In this course, students will use the graphical programming language StarLogo The Next Generation (SLTNG) to develop their own agent-based simulations of biological processes. Agents may be chosen to represent molecules, cells, or organisms. Examples might include such phenomena as population genetics, predator-prey dynamics, cell-cell communication, or enzyme-substrate interactions. Recommended background: completion of at least one 3000 or 4000 level biology or biochemistry course. No prior programming experience is required.
Computer simulations are becoming increasingly important in understanding and predicting the behavior of a wide variety of biological systems, ranging from metastasis of cancer cells, to spread of disease in an epidemic, to management of natural resources such as fisheries and forests. In this course, students will learn to use a graphical programming language to simulate biological systems. Most of the classroom time will be spent working individually or in groups, first learning the language, and then programming simulation projects. We will also discuss several papers on biological simulations from the primary scientific literature. In constructing and comparing their simulations, students will demonstrate for themselves how relatively simple behavioral rules followed by individual molecules, cells, or organisms can result in complex system behaviors. Recommended background: Students taking this course must have a solid background in a biological areathey would like to simulate, at about the depth provided by a BB 3000 level class. No programming experience is assumed. This course will be offered in2014-15 and in alternating years thereafter
Cat. II This course will provide an overview of bioinformatics, covering a broad selection of the most important techniques used to analyze biological sequence and expression data. Students will acquire a working knowledge of bioinformatics applications through hands-on use of software to ask and answer biological questions. In addition, the course will provide students with an introduction to the theory behind some of the most important algorithms used to analyze sequence data (for example, alignment algorithms and the use of hidden Markov models). Topics covered will include protein and DNA sequence alignments, evolutionary analysis and phylogenetic trees, obtaining protein secondary structure from sequence, and analysis of gene expression including clustering methods. Recommended background: BB 2920, BB 2950, and MA 2610 or 2611. This course will be offered in 2014-15 and in alternating years thereafter.
Cat. II This course will use interactive visualization to model and analyze biological information, structures, and processes. Topics will include the fundamental principles, concepts, and techniques of visualization (both scientific and information visualization) and how visualization can be used to study bioinformatics data at the genomic, cellular, molecular, organism, and population levels. Students will be expected to write small to moderate programs to experiment with different visual mappings and data types. Recommended background: CS 2102, CS 2223, and one or more biology courses. This course will be offered in 2014-15 and in alternating years thereafter.
Cat. II This course will investigate computational techniques for discovering patterns in and across complex biological and biomedical sources including genomic and proteomic databases, clinical databases, digital libraries of scientific articles, and ontologies. Techniques covered will be drawn from several areas including sequence mining, statistical natural language processing and text mining, and data mining. Recommended Background: CS 2102, CS 2223, MA 2610 or MA 2611, and one or more biology courses. This course will be offered in 2013-14 and in alternating years thereafter.
Cat. II This course provides students with knowledge and understanding of the applications of statistics in modern genetics and bioinformatics. The course generally covers population genetics, genetic epidemiology, and statistical models in bioinformatics. Specific topics include meiosis modeling, stochastic models for recombination, linkage and association studies (parametric vs. nonparametric models, family-based vs. population-based models) for mapping genes of qualitative and quantitative traits, gene expression data analysis, DNA and protein sequence analysis, and molecular evolution. Statistical approaches include log-likelihood ratio tests, score tests, generalized linear models, EM algorithm, Markov chain Monte Carlo, hidden Markov model, and classification and regression trees. Recommended background: MA 2612, MA 2631 (or MA 2621), and one or more biology courses. This course will be offered in 2013-14 and in alternating years thereafter.