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Bio 2010: Transforming Undergraduate Education for Future Research Biologists
They should acquire an understanding of how computers work, basic programming skills, and fluency in using networks and databases. A course at this level should include simple programming assignments. To give it a biological accent, there should be laboratory experiences using Medline, Genbank, and other biological databases, as well as physiological and ecological simulations. One assignment might ask students to use computer searches to track down all known information about a given gene and the protein it encodes, including both structure and function. This would involve exploring the internal structure of the gene (exons, introns, promoter, transcription factor binding sites); the regulatory control of the gene; sequence homologs of the gene and the protein; the structure and function of the protein; gene interaction networks and metabolic pathways involving the protein; and interactions of the protein with other proteins and with small molecules.
The NRC report Being Fluent with Information Technology lays out the structure and objectives of such a course in detail, but is not oriented specifically toward biologists.
Capability in Program Design for Computational Biology and Genomics Applications
A course at this level provides the minimal skills required to be an effective computer user within a computationally oriented biology research team. A good example is a course by Adam Arkin at Berkeley. His course introduces students to structured software development and selected principles of computer science, with applications in computational biology and allied disciplines. The principal language used for instruction is Java, with a course module on Perl. Examples and tutorials are drawn from problems in computational biology. The course requires one significant programming project, preferably biologically oriented.
Capability in Developing Software Tools for Use by the Biology Community
A foundation for reaching this level is provided by courses in discrete mathematics, data structures, and algorithms. According to the student’s interests, these could be followed by courses in database management systems, information systems, software engineering, computer graphics, or computer simulation techniques. Biologists could select courses that teach