Biological Theory Alliance Classes Below is a list of courses that are related to conceptual and mathematical modeling in biology.

If you know of a relevant class that we have missed, let us know: biota@umn.edu.

##### ANTH 5403 - Quantitative Methods in Biological Anthropology

(4.0 cr.; A-F or Audit; prereq Basic univariate statistics course or #; fall, spring, even years)

Quantitative methods used by biological anthropologists. Applying these methods to real anthropometric data. Lectures, complementary sessions in computer lab.

##### BIOL 3270 - Introduction To Systems Biology

(3.0 cr; Prereq-Recommended prereq MATH1241, BIOC3021; A-F only, spring, every year)

Build model test. Determine validity by comparing emergent properties to experimental data.

##### BIOL 3272 - Applied Biostatistics

(3.0 cr; Equiv.: BIOL 5272; Prereq-High school algebra; 2003 recommended; A-F only, fall, every year)

Conceptual basis of statistical analysis. Statistical analysis of biological data. Data visualization, descriptive statistics, significance tests, experimental design, linear model, simple/multiple regression, general linear model. Lectures, computer lab.

##### BIOL 5272 - Applied Biostatistics

(3.0 cr; Credit not given if already received for BIOL 3272; Prereq-One semester of college-level calculus or statistics or computer programming, general biology; A-F only, fall, every year)

Conceptual basis of statistical analysis. Statistical analysis of biological data. Data visualization, descriptive statistics, significance tests, experimental design, linear model, simple/multiple regression, general linear model. Lectures, computer lab.

##### CSCI 3003 - Introduction to Computing in Biology

(3.0 cr; Prereq-1002H or Biol 1002 or 1009H or Biol 1009 or equiv; spring, every year)

Emphasizes computing tasks common in biology. Programming techniques: variables, flow control, input/output, strings, pattern matching, arrays, hash tables, functions, subroutines. Concepts in computing: algorithms, complexity, documentation, regular expressions/grammars, local variables, encapsulation. Students complete lab projects in Perl language.

##### CSCI 5461 - Functional Genomics, Systems Biology, and Bioinformatics

(3.0 cr; Prereq-3003 or 4041 or equiv; spring, every year)

Computational methods for analyzing, integrating, and deriving predictions from genomic/proteomic data. Analyzing gene expression, proteomic data, and protein-protein interaction networks. Protein/gene function prediction, Integrating diverse data, visualizing genomic datasets.

##### CSCI 8725 - Databases for Bioinformatics

(3.0 cr; Prereq-4707 or 5707 or equiv; spring, offered periodically)

DBMS support for biological databases, data models. Searching integrated public domain databases. Queries/analyses, DBMS extensions, emerging applications.

##### EEB 5053 - Ecology: Theory and Concepts

(4.0 cr; Prereq-Biol 3407 or equiv; fall, odd academic years)

Classical and modern mathematical theories of population growth, interspecific interactions, ecosystem dynamics and functioning, with emphasis on underlying assumptions and on effects of added biological reality on robustness of predictions, stability, interspecific interactions, ecosystem structure and functioning.

##### EEB 5371 - Principles of Systematics

(3.0 cr.; prereq Grad student or #; spring, even years)

Theoretical/practical procedures of biological systematics. Phylogeny reconstruction. Computer-assisted analyses, morphological and molecular approaches, species concepts/speciation, comparative methods, classification, historical biogeography, nomenclature, use/value of museums.

##### ESPM 3012 - Statistical Methods for Environmental Scientists and Managers (MATH)

(4.0 cr; Equiv.: STAT 5021, STAT 3011, ANSC 3011; Prereq-Two yrs of high school math; A-F or Aud, spring, every year)

Introduction to statistical principles, foundations, and methods for examining data and drawing conclusions. Regression modeling of relationships in environmental and natural resource science and management problems.

##### FW 4001 - Biometry (WI)

(4.0 cr; Prereq-Math 1031; A-F or Aud, fall, every year)

Covers the basic foundations of statistical methods, emphasizing simulation-based approaches to inference (randomization tests, bootstrapping). Descriptive statistics, one and two sample tests, linear and multiple regression. Computer lab uses the R programming language.

##### FW 5051 - Analysis of Populations

(4.0 cr; Prereq-4001 or STAT 3011 or ESPM 3012, BIOL 3407 or BIOL 3408W or BIOL 3807, Senior or grad student; spring, every year)

Regulation, growth, general dynamics of populations. Data needed to describe populations, population growth, population models, regulatory mechanisms.

##### FW 8051 - Statistical Modeling of Ecological Data using R and WinBugs/JAGS

(4.0 cr; Prereq-Graduate-level statistics class, working knowledge of program R or equiv.; spring, every year)

Regression methods for modeling ecological data. Real world examples from ecology, as well as environmental/natural resource sciences/management. Computer-based solutions using R/Bayesian modeling software.

##### MATH 1241 - Calculus and Dynamical Systems in Biology (MATH)

(4.0 cr; Prereq- 4 yrs high school math including trig or satisfactory score on placement test or grade of at least C- in 1151 or 1155, CBS student; fall, spring, every year)

Differential/integral calculus with biological applications. Discrete/continuous dynamical systems. Models from fields such as ecology/evolution, epidemiology, physiology, genetic networks, neuroscience, and biochemistry.

##### MATH 2241 - Mathematical Modeling of Biological Systems

(3.0 cr, Prereq-Math 1241 or 1271 or 1371 or equivalent)

Development, analysis and simulation of models for the dynamics of biological systems. Mathematical topics include discrete and continuous dynamical systems, linear algebra, and probability. Models from fields such as ecology, epidemiology, physiology, genetics, neuroscience, and biochemistry.

##### MATH 4428 - Mathematical Modeling

(4.0 cr; Prereq-2243 or 2373 or 2573; spring, every year)

Modeling techniques for analysis/decision-making in industry. Optimization (sensitivity analysis, Lagrange multipliers, linear programming). Dynamical modeling (steady-states, stability analysis, eigenvalue methods, phase portraits, simulation). Probabilistic methods (probability/statistical models, Markov chains, linear regression, simulation).

##### MATH 5445 - Mathematical Analysis of Biological Networks

(4.0 cr; Prereq-Linear algebra, differential equations; spring, every year)

Development/analysis of models for complex biological networks. Examples taken from signal transduction networks, metabolic networks, gene control networks, and ecological networks.

##### MATH 8505 - Applied Dynamical Systems and Bifurcation Theory I

(3.0 cr; Prereq-5525 or 8502 or equiv.; A-F or Aud)

Static/Hopf bifurcations, invariant manifold theory, normal forms, averaging, Hopf bifurcation in maps, forced oscillations, coupled oscillators, chaotic dynamics, co-dimension 2 bifurcations. Emphasizes computational aspects/applications from biology, chemistry, engineering, physics.

##### MATH 8540 - Topics in Mathematical Biology

(1.0 - 3.0 cr max 12.0 cr; A-F or Aud, fall, spring, every year)

Offered for one year or one semester as circumstances warrant.

##### PHIL 4607 - Philosophy of the Biological Sciences

(3.0 cr; Prereq-Courses in philosophy or biology or equiv.; fall, spring, offered periodically)

Structure/status of evolutionary theory. Nature of molecular biology, genetics. Reductionism in biology. Legitimacy of teleology. Species concept.

##### PHIL 5222 - Philosophy of Mathematics

(3.0 cr; Prereq-College level logic or mathematics course or equiv.; fall, spring, offered periodically)

Major philosophical questions arising in connection with mathematics. What is mathematics about? How do we know the mathematics we do? What is the relation between mathematics and the natural sciences? Selected readings of leading contributors such as Frege, Dedekind, Russell, Hilbert, Brouwer, Godel, Quine.

##### PHIL 8620 - Seminar: Philosophy of the Biological Sciences

(3.0 cr, max 6.0 cr; fall, every year)

Topics vary by offering.