POSITION DESIRED:  Bioinformatics Software Engineer
LOCATION DESIRED:  France
TIME PERIOD:  some time in the future for 2 or 3 years duration

QUALIFICATIONS:

  Thirty years experience software engineering
  Two years+ bioinformatics software engineering
  Excellent written and verbal communication skills
  Development Environments: UNIX, GNU/Linux, AIX, Solaris
  Programming Languages: C, PERL, SHELL, HTML, SQL, PHP, JavaScript
  Bioinformatic Toolsets: BLAT, BLAST, Repeat Masker, BlastZ, BioPERL
  System Administration: Apache WEB server, MySQL database server, UNIX/Linux

EXPERIENCE:

Bioinformatics Software Engineer                              May 2003 - present
  Center for Biomolecular Science and Engineering
       University of California, Santa Cruz
  UCSC Genome Browser software engineering
  Built genome browsers for genome assemblies: human, mouse, rat,
      opossum, C. elegans and C. briggsae.
  Developed "wiggle" track display for the UCSC genome browser
  Experienced with parallel computing resources: the UCSC KiloKluster
      super computer, and the Parasol Parallel batch processing system.
  Customer support for the UCSC Genome Browser product

Volunteer, Bioinformatics research                            Dec 2002 - July 2006
  The Zahler Lab at U.C. Santa Cruz
  Investigating conserved regions of alternative gene splice signals
  between C. elegans and C. briggsae.  Built updated installations of
  Jim Kent's Intronerator and added specific tracks to the UCSC Genome browser,
  assisted with data analysis.  Project completed publication:
  Intronic alternative splicing regulators identified by comparative genomics in nematodes
  Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, Zahler AM, Stormo G
  (2006) PLoS Computational Biology 14 July 2006 2(7):e86
  PMID: 16839192

SETI@Home porting manager                                  April 1999 - Jan 2003
  Volunteer position, SETI@Home project at U.C. Berkeley
  Coordinated the porting efforts of 20 engineers to produce SETI@Home
  client versions for 44 different operating system environments
  on 12 different CPU types.  SETI@Home profile.

Senior Software Engineer                                   Dec 1987 - March 2002
  SCO - The Santa Cruz Operation                                  Santa Cruz, CA
  Keynote projects:
  SCO UnixWare 7
      Created a highly successful development toolkit for third party video
      device driver engineers that reduced typical driver development time
      from several months to several weeks, which also allowed the same
      driver code to be used on three different operating systems,
      OpenServer 5, UnixWare 7 and IBM AIX-5L
  IBM-SCO Project Monterey 64
      Successfully worked through start-up problems on prototype Intel IA64
      hardware, prototype compilers and development systems on Microsoft NT
      simulators, and initial versions of the IBM AIX-5L operating system
      to provide the IBM engineering team with a fully functional SCO video
      driver interface, example drivers, and driver development toolkit.
  Mozilla browser project
      Satisfied the important customer request for a new WEB browser on
      SCO UNIX systems by preparing the code changes and porting process
      to OpenUNIX 8 and OpenServer 5 two months ahead of schedule for the
      Mozilla v1.0 release.
  Caldera Volution project
      Ported the Volution cross-platform administration system from Linux
      to UnixWare 7 and OpenUnix 8.  Completed the project on time with
      packaging, documentation, and Volution team training on the
      operation of the product for these new operating systems.
  SCO-Caldera OpenUNIX 8 project
      Provided the CDE component for the project, worked with new video
      driver code from Matrox, performed system testing, project source
      code management, build processes, system integration, and
      documentation review.

Software Engineer and Group Manager                        March 1983 - Feb 1985
  Ryan-McFarland Corporation                                   Aptos, California
  Develop RM/COBOL compilers on the IBM/MS-DOS operating system

Software Control Engineer                            September 1979 - March 1980
  MEASUREX Corporation                                        Frankfurt, Germany
  Install and maintain process control software at Measurex
      installations in Austria.

Software Field Support Engineer                             July 1978 - Feb 1979
  MEASUREX Corporation                                     Cupertino, California
  Telephone assistance to on-site Technical Representatives for
      process control software installations

Field Engineer and Technical Representative               March 1977 - July 1978
  MEASUREX Corporation                                       Hanford, California
  Maintenance of hardware and sensor electronics for the MEASUREX
      process control system #222 at the Armstrong Tire Company

Lab Assistant                                           October 1973 - July 1975
  Space Sciences Lab                                               U.C. Berkeley
  Provide programming support for X-RAY astronomy research
  Assemble electronics and write programming to "Search for
      Extraterrestrial Radio Emissions from Nearby Developed
      Intelligent Populations" SERENDIP

Computer Programmer                                         June 1970 - Sep 1970
  Collins Radio Company                                Newport Beach, California
  Write FORTRAN programs to simulate and test the logic design of
      integrated circuits

PUBLICATIONS:

  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
      Adam Siepel, Gill Bejerano, Jakob S. Pedersen, Angie S. Hinrichs,
      Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth,
      LaDeana W. Hillier, Stephen Richards, George M. Weinstock,
      Richard K. Wilson, Richard A. Gibbs, W. James Kent,
      Webb Miller and David Haussler
      (2005) Genome Research Aug 15(8):1034-50. Epub 2005 Jul 15
      PMID: 16024819
      ISSN 1088-9051

  Exploring relationships and mining data with the UCSC Gene Sorter
      W.J. Kent, Fan Hsu, Donna Karolchik, Robert M. Kuhn,
      Hiram Clawson, Heather Trumbower and David Haussler
      (2005) Genome Research May 15(5):737-41
      PMID: 15867434
      ISSN 1088-9051

  The ENCODE (ENCyclopedia Of DNA Elements) Project
      (2004) Science Oct 22;306(5696):636-40

  Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
      Mathieu Blanchette, W. James Kent, Cathy Riemer, Laura Elnitski,
      Arian F.A. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom,
      Hiram Clawson, Eric D. Green, David Haussler and Webb Miller
      (2004) Genome Research 14:708-715
      PMID: 15060014
      ISSN 1088-9051

  Genome sequence of the Brown Norway rat yields insights into mammalian evolution
      Rat Genome Sequencing Project Consortium
      (2004) Nature 428(6982):493-521
      PMID: 15057822

EDUCATION:

  U.C. Santa Cruz Extension - Bioinformatics Certificate - November 2003
  U.C. Santa Cruz Extension PERL programming - 60 hours - November 2002
  U.C. Berkeley Extension JAVA Programming - 30 hours - March 2000
  U.C. Berkeley B.S. EECS - June 1974

EXTRA CURRICULAR ACTIVITIES:

  Solar Eclipse chasing and Astrophotography (20 minutes lunar shadow time)
  World Travel - eight years of educational travel in 50 countries
      on 5 continents and all 50 states
  Second degree black belt in the martial art of Aikido, a study
      in conflict resolution
  Photography

CONTACT:

  Hiram Clawson
  email: hiram@soe.ucsc.edu
  web: www.soe.ucsc.edu/~hiram/