# BIO405: Computational Biology

Unit 1: Introduction to Computational Biology   *This unit will serve as your introduction to the basic principles and procedures of computational biology.  We will begin by discussing the application of mathematics to biological phenomena and then learn in detail how computers can be used to create and manipulate mathematical models.

How does a scientist extract variables from a natural process in order to create a predictive mathematical formula and then use that formula to create a computer program through which he can quickly manipulate variables to simulate a variety of circumstances within a complex environment?  You will learn each step of that process here.  Upon completion of this unit, you should have a clear understanding of the process of creating a computational model in biology.*

This unit should take approximately 21 hours to complete.

☐    Subunit 1.1: 5 hours

☐    Subunit 1.2: 1 hour

☐    Subunit 1.3: 7 hours

☐    Subunit 1.4: 4 hours

☐    Subunit 1.5: 4 hours

Unit1 Learning Outcomes
Upon completion of this unit, the student will be able to: - Define computational biology. - Explain the role of models and variables. - Describe what networks are and how they are used. - Define several types of mathematical algorithms.

1.1 What is Computational Biology?   - Reading: Wikipedia’s “Computational Biology” Link: Wikipedia’s “Computational Biology” (HTML)

`````` Instructions: Read this webpage, paying particular attention to the
description of computational biology and the related fields of
study.

Reading this material should take approximately 30 minutes.

displayed on the webpage above.
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1.1.1 Biology   - Reading: Nature News: Lucas Laursen’s “Computational Biology: Biology Logic” Link: Nature News: Lucas Laursen’s “Computational Biology: Biology Logic” (HTML)

`````` Instructions: Please read the linked article above, which will give
you an idea of how computer models are being developed to understand
biological systems.

Reading this material should take approximately 30 minutes.

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1.1.2 Applied Mathematics   - Reading: PLoS Biology: J. Cohen’s “Mathematics Is Biology’s Next Microscope, Only Better; Biology Is Mathematics’ Next Physics, Only Better” Link: PLoS Biology: J. Cohen’s “Mathematics Is Biology’s Next Microscope, Only Better; Biology Is Mathematics’ Next Physics, Only Better” (HTML)

`````` Instructions: Please read the linked material.  In it, the author
provides an historical sketch of how biology and math are connected
and describes the increasingly strong relationship between math and
biology.

Reading this material should take approximately 30 minutes.

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1.1.3 Computer Science   - Reading: OMICS Publishing Group’s “Journal of Computer Science and System Biology” Link: OMICS Publishing Group’s “Journal of Computer Science and System Biology” (HTML)

`````` Instructions: This is the home page for the journal.  If you
explore the site, you will find many articles related to the use of
computer science in biology.  Click the current issue or previous
issue links to find articles.  You should see this site as a
resource and take the time to read a couple of articles that are
related to material in the course.

Reading this material should take approximately 2 hours.

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1.1.4 Statistics   - Lecture: Mathematical Sciences Research Institute: “Algebraic Statistics for Computational Biology” Link: Mathematical Sciences Research Institute: “Algebraic Statistics for Computational Biology” (QuickTime)

`````` Instructions: This lecture presents a variety of statistics that
are used in computational biology; please watch it in its entirety
and pay particular attention to the statistics that are presented.
You will need QuickTime 6.5 or higher to view this resource.

Viewing this lecture should take approximately 1.3 hours.

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1.2 Mathematical Treatment of Biology   1.2.1 Creating a Mathematical Equation   - Reading: University of Utah: D. Dobson’s “Lecture Notes on Mathematical Modeling” Link: University of Utah: D. Dobson’s “Lecture Notes on Mathematical Modeling” (PDF)

`````` Instructions: Click on the “Lecture Notes” link.  This reading
provides a general description of the modeling process and lists a
variety of reasons for modeling.

Reading this material should take approximately 45 minutes.

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• Reading: eHow’s “How to Build a Mathematical Model” Link: eHow’s “How to Build a Mathematical Model” (HTML)

Instructions: Read this step-by-step procedure for building a model.  This is a very general overview; it only touches on the general process.

Reading this material should take approximately 15 minutes.

1.3 Networks in Biology   - Reading: MIT: Dr. George Church’s “Networks 1-3” Link: MIT: Dr. George Church’s “Networks 1-3” (JWPlayer)

`````` Instructions: Listen to the three audio lectures titled Networks 1,
2, and 3 from this course on Genomics and Computational Biology from
the “Lecture Slides” PDF that accompanies each audio lecture and
view it while listening.

Viewing these lectures should take approximately 4.45 hours.

Institute of Technology: MIT OpenCourseWare), <http://ocw.mit.edu>
(Accessed August 28, 2012).  License: [Creative Commons BY-NC-SA
``````

1.3.1 Random Networks   - Reading: University of Arizona: Robert May’s “Networks” Link: University of Arizona: Robert May’s “Networks” (PDF)

`````` Instructions: Scroll down the page to the section on “Papers” and
look for May: “Network structure and the biology of populations”
TREE 21: 394.  This paper discusses several types of networks,
including random networks.

Reading this material should take approximately 1 hour.

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1.3.2 Small-World Phenomenon   - Reading: Cornell University: Jon Kleinberg’s “The Small-World Phenomenon” Link: Cornell University: Jon Kleinberg’s “The Small-World Phenomenon” (HTML)

`````` Instructions: This reading describes the phenomena of the small
world before introducing a network model and its related
algorithms.

Reading this material should take approximately 1.3 hours.

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1.3.3 Scale-Free Network Model   - Reading: Scholarpedia’s “Scale-free Network Model” Link: Scholarpedia’s “Scale-free Network Model” (HTML)

`````` Instructions: The page discusses several different models and lists
some of their respective mathematical properties.  Pay attention to
how scale free networks are defined.

Reading this material should take approximately 30 minutes.

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1.4 Algorithms   1.4.1 Classes of Algorithms   - Reading: Connexions’ “Introduction to Algorithms” Link: Connexions’ “Introduction to Algorithms” (HTML)

`````` Instructions: This reading covers subunits 1.4.1.1-1.4.1.4.  Please
and how they are classified.  This page also includes a number of
different types of algorithms.

Reading this material should take approximately 2 hours.

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1.4.1.1 Recursive   Note: The reading for this subunit is covered by the material under subunit 1.4.1, “Algorithms.”

1.4.1.2 Logical   Note: The reading for this subunit is covered by the material under subunit 1.4.1, “Algorithms.”

1.4.1.3 Distributed   Note: The reading for this subunit is covered by the material under subunit 1.4.1, “Algorithms.”

1.4.1.4 Approximated   Note: The reading for this subunit is covered by the material under subunit 1.4.1, “Algorithms.”

1.4.2 Graph Drawing   1.4.2.1 Dijkstra’s Algorithm   - Reading: Wikipedia’s “Dijkstra’s Algorithm” Link: Wikipedia’s “Dijkstra’s Algorithm” (HTML)

`````` Instructions: Read this entry on Dijkstra’s algorithm and the
coding associated with it.  The description of the algorithm on the
page may be a useful starting point.

Reading this material should take approximately 1 hour.

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1.4.2.2 Kruskal’s Algorithm   - Reading: Wikipedia’s “Kruskal’s Algorithm” Link: Wikipedia’s “Kruskal’s Algorithm” (HTML)

`````` Instructions: The reading describes Kruskal’s algorithm, its
performance, and includes a proof of correctness.  Try comparing
this algorithm to Dijkstra’s algorithm from above.

Reading this material should take approximately 1 hour.

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1.5 Dynamic Programming   1.5.1 Principle of Optimality   - Reading: Duke University: Steven Skiena’s “Principle of Optimality” Link: Duke University: Steven Skiena’s “Principle of Optimality” (PDF)

`````` Instructions: Click on “lecture13.pdf” to download the PDF.  The
reading briefly discusses the principle of optimality and then
provides details dynamic programming.

Reading this material should take approximately 1 hour.

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1.5.2 Optimal Substructure   1.5.2.1 Recursion   - Reading: Wikipedia’s “Recursion” Link: Wikipedia’s “Recursion” (HTML)

`````` Instructions: The article defines recursion and discusses recursion
data, programs, and algorithms.

Reading this material should take approximately 1.15 hours.

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1.5.2.2 Bellman-Ford Algorithm   - Reading: CSAnimated’s “Bellman-Ford Algorithm” Link: CSAnimated’s “Bellman-Ford Algorithm” (Flash)

`````` Instructions: This is an animated slide show that describes the
algorithm.  It has an audio component associated with it so make
sure you are on a computer where you can hear it while viewing the
animated slide show.

Viewing this material should take approximately 1 hour.

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