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NIMBioS Tutorial

Algebraic and Discrete Biological Models for Undergraduate Courses

Tutorial group photo.

Topic: Algebraic and discrete biological models for undergraduate courses

Meeting dates: June 18-20, 2014. Participants arrive on June 17 and depart on June 21.

Location: NIMBioS at the University of Tennessee, Knoxville

Organizers:
Raina Robeva, Mathematical Sciences, Sweet Briar College
Robin Davies, Biology, Sweet Briar College
Terrell Hodge, Mathematics, Western Michigan Univ.
Matthew Macauley, Mathematical Sciences, Clemson Univ.

Description: The field of mathematical biology has been transformed over the past 15 years by researchers using novel tools from discrete mathematics and computational algebra to tackle old and new problems. This tutorial exposed participants to algebraic and discrete approaches to problems from modern biology including gene regulation, gene identification, RNA folding, phylogenetics, and metabolic pathway analysis. The tutorial format included interactive lectures with quick exercises on each topic, followed by structured hands-on activities during which participants worked in small groups on exercises and projects. During lectures and interactive sessions, participants learned web-based software systems and databases that students in their courses can use.

This tutorial was appropriate for both mathematics and biology faculty. In particular, it targeted undergraduate faculty teaching modern algebra, finite mathematics or mathematical modeling, or intermediate and advanced undergraduate biology, but many topics were also appropriate for introductory biology courses. All introductory lectures to the tutorial topics were accessible for both math and biology faculty and covered basic biology and mathematical methods, models, heuristics, computational approaches, and relevant software. Participants had the opportunity to customize their tutorial experience by opting for lectures and activities at two different levels - one introductory and one more advanced.

Tutorial objectives:

  • Participants were introduced to the importance of algebraic and discrete methods and models in modern biology, as an alternative to classical continuous methods based on calculus and differential equations. They learned how to use such methods and/or build and analyze models in the context of the tutorial's topics and worked in small groups to experience how to use the methodology to describe, simulate, and analyze the relevant biological systems.
  • Participants were exposed to software that implements the mathematical methods, aids visualization, and facilitates the computations and analyses.
  • Participants learned of existing curricular resources related to the tutorial's topics, including exercises, projects, solution guidelines, and/or computer code and data. They received guidance on how the tutorial materials may fit into mathematics and biology courses or be used as an introduction to independent studies or undergraduate research.

Databases and software covered included (but were not limited to) DVD and ADAM (for visualization and analysis of Boolean and finite dynamical systems models), CpG Educate (for CpG island identification), BioNJ and TreeDyn and/or related analogues (for phylogenetic tree reconstruction), Metacyc, KEGG, and/or BIGG (for metabolic pathways), and Pfold (for RNA secondary structures).

Possible courses this tutorial would apply to in either math or biology or integrated curriculum: finite mathematics, discrete structures, linear algebra, modern algebra, graph theory, topology, probability, statistics, modeling, bioinformatics and biostatistics, cell and molecular biology, biochemistry, ecology, phylogenetics, and evolution.

Descriptive Flyer

Algebraic and Discrete Biological Models for Undergraduate Courses WordPress Site.

Presentations were available for viewing via live streaming during the workshop. A live chat took place via Twitter with the hashtag #biomodelTT.

Playlist of online videos

photo. Summary Report. TBA