Bioinformatics: A new field in engineering education

Journal of Engineering Education, Jan 2003 by Hughey, Richard, Karplus, Kevin

An Educational Brief

ABSTRACT

Bioinformatics is a new engineering field poorly served by traditional curricula. Bioinformatics concerns the use of computer and statistical methods to understand biological data, such as the voluminous data produced by high-throughput biological experimentation. As the demand has outpaced the supply of bioinformaticians, the University of California, Santa Cruz, School of Engineering is establishing undergraduate and graduate degrees in bioinformatics. In this paper we explore the blend of mathematics, engineering, science, and bioinformatics topics and courses needed for an undergraduate degree in this new field.

I. INTRODUCTION

Bioinformatics is a new engineering field poorly served by traditional curricula. Bioinformatics crosses many disciplines, making the design of bioinformatics degree programs particularly challenging.

Bioinformatics can be broadly defined as the application of computer techniques to biological data. This field has arisen in parallel with the development of automated high-throughput methods of biological and biochemical discovery that yield a variety of forms of experimental data, such as DNA sequences, gene expression patterns, and three-dimensional models of macromolecular structure. The field's rapid growth is spurred by the vast potential for new understanding that can lead to new treatments, new drugs, new crops, and the general expansion of knowledge.

Bioinformatics encompasses everything from data storage and retrieval to computational testing of biological hypotheses. The data and the techniques can be quite diverse, including such tasks as finding genes in DNA sequences, finding similarities between sequences, predicting structure of proteins, correlating sequence variation with clinical data, and discovering regulatory elements and regulatory networks. Bioinformatics systems include multi-layered software, hardware, and experimental solutions that bring together a variety of tools and methods to analyze immense quantities of noisy data.

As the demand has outpaced the supply of bioinformaticians, the University of California, Santa Cruz (UCSC) School of Engineering (SOE) is establishing undergraduate and graduate degrees in bioinformatics. Although many schools have or are proposing graduate programs in bioinformatics, few are creating undergraduate programs. In forming our graduate program, we realized a fundamental problem: where would we find qualified graduate students? This quickly lead to the development of an undergraduate curriculum that we believe will serve students heading either to graduate school or to industry.

We are, of course, part of a wave of activity in the development of academic programs in bioinformatics [2, 3, 5]. More details can be found at the Web site of the International Society for Computational Biology (ISCB), http://www.iscb.org [10], including information about textbooks, degree programs, and the annual Workshops on Education in Bioinformatics held at the Intelligent Systems for Molecular Biology conferences.

In the following sections, we discuss the history of bioinformatics at UCSC and the new undergraduate bioinformatics curriculum.

II. BIOINFORMATICS AT UCSC

UC-Santa Cruz is well known in the field of bioinformatics for pioneering work on applications of hidden Markov models (HMMs) and stochastic context-free grammars to biological sequence data and for the development of software tools for sequence analysis [8, 11]. Our efforts include participation in the international Human Genome Project [1], development of the gene-finding software chosen to annotate the human and Drosophila (fly) genomes [9], creation of the UCSC Genome Browser (http://genome. ucsc.edu), success in international protein-structure prediction experiments [7], and construction of a SIMD programmable accelerator for sequence analysis [6]. We are planning a Department of Biomolecular Engineering, which in addition to bioinformatics will have undergraduate and graduate degree programs considering the engineering and manipulation of biomolecules, and the technologies necessary for such tasks.

Our experiences with undergraduate and graduate research enabled us to develop integrated curricula and training programs in bioinformatics. These curricula emphasize the foundations of basic molecular biology and biochemistry coupled with substantial training in mathematics and computer engineering and science.

Our goal at all levels is to hone the engineering design skills and scientific understanding required to develop new bioinformatics tools and methods to solve real problems. At the undergraduate level, bioinformatics students may continue to graduate school in bioinformatics or a related discipline, or proceed directly to the workplace. Our program has a strong emphasis on research, and most of our undergraduate bioinformatics research students have continued on to graduate school, while the rest have joined the local biotechnology industry. The first two graduates received their B.S. in the double major of Bioinformatics and Molecular, Cellular, and Developmental (MCD) Biology in Spring 2002, and one is now in our graduate program.