In addition to courses or lab modules that teach the use of tools, some students will want a deeper understanding of the way bioinformatics tools address biological questions. For that, there is a need for an undergraduate course that focuses on the fundamental biological, mathematical and algorithmic chain of reasoning leading to the models that lie behind these tools. Such a course requires more sophistication in mathematics, and some intuitive understanding of can be accomplished by computer programming, but does not require extensive exposure to programming. Such a course is currently being developed in the computer science department.
It is also desirable to have some students, both biology and non-biology majors (particularly engineering majors), develop the deep programming and computer skills to modify, develop and implement new bioinformatics tools. It may be possible to reserve some space in undergraduate programming and database courses for biology students, and some space in laboratory biology courses for some computer science students. We should also give some thought to a hybrid major between biology and computer science (or possibly in bioengineering, depending on the direction that new department takes) to serve the appropriate students.
Also, see the Altman Proposal for a bioinformatics curriculum in Bioinformatics, Vol. 14, no 7 1998 pages 549-550.