From UVaCompBio

Contents 1 About, general motivation... 2 Announcement 2.1 What is this? 2.1.1 What, exactly, is this? 2.2 What should I do? 3 Resources 3.1 Textbooks 3.2 Review articles & Primers 3.2.1 Historical accounts; General overviews 3.2.2 Primers; Tutorials 3.3 Additional resources 4 Major discussion areas 4.1 Computational biology & Bioinformatics 4.2 Molecular biophysics 4.2.1 Simulation methods 4.2.2 Electrostatics calculations 4.2.3 Docking calculations 5 Timeline, Lectures / Discussions 5.1 Spring 2011 (←click for materials) 5.2 Calendar 6 Participants 7 Acknowledgements 8 Wikis: Getting started

About, general motivation...

This new, Mead-funded educational series is being developed by Cameron Mura over Spring 2011, in order to introduce UVa undergraduates to scientific research areas that span the biological and computational sciences. Much of the motivation stems from the fact that the bio-* sciences (biochemistry, molecular biology, etc.) will continue to become increasingly quantitative and computational in nature.

Announcement

Are you a highly-motivated UVa second- or third-year undergrad who is considering (or already pursuing) a major in Biology, Chemistry, Physics, Computer Science, or related areas ?? If so, and if you're interested in learning about an exciting, relatively new scientific field known as "computational biology" (henceforth abbreviated as 'CB' or 'CompBio'), then please read on...

What is this?

• Computational biology is a relatively young scientific discipline (< 30 yrs old) that has developed at the intersection of biological and computational sciences. With ever-increasing quantities of biological data (and methods for handling such data), it can be argued that nearly every biological sub-discipline (biochemistry, molecular biology, genetics, etc.) is becoming quantitative and computational (both in principle and in practice).

• A helpful definition from Wikipedia follows:
  "Computational biology is an interdisciplinary field that applies the techniques of computer science, applied mathematics and statistics to address biological problems. The main focus lies on developing mathematical modeling and computational simulation techniques."

• See also the Wikipedia entries for terms such as "Computational Biology" and the closely related (but not perfectly identical) subfield known as "Bioinformatics". Bioinformatics can be considered as a subset of CompBio. Interesting perspectives are available at http://www.bioinformatics.org/wiki/Computational_biology (Durbin quote) and http://www.bioinformatics.org/wiki/Bioinformatics#The_Loose_definition. (I may occasionally slip and use the terms interchangeably.)

What, exactly, is this?

This is not an official UVa course (i.e., no credit hours). This very new endeavor will be run as a semi-formal gathering, or seminar series, with a small number of students and myself meeting for a couple hours every couple weeks to discuss a concept (e.g., substitution matrices), algorithm (e.g., dynamic programming), etc. I will lead the discussions, but some level of student participation will be vital (especially after the first few sessions). As can be seen from this, the initial intention is more exposure to CompBio rather than formal pedagogy or lectures. We will also sample the primary and secondary literature (review articles) on occasion. It is anticipated that the series will run from late February until the end of Spring semester.

What should I do?

If interested, please email (as PDFs) the following three items to me (cmura@virginia.edu) by 24-Jan-2011:

• A most recent copy of your transcript (unofficial copy is fine) and your CV (even brief).
• A brief (<½-pg) statement describing your potential interest in such a series.

Resources

Textbooks

We'll aim at approximately the level of the following book:

• JP: Jones & Pevzner's "An Introduction to Bioinformatics Algorithms" (book website | publisher)

The following is a classic, indispensable text in the field:

• DEKM: "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids", by Durbin, Eddy, Krogh, & Mitchison

Review articles & Primers

Historical accounts; General overviews

• Russell F. Doolittle. "The Roots of Bioinformatics in Protein Evolution" PLoS Comput Biol, 6(7):e1000875+, July 2010.

Primers; Tutorials

• Sean Eddy authored many useful primers in Nature Biotechnology a few years back. They can be found via the following PubMed query:
  "eddy sr[au] & "nature biotechnology"[jt]"
  Here are some:
  • Eddy S. "What is Bayesian statistics?" (2004) Nat Biotechnol, 22(9):1177-8.
  • Eddy S. "What is dynamic programming?" (2004) Nat Biotechnol, 22(7):909-10.

Additional resources

• Courses:
  • Biochem 508, "Computer Analysis of DNA and Protein Sequences", is a grad course taught by Dr William Pearson & others, and is being offered Sp2011 semester.

Major discussion areas

Computational biology & Bioinformatics

One can consider the following to be bioinformatics proper — i.e., the information(informatics/statistics/data)–based realms of computational biology:

• Primers on bioinformatics
  • What are amino acid substitution matrices?
  • How are they used? An intro to sequence alignment
  • Multiple sequence alignment
    • Guide trees
• Molecular evolution
  • Phylogenetic tree estimation
    • Relationship to clustering algorithms
    • Distance-based tree reconstruction
    • Character-based tree sampling
• Information theory?

Molecular biophysics

One can consider the following areas to be chemistry–/physics–based approaches in computational biology. The following are quite interesting fields too (and are captured under the umbrella term CompBio), but due to time constraints we probably won't get to much molecular biophysics this time...

Timeline, Lectures / Discussions

Spring 2011 (←click for materials)

Mtng 1 is scheduled for 6:30 → 8:00 PM, Wed, March 23 in Room 290 Chemistry (←click for directions).
Mtng 2 is scheduled for 6:00 → 7:30 PM, Thu, March 31.
Mtng 3 is scheduled for 6:00 → 7:30 PM, Wed, April 6.
Mtng 4 is scheduled for 6:00 → 7:30 PM, Wed, April 13.
Mtng 5 is scheduled for 6:00 → 7:30 PM, Wed, April 20.
Mtng 6 is scheduled for 6:00 → 7:30 PM, Mon, April 25.
Mtng 7 is scheduled for 6:00 → 7:30 PM, Mon, May 9.
BioTrac40 ("Protein Bioinformatics"): May 17 (~6 AM) ⟶ May 19 (~9 PM) at the NIH campus in Bethesda, MD.

Calendar

Participants

Brown, Brielin [student; CS, Physics]	Evans, David [CS prof]	Hatch, John [student; Biol, CogSci]	Horton, Scott [student; ChemE, BME]	King, Julia [student; Biochem, Neurosci]
Le, Peter [student; CS]	Lee, Chris [student; Biochem, CS]	Lee, Jeong-Hyun [honorary student; Biochem]	Mura, Cameron [Chem prof; coordinator]	Ye, Jerry [student; CS, BME]

Acknowledgements

Financial support from UVa's Mead Endowment ($3K) is gratefully acknowledged for making this effort possible, as are additional funds from the College of Arts & Sciences ($1K) and Dept of Chemistry ($1.5K).

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