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Mark A. Martin

0610 SW Nevada St Apt H, Portland, OR 97219



Software Development


Protocols and Interfaces



I began programming in 1978 in Basic and Fortran via CRT, teletype, and punch cards on HP minicomputers and IBM mainframes. Since then, I have authored or contributed to a wide variety of projects in many languages on many platforms. The projects have ranged from small programs in a single language to projects consisting of tens of thousands of lines of code in multiple languages. I have designed and written procedural and object-oriented programs, have constructed graphical user interfaces and animations, and have written or participated in the development of distributed applications. Most recently, I played several software development roles at a bioinformatics company. In this capacity, I was a lead designer of software for mathematically modeling prokaryotic organisms as networks of metabolic reactions and maintaining the company's biochemical pathway collection and a leader of the effort to provide the infrastructure for using legacy tools and methods for developing and maintaining the pathway collection.



After leaving Integrated Genomics, I continued my research into the dynamics of populations of marine plankton in response to climatic changes.


During this time, I was a Computational Scientist at Integrated Genomics, Inc.

1998 - 2000

This period of time includes the last two years of my Ph.D. work and work done after completing my Ph.D. During this time, my primary goal was finishing my degree and nearly all of my work was performed on Linux systems that I administer. Most of my work focused on analyzing mathematical models of marine plankton, analyzing oceaongraphic data for use in the models, and presenting the results of my research.

1996 - 1997

During this period of time, I was a systems administrator for Boeing Information and Support Services and for the Department of Applied Mathematics at the University of Washington. At Boeing, I was the lead administrator for a team of 7 administrators responsible for maintaining terabyte-scale Sequent Symmetry 5000 and Sequent NUMA-Q 2000 data servers. At the University of Washington, I helped maintain a network of workstations and Xterminals. See Systems Administration for details. I also continued my studies, performing most of my work on a Linux system that I administered.

1992 - 1995

At this time, I was a graduate student in the Department of Applied Mathematics at the University of Washington, studying mathematical ecology, biological oceanography, boundary-layer meteorology, and climatology. I also had a notable summer job writing radiation treatment planning software for the University of Washington Department of Radiation Oncology.

1988 - 1991

During these years, I studied numerical analysis as a graduate student in the Applied Mathematics departments at the University of Colorado and the University of Washington and contributed to an effort to create a large-eddy simulation cloud model at University of Washington.

1986 - 1987

I was a graduate student in Mathematics at the University of Arizona at this time.

1978 - 1985

My first exposure to programming was learning Basic and Fortran and programming HP RPN calculators in High School in 1978. Later, I wrote programs for physics classes as an undergraduate.

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Last modified: Thu Jul 4 18:09:23 CDT 2002