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Sweet Briar College
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All content following this page was uploaded by Raina Robeva on 21 January 2014.
tional ideas (hierarchical clustering, pat- We do not argue against the mathematical References and Notes
1. National Research Council, BIO2010, Transforming
tern classification, and feature selection) are courses included in current undergraduate Undergraduate Education of Future Research Biologists
introduced as part of the “story” to promote biology curricula. But we believe that these (National Academies Press, Washington, DC, 2003).
ease of understanding by students. Such courses should be revised and extended. 2. W. Bialek, D. Botstein, Science 303, 788 (2004).
3. P. A. Pevzner, Bioinformatics 20, 2159 (2004).
examples may also instill in students the Many key computational ideas can be bet- 4. L. M. Iyer et al., Genome Biol. 2(12), RESEARCH0051.1
real-life impact of computational methods. ter communicated and absorbed by biology (2001).
This research, for example, led to the first undergraduates with few prerequisites, in a 5. P. Grindrod et al., Math. Today 44, 80 (2008).
6. N. Wingreen, D. Botstein, Nat. Rev. Mol. Cell Biol. 7, 829
cancer diagnostic chip to be approved by way that will make the students excited about (2006).
the U.S. Food and Drug Administration; it is bioinformatics as a scientific discipline and 7. L. J. van ’t Veer et al., Nature 415, 530 (2002).
currently used to determine which patients more creative when they employ bioinfor- 8. L. J. Gross, Cell Biol. Educ. 3, 85 (summer 2004).
may benefit from additional chemotherapy. matics methods and ideas in the future. We 9. R. Brent, Cell Biol. Educ. 3, 88 (summer 2004).
10. We are grateful to all participants of RECOMB Bioinformat-
The question of whether similar inno- feel that the best way to engage biology ics Education conference (La Jolla, 14 and 15 March 2009)
vative courses can be implemented at the undergraduates in bioinformatics is to appeal for many comments on various aspects of bioinformatics
undergraduate level at many universities to their innate intuition and common sense education. We are also grateful to V. Bafna, N. Bandeira,
A. Tanay, and G. Tesler for many interesting discussions
remains subject to debate (8, 9). Never- and to avoid mathematical formalism as and suggestions. The conference was supported by the
theless, such courses are pioneering steps much as possible. The proposed course may Howard Hughes Medical Institute Professors Program.
EDUCATION
Beyond Calculus
to biologists and mathematicians.
I
n 2003, the National Research
Council’s BIO2010 report M
recommended aggressive )
curriculum restructuring to
educate the “quantitative biol- Ge E Le
ogists” of the future (1). The
number of undergraduate and
graduate programs in math- L
ematical and computational
biology has since increased, DE and Boolean models of the lac operon mechanism. Each component of the shaded part of the wiring
and some institutions have added diagram is a variable in the model, and the compartments outside of the shaded region are parameters.
courses in mathematical biology related to Directed links represent influences between the variables: A positive influence is indicated by an arrow; a
biomedical research (2, 3). The National negative influence is depicted by a circle.
Science Foundation (NSF) and the National
Institutes of Health are funding development systems biology. At the molecular level, this regulatory networks (10). They have proven
workshops and discussion forums for fac- involves understanding a complex network of useful in cases where network dynamics
ulty (4, 5), research-related experiences (6, interacting molecular species that incorpo- are determined by the logic of interactions
7), and specialized research conferences in rates gene regulation, protein-protein inter- rather than finely tuned kinetics, which often
mathematical biology for students (8, 9). actions, and metabolism. Two types of mod- are not known. Published algebraic models
This new generation of biologists will els have been used successfully to organize include the metabolic network in Escheri-
routinely use mathematical models and com- insights of molecular biology and to capture chia coli (11) and the abscisic acid signaling
putational approaches to frame hypotheses, network structure and dynamics: (i) discrete- pathway (12).
design experiments, and analyze results. To and continuous-time models built from dif- The use of algebraic methods is extend-
accomplish this, a toolbox of diverse math- ference equations or differential equations ing beyond systems biology. Methods
ematical approaches will be needed. (DE) models, which focus on the kinetics from algebraic geometry have been used
Nowhere is this trend more evident than in of biochemical reactions; and (ii) discrete- in evolutionary biology to develop new
time algebraic models built from functions approaches to sequence alignment (13), and
of finite-state variables (in particular Boolean new modeling of viral capsid assembly has
1
Department of Mathematical Sciences, Sweet Briar Col-
lege, Sweet Briar, VA 24595, USA. 2Virginia Bioinformatics networks), which focus on the logic of the been developed using geometric constraint
Institute, Virginia Tech, Blacksburg, VA 24061, USA. network variables’ interconnections. theory (14). Algorithms based on algebraic
*To whom correspondence should be addressed. E-mail: Algebraic models were introduced in combinatorics have been used to study RNA
Robeva@sbc.edu. 1969 to study dynamic properties of gene secondary structures (15).
Because of the success of DE methods tative while Boolean models are qualitative DE models in the courses already in place
for modeling biochemical networks, they in nature. will only reinforce the conceptual frame-
have been the primary focus of curriculum To illustrate, we use one of the sim- work and further elevate students’ mathe-
reform efforts, whereas algebraic models plest and best-understood mechanisms of matical sophistication.
have received less attention. But algebraic gene regulation: the lactose (lac) operon
models have many features needed to inte- that controls the transport and metabolism References and Notes
grate mathematics and biology into the train- of lactose in E. coli (fig. S1). A wiring dia- 1. National Research Council, BIO2010: Transforming
ing of students at all levels; thus, their inclu- gram is constructed to represent major com- Undergraduate Education for Future Research Biologists
(National Academies Press, Washington, DC, 2003).
sion in curricula is necessary and timely. ponents and causal interactions of the sys- 2. N. Wingreen, D. Botstein, Nat. Rev. Mol. Cell Biol. 7, 829
tem (see figure, page 542). (2006).
DE Versus Algebraic Models The wiring diagram on the left of the fig- 3. R. Robeva, Methods Enzymol. 454, 305 (2009).
4. Over the Fence: Mathematicians and Biologists Talk
Many institutions now offer DE-focused ure depicts both DE and Boolean models of About Bridging the Curricular Divide, Mathematical
courses that include problems from the life the lac operon. Although it involves only three Biosciences Institute workshop, Columbus, OH, 1 and 2
sciences, rather than just the traditional variables, the DE model is complex, involv- June 2007.
linkages with physics and engineering. For ing additional parameters reflecting the reac- 5. Computational and Mathematical Biology, Mathematical
Association of America, Professional Enhancement
example, in bio-calculus and precalculus- tion kinetics. The Boolean model is simpler, Programs, 2003, 2004, 2005, 2006, and 2007.