Assistant Project

James R. Thurmond

Scientific and Web Programmer

**** **** **. #*, *** Alamos NM 87544

Home phone: 505-***-****, work: 505-***-****

E-mail: ********@****.***, ***.********@*****.***

Website: http://www.cox-thurmond.net/

Education: Master of Science in Bioinformatics, May 2006

Indiana University, Bloomington, Indiana

GPA: 4.0 on a 4-point scale

50+ hrs of additional graduate credit in mathematics, 1996 2000

Western Michigan University, Kalamazoo, Michigan

Master of Arts in Mathematics, August 1993

Southwest Texas State University, San Marcos, Texas

30+ hours of coursework in computer science

UT Austin, WMU, and IU

40+ hrs coursework/graduate credit in biology, 1987 1989

University of Texas, Austin, Texas

Bachelor of Arts in Physics, May 1985

University of Texas, Austin, Texas

Work Database Programmer July 2006 present

Experience: Responsible for database maintenance, perl and Mason web tool maintenance, and tool development

and upgrades on the HIV, hepatitis C, and influenza viral genome sequence databases, at the Los

Alamos National Laboratory. Developed bulk input web tool for power database users to add batch

sequence data. Merged a set of HCV software tools with a similar set of tools used by the HIV

sequence database. Worked in an linux/apache environment, used version-control software (SVN).

Participated in academic atmosphere by attending lectures, symposia, and journal clubs.

Please visit these LANL websites: http://hiv.lanl.gov, http://hcv.lanl.gov, and http://www.flu.lanl.gov.

Research Assistant January 2005 May 2006

Dr. Santiago Schnell, in the School of Informatics at IU, supervised and funded my Capstone project, a

web-based tool for analyzing enzyme kinetics data, using a unique and mathematically powerful new

algorithm. Built this project from the ground up, starting with a clean linux PC. Installed Apache

server software, wrote all of the HTML and CSS, javascript, Perl scripts and CGI, and some Fortran

code, integrating these parts into a working website.

Please visit the BioFitWeb site at http://156.56.92.83/BioFitWeb.htm, or mirrored at

http://biofitweb.cox-thurmond.net/BioFitWeb.shtml.

Teacher 1990 2004

I taught mathematics and science for 15 years, at a wide range of levels and to a great variety of

students. My duties have included committee work, new curriculum development, research projects,

and management of other teachers. Details of my teaching career are available upon request.

Laboratory Assistant 1989

I worked in Dr. Ian Molineux s microbiology laboratory investigating host-phage interactions between

E. coli and bacteriophage T7. My research included culturing and plating bacteria and phages,

mutating and transfecting with genes of interest, purifying proteins, isolating and sequencing DNA,

and analyzing data.

Publications: J. Thurmond, H. Yoon, C. Kuiken, K. Yusim, S. Perkins, J. Theiler, T. Bhattacharya, B. Korber, W.

Fischer. T-cell Vaccine Design and Epitope Coverage Tool Suite. (submitted)

S. Schnell, J. Thurmond. The condition for pseudo-first-order kinetics to be valid in receptor-ligand

associations is derived using phase-plane analysis. (submission pending)

C. Kuiken, P. Hraber, D. Aggarwal, V. Hamine, J. Thurmond. A New Hepatitis C Sequence Database

in Los Alamos. Nucleic Acids Research Journal. (submitted)

P Hraber, R Leach, L Reilly, J Thurmond, K Yusim, C Kuiken, and the Los Alamos HIV Database

Team. Los Alamos hepatitis C virus sequence and human immunology databases: An expanding

resource for antiviral research. Antiviral Chemistry and Chemotherapy 18(3):113-124, 2007.

Skills: Programming

Fluent in perl, PHP, java, C++, and several other languages. Familiar with Windows, Unix, Linux, and

Mac environments. Well-versed with many technical software packages such as Matlab, Systat, Excel,

etc. Experience using version control software.

Web design

Skilled with HTML, javascript, PHP, and CSS. Experience installing and maintaining Apache and

Tomcat web server software.

Inter-personal

Excellent communicator, verbally and in writing. Strong collaboration skills. I learn quickly and can

teach well.

Projects: Montessori Online Menu

Web application tool package automating parent menu selection and school administration

maintenance for a private school in Bloomington, IN. PHP with MySQL database access.

Volunteer project.

http://montessori.dreamhosters.com/index.php (Menu tools are restricted access; ask for account)

BioFitWeb

Web application for enzyme kinetics data analysis. Integrates fortran code, perl CGI and Gnuplot

scripts, javascript forms, and SQL querying capability administrated on a Linux Fedora system running

Apache server software. Capstone project for bioinformatics masters degree.

http://156.56.92.83/BioFitWeb.htm or http://biofitweb.cox-thurmond.net/BioFitWeb.shtml

Sequence Alignment

Perl-CGI web tool for DNA or protein sequence alignment using the Smith-Waterman and

Needleman-Wunsch dynamic programming algorithms with a unique weighted scoring system.

Java Application

Towers of Hanoi game implemented with a GUI, full animation of player moves, autoplay and play

speed controls.

References: Dr. Santiago Schnell

Assistant Professor, School of Informatics

Mail to: Eigenmann Hall

1900 E.10th Street, Rm. 906

Indiana University at Bloomington

Bloomington, IN. 47406

E-mail: *******@*******.***

Telephone: 812-***-****

Dr. Carla Kuiken

Staff Scientist, Hepatitis C Virus Sequence Database

Mail to: TA-03, Building 0410, Room 110B

Mailstop K710

Los Alamos National Laboratory

Los Alamos, NM. 87545

E-mail: ******@****.***

Telephone: 505-***-****

Dr. Catherine Macken

Staff Scientist, Influenza Sequence Database

Mail to: TA-03, Building 0410, Room 110A

Mailstop K710

Los Alamos National Laboratory

Los Alamos, NM. 87545

E-mail: *******@****.***

Telephone: 505-***-****

Contact this candidate