Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this…

This article describes a computational project designed for undergraduate students as an introduction to mathematical modeling. Students use an ordinary differential equation to describe fish weight and assume the instantaneous growth rate depends on the concentration of dissolved oxygen. Published laboratory experiments suggest that continuous…

Most biological scientists conduct experiments to look for effects, and test the results statistically. One of the commonly used test is Student's t test. However, this test concentrates on a very limited question. The authors assume that there is no effect in the experiment, and then estimate the possibility that they could have obtained these…

How effective is training frogs to jump? This is perhaps the most frequent question in biology that is subjected to statistical analysis: does a treatment make a difference? One can examine whether there is indeed a training effect, by first assuming the opposite. That is, the authors assume that training has no effect on the mean distance jumped.…