title: Computer Simulation and Data Analysis in Molecular Biology and Biophysics: An Introduction Using R (Biological and Medical Physics, Biomedical Engineering)
author: Victor Bloomfield
description: From the reviews: This book targets biochemistry and molecular biophysics students who have prior knowledge of a few subjects, including mathematics, statistics, and modeling, and possess very basic programming skills. Examples and illustrations are ample throughout the text, and the writing style is plain and efficient.  this book mostly appropriate for students or researchers who have prior exposure to the related subjects. Summing Up: Recommended. Upper-division undergraduates through researchers/faculty. (D. Papamichail, Choice, Vol. 47 (5), January, 2010)
zlib_text: C H A P T E R
  8
  A Qualitative Biochemistry 
  and Its Application to the 
  Regulation of the Tryptophan Operon
  Peter D. Karp
  1 Introduction
  This article is concerned with the general question of how to represent
  biological knowledge in computers such that it may be used in multiple prob-
  lem solving tasks. In particular, I present a model of a bacterial gene regula-
  tion system that is used by a program that simulates gene regulation experi-
  ments, and by a second program that formulates hypotheses to account for
  errors in predicted experiment outcomes. This article focuses on the issues of
  representation and simulation; for more information on the hypothesis for-
  mation task see (Karp, 1989; Karp, 1990). 
  The bacterial gene regulation system of interest is the tryptophan (trp)
  operon of E. coli (Yanofsky, 1981). The genes that it contains code for en-
  zymes that synthesize the amino acid tryptophan. My model of the trp oper-
  
  on—called GENSIM (genetic simulator)—describes the biochemical