Thursday, May 29, 2008

Biomedical Ruby Programming

If you're a regular reader of this blog, you've read some of my prior essays about the Ruby Programming Language. My book teaches Ruby, but its content is not exclusively focused on the Ruby Language (there are many excellent Ruby language books available to programmers). My book is mostly about the tasks that confront students and professionals in the biomedical fields... and how you can use Ruby to solve those tasks. So in the book chapters, I may spend more words describing the biomedical tasks (which can be hard to understand) and many fewer words on the Ruby scripts (which are usually quite short).

The basic theme in my books is that if all biomedical workers knew how to program, they would gain some independence (from application vendors), and become more creative.

Once you start using Ruby, you may find that you can integrate your knowledge of medicine and biology with your knowledge of programming, to solve a wide range of new and interesting problems.

I recommend either Perl, Python, or Ruby as excellent languages for anyone in the biomedical sciences. I wouldn't claim that these are the best languages for programmers, in general. But they are superb languages for individuals whose primary interest lies in biology or medicine and who use programming as a creative tool to discover and solve new questions in their fields. These languages are easy to learn, and each has an active community that contributes open source libraries and modules to the language.

- Jules J. Berman

Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.