Bioinformatics for undergraduates: Steps toward a quantitative bioscience curriculum*

Abstract

We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and reasoning, using a computer-assisted, problem-based learning model. Here we report on the course design, methods of assessment for the course and materials, and analysis of results obtained in initial offerings of the course.Keywords: Bioinformatics, course design, interdisciplinary curriculum, problem-based learning.In their 2003 report, BIO 2010, a committee of the National Research Council charted a course for educating 21st century biological scientists. The ambitious proposal, aimed at implementation by the year 2010, envisions interdisciplinary undergraduate experiences that seamlessly integrate biology with mathematics, statistics, computer science, physics, and chemistry. The research community has enthusiastically endorsed this new, quantitative bioscience curriculum, viewing the proposed restructuring as essential to transcend the traditional barriers between biology and mathematics-based sciences [2]. The changes, they say, will benefit students in mathematics and the physical sciences by providing biological systems to model while preparing biology students for the new world of quantitative biology. The relatively new discipline known as bioinformatics already provides a bridge from molecular and structural biology to computer science, statistics, and information theory. Adding a bioinformatics course to the undergraduate biology curriculum thus represents an easy, natural step toward the goal of providing quantitative, interdisciplinary coursework for all bioscience students. DESIGN ISSUESThe Central Concept-For students, understanding the fundamental concept of a course can illuminate every aspect of their learning experience. A central, powerful concept provides a framework for thinking, not only through the topics explored in the class but also through related courses and experiences in the real world. For course designers, the explanatory power of a fundamental concept provides an organizing principle. Construction of a course around a primary concept increases the likelihood that students will take away the essence of the discipline and a usable set of thinking skills [3].At its core, bioinformatics is the extraction of biological information (or meaning) from biological data stored in databases. All other topics and questions in bioinformatics, such as how biological data are collected and stored, how protein structure and function can be predicted from sequence data, or how metabolic networks may be visualized, can be understood in relation to this primary concept. The overall design of our undergraduate bioinformatics course reflects our effort to keep this fundamental idea in focus.Curricular Goals-The curriculum project aimed to establish a foundatio...

Making authentic science accessible—the benefits and challenges of integrating bioinformatics into a high-school science curriculum

“…This is reflected in the tremendous accumulation of bioinformatics tools and databases to empower scientific research, compared with a relatively minor increase in the number of educational resources in bioinformatics [12, 13]. While most bioinformatics educational resources and courses were designed for the undergraduate level (for example [14]), bioinformatics educational reform is sporadic at the secondary level [15, 16]. In addition, better incorporation of bioinformatics into states’ science standards is required [17].…”

Assessment of a bioinformatics across life science curricula initiative

“…The use of bioinformatics in model systems such as fruit flies, mice, yeast, Arabidopsis thaliana, and Caenorhabditis elegans has allowed advances in understanding the complex interactions among genes and the dissection of pathways regulating gene expression under various conditions. Awareness of and familiarity with bioinformatics have become essential for biologists in all fields, but student training in this field has largely been limited to molecular/cell biology-related courses and programs [2][3][4][5][6]. In our own institution, individual instructors had been addressing bioinformatics-related topics in their specific courses for many years, but a common set of experiences among life science students was lacking.…”

“…To address the lack of shared experiences and to broaden student exposure to bioinformatics, we have implemented a program to incorporate Bioinformatics across Life Science Curricula (BLSC) 1 at UW-La Crosse [7]. Prior efforts at incorporating bioinformatics exercises into the curriculum have largely centered on specific courses or specific exercises [2][3][4][5][6]. Our approach differs in that we include bioinformatics in essentially all of our "core" courses, from introductory to junior/senior level courses, and that the material becomes more complex as students advance through the curriculum, building on a common background obtained in the introductory courses.…”

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

“…Educators have responded by incorporating bioinformatics into diverse life science curricula [42]–[44]. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms [45].…”