Okgu Kim


Education:

B.S.: Kyungpook National University College of Engineering,
     Department of Electronic Engineering,
     Information Communication Major (Digital Communication) (1993.03 ~ 1998.02)

M.S.: Seoul National University College of Natural Sciences,
     Interdisciplinary Program in Bioinformatics (2003.09 ~ 2005.08)


Research Interests and Current Work:

Bioinformatics

  • T.A. Brown. GENOMES 2nd Edition. Wiley-Liss, 2002 (studied)
  • Andres D. Baxevanis, B.F. Francis Ouellette. Bioinformatics. Wiley-Interscience, 2001
  • Biochemistry, Molecullar Cell Biology, Medicinal Chemistry

  • David L. Nelson, Michael M. Cox. Lehninger Principles of Biochemistry 3rd Edition. Worth Publisher, 2000 (studied)
  • Bruce Alberts, et. al. Essential Cell Biology: An introducton to the Molecular Biology of the Cell. Garland Publishing, 1997 (studied)
  • Graham L. Patrick. An Introduction to Medicinal Chemistry. Oxford University Press, 2001 (studied)
  • Anatomy, Physiology, Pathology, Clinical Microbiology, Cancer, Pharmacology, and Pharmacogenetics

  • David Shier, Jackie Butler, Ricki Lewis. Hole's Human Anatomy & Physiology 10th Edition. McGraw-Hill, 2004 (on studying)
  • Geoffrey M. Cooper. Elements of Human Cancer. Jones and Bartlett, 1992 (studied)
  • Wendell W. Weber. Pharmacogenetics. Oxford University Press, 1997 (on studying)
  • Joseph G. Cannon. Pharmacology for Chemists. American Chemical Society, 1999 (studied)
  • Pharmacoepidemiology (just interest)

  • Informatics Applicatoin
  • Epidemiology
  • Post-Marketing Surveilance (PMS)
  • Adverse Event Reporting System
  • Database development for Pharmacoepidemiology
  • PhactaX: Clinical Trial Process Management System Development
         (on development, funded by National Research Laborary Project
              of the Ministry of Science and Technology)

  • PhactaDesigner: eCRF design program
  • PhactaManager: Clinical Trial Data Management System (XML based, Web based, and for Multicenter)
  • PhactaForm: Common Data Element and Common eCRF Section Management Website
  • PhactaDictionary: Standard Coding Dictionary System Management Website (MedDRA 5.0, 5.1, 8.0, COSTART, ICD-10, WHOART)



  • Publications:

  • Okgu Kim, Byung Ju Park, Introduction to electronic document standards and guidelines for the management, exchange, and submission of clinical trial data. Journal of Korean Clinical Pharmacology. 2004;12(2)
  • Okgu Kim, Byung Ju Park. Introduction of electronic adverse event reporting system. Journal of Korean Clinical Pharmacology. 2004;12(1):13-15
  • Okgu Kim, Seon Ha Kim, Ju Han Kim, Kyun Seop Bae, Hwa Jung Kim, Byung Joo Park. Information technologies for solving the problems of paper based clinical trial. Journal of Korean Clinical Pharmacology. 2003;11(2):75-82



  • Proceedings:

  • Okgu Kim, Sun-Ha Kim, Young-Shin Kim, Hee-Jung Ahn, Young Koh, Hyoung-Joo Lim, Jin-Young Jang, Ju Han Kim, Byung Joo Park. PhactaX - a package of data management system and related web sites for conducting medical researches and clinical trials. Journal of Korean Society of Medical Informatics. 2005;11(Suppl 1)
  • Okgu Kim, Young Shin Kim, Seon Ha Kim, Hwa Jung Kim, Nam-Kyong Choi, Jung-Lim Jung, Ju Han Kim, Byung Joo Park. XML Grammar development for system independent and reusable electronic case report form with online data verification support. Journal of Korean Society of Medical Informatics. 2004;10(Suppl 2)



  • Work Experience (1998.03 ~ 2005.08):

    By Field

    Principal Database:

  • Oracle SQL tuning
  • Oracle Pro*C/C++
  • Oracle OCI
  • Oracle PL/SQL
  • Principal Programming Languages:

  • C/C++ (for core engine)
  • MFC (for interface)
  • x86 Assembly (only for speed and code optimization)
  • High Performance Computing:

  • MPI based and native clustering
  • OpenMP and native multithreading
  • Distributed Computing:

  • CORBA on C/C++ and Java
  • Principal Web Server Script Language:

  • PHP
  • By Application

    High-throughput Message Broker
         (at Greathuman Corp., Server Development Team)

  • Core based on AVL Tree Message Mangement Algorithm
  • Embedded in Instant Messaging Server
  • Message delivery between H.323 (VoIP) Gatekeeper and Internet Phone Client
  • Database for Internet Phone Call Log Management
         (at Greathuman Corp., Server Development Team and as a Freelancer)

  • Cache for call logging (hundreds of logs per one second scale)
  • Large-scale call log traversing (tens of million scale)
  • Asset & Liability Management (ALM) System
         (at Samsung Life Insurance Corp., Enterprise Risk Management Team)

  • Runs on a cluster of three 8-way SMP systems and four 4-way SMP systems
  • Implements clustering and multi-threading
  • Implements Risk Management Algorithms (Direct Cashflow, PVDE, MVS)
  • Handles 1 ~ 20 GB data at one computation cycle (30 min. ~ 4 hours)
  • PhactaX : A package of clinical trial data management programs and websites
         (at Seoul National University Hospital Clinical Trial Center)

  • XML based eCRF description language specified using XML Schema language
  • Multi-center clinical trial management support
  • Various Adverse Event Coding Dictionary support using website and Simple Object Access Protocol (SOAP)
  • Common Data Element (CDE) and Common eCRF Section management website



  • Undergraduate Student Extracurricular Activity (1993.03 ~ 1998.02):

    Hanulso Club (the 7th-term member)

    Tiny Operating System (1993)

  • Whole Assembly language in 286 Protected Mode
  • Basic Keyboard and Screen APIs
  • Guest Book Program (1993)

  • With other members
  • Voice play function
  • Guest book recording
  • Presented at Hanulso Software Exhibition '1993
  • Usenet Data Retriever (1994)

  • Consists of a client program and a proxy server
  • Manages concurrent TCP connections for large data transfer
  • Multi-process management
  • Network News Transfer Protocol (NNTP) Processing
  • Automatic uudecode and file assembly
  • X Window Graphic File Viewer, 'Hanaro'(1994 ~ 1995)

  • BMP, PCX, GIF, JPEG, TIFF file view
  • Image Processing (Convex Effect, Sharpening/Smoothing, Boundary Detection in YIQ space,
         Discrete Cosine Transform (DCT) Analysis, etc)
  • Presented at Hanulso Software Exhibition '1994
  • X Window Text Editor, 'Vada for X Window' (1994 ~ 1995)

  • Text editor
  • Embedded C/C++ Compliation
  • Regular Expression Search
  • Remote file edit through FTP/TFTP and ZMODEM on Telnet Protocols
  • Presented at Hanulso Software Exhibition '1994
  • Won the best prize of Software Exhibition of Department of Electronic Engineering '1995 (1995)
  • Class Scheduler (1997)

  • Based on Network Computing Architecture (NCA, 3-tier) of Oracle Corporation
  • Load balancing among clustered PCs
  • Won the best prize of Software Exhibition of Department of Electronic Engineering '1997 (1997)
  • Undergraduate Student Intern:

    Telecommunication Lab.(1994~1995)

  • Ethernet (IEEE 802.3) Protocol Study
  • Asynchoronous Transfer Mode (ATM) Protocol Study
  • Other Protocol Studies: FDDI, Token Ring (IEEE 802.5), Logical Link Control (LLC, IEEE 802.2), DQDB
  • Cryptography Lab.(1996)

  • RSA, DES, IDEA, Diffie-Hellman Cryptography and MD5 Hashing Implementation using C
  • Large-number manupulation (addition, multiplication, exponential, residue in Galois Field (GF)) Impelementation using C
  • Large Prime Number Generation Impelementation using C
  • Eliptic Curve Cryptography (ECC) Study
  • Discrete Logarithm Problem, Montgomery Algorithm, Euler and Euclid Theorem Study
  • Real-time and Embed Lab.(1997)

  • CORBA Programming using C
  • Database Programming (Oracle Database)
  • Software Engineering and Artificial Intelligence Study
  • Real-time Intrusion Detection Research
  • Undergraduate Student Research Project:

    Legacy-Transparent Crypto-Communication Program (1997)

  • Funded by Ministry of Information and Communication
  • Implemented symmetric and assymmetric cryptography algorithms
  • Transparent to legacy network communication clients and servers
         (different to telnet and ftp programs that use SSL with different TCP ports)
  • Operates in UNIX environment (Linux, AIX(IBM RS6000), Solaris(Sun Sparc20), Digital OS)