Software Development

Biology and other science have always been part of my software career in one way or another, whether creating biomedical applications, educational software, or doing computer simulations as part of my biological research. Below are some of the projects I've worked on, followed by some research papers and poster presentations. For more details, see my resume. (Download [industry style Resume] [academic style CV].)


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Demos: JavaScript, PHP
Evo-devo project
Notochord simulation project
Biomedical and educational software
Selected publications and presentations


Evo-devo project

Most recently, I spent two years at the Konrad Lorenz Institute for Evolution and Cognition Research (KLI), near Vienna, Austria, where I began a research project aimed ultimately (see my 2002 poster abstract) at achieving in silico evolution of simulated multicellular organisms, complete with embryonic development (hence, Evo-Devo). In the short term, it has been all about cell biomechanics and locomotion. Written in C on a Mac. See my 2005 paper.



The simulation is based on mechanical properties of cells – adhesion, viscoelasticity, and tension in the cell cortex (outer layer). Here, the green cells are stickier than the blue cells, and therefore sort to the interior of the cell aggregate, in agreement with the differential adhesion hypothesis. View a poster, complete with QuickTime movies of running simulations , that I presented at the 2005 conference, Society for Integrative and Comparative Biology.



I gave an informal and nearly-impromptu talk on this research, at the Grey Thumb Silicon Valley meeting, June 24, 2008, at the Internet Archive, San Francisco.
[View my talk on Google video (30 minutes)]



Notochord simulation project

I got my start in biological simulations with this project at U.C. Berkeley. We were trying to understand the morphogenesis of the notochord (i.e., the changes in tissue shape that take place as this early embryonic organ develops). By simulating the behavior of the individual cells according to alternative sets of behavioral rules, taking into account the mechanical properties of cells and tissues, we could test which sets of rules would produce shape changes (in individual cells as well as in the whole tissue) similar to those observed in real embryos.


The diagrams above show the changes unfolding over time in a simulated patch of cells. As in a real notochord, the elongation of individual cells as they squeeze between one another (horizontal in the diagrams) causes the elongation of the tissue in the orthogonal direction (vertical in the diagrams). See my co-authored 1990 and 1991 papers.



Applied biomedical and educational software

In the early days I developed some biomedical applications, as well as educational software – some science and math oriented, some not. Apple II+, Atari 800, and the DEC 20; Pascal, Fortran, BASIC, 6502 Assembler! Those were the days! The simple educational game below won Learning Magazine's 1983 Outstanding Software of the Year Award (image found on the web from an old ad by Scholastic, the publisher).



Selected publications and presentations

Minsuk, S. B. (2005). Toward an open-ended and mechanically realistic model of biological cells. In: Workshop on Artificial Chemistry and Its Applications. The 8th European Conference on Artificial Life (ECAL) Workshop Procedings. Mathieu Capcarrere (ed.). [download pdf]

Minsuk, S. B. (2004). First steps toward a generalized model cell for evo-devo computer simulations. Abstract: Integrative and Comparative Biology 44:729. (A poster presented at the Society for Integrative and Comparative Biology, Jan. 2005.)
[View poster, with QuickTime movies of simulations]

Minsuk, S. (2002). A proposal for an artificial life simulation of evolving multicellular ontogeny. (A poster presented at Artificial Life VIII [8th International Conference on the Simulation and Synthesis of Living Systems], Dec. 2002.)
[abstract only]

Weliky, M., S. Minsuk, R. Keller and G. Oster (1991). Notochord morphogenesis in Xenopus laevis: simulation of cell behavior underlying tissue convergence and extension. Development 113:1231-1244.

Oster, G., M. Weliky, and S. Minsuk (1990). Morphogenesis by cell intercalation. In: 1989 Lectures in Complex Systems. Santa Fe Institute Studies in the Sciences of Complexity Series, Lect. Vol. II. 501-512. Erica Jen (ed). Reading, MA:Addison-Wesley.