz J., Kasprzak M., Jackowiak P., Janny D., Jarczynski D., Nalewaj M., Nowierski B., Styszynski R., Szajkowski L., Widera P.: ASM: DNA Assembly Application Poznan Supercomputing and Networking Center internal report, no. RA-001/2004

Available upon request