Chris Bazinet

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Genomics at St. John's University

Course Overview


Bioinformatics has been offered as an upper-level undergraduate course at St. John’s University since 2005. In previous years, the course has been organized along traditional lines, with emphasis on lectures, and accompanying laboratory exercises (generally, web-based bioinformatics exercises) that illustrate the point(s) of the lectures. For the spring of 2013, we have joined the Genomics Education Partnership, organized by Professor Sarah Elgin at Washington University, St. Louis, in which the assembly and annotation of various Drosophila genomes, or portions thereof, are “crowd-sourced” to (primarily undergraduate) student groups around the U.S. This work in progress reverses the intellectual priority in the course, with our lecture/discussion driven by what we need to understand in order to accomplish our sequence finishing and/or annotation goals with the GEP. Engagement in a true genomics research project, where the solution to a finishing or annotation assignment is not known beforehand and may present novel problems requiring original thinking, models the real scientific process, and promises to engage students more genuinely and deeply in an exploration of basic genomics.

Implementation

This first year, students have worked on annotation of the D. ananassae dot chromosome and a control region on chromosome 3L. We hope to do sequence assembly/finishing projects in the spring of 2014, in addition to annotation projects.

Lessons Learned and Future Plans

Students have been wonderfully engaged in the annotation project. Our first hint of this was when, early in the course, the scheduled laboratory period ended—and most of the students stayed at their computers, actively working on and discussing their annotation projects. We have found also that many of the issues students have with their annotation projects stem from incomplete understanding of basic concepts about gene structure and function, the biochemistry of nucleic acids and proteins, and many details of gene expression. The genomics lab thus affords many teachable moments in which students have the opportunity to integrate many lower level concepts that have previously been experienced separately, in different courses, and not related to each other. This is where they have a great opportunity to put the big picture together, with a perspective that relates many lower level biological concepts. We hope to add sequence annotation/finishing in future iterations of the course, and to fine-tune lecture topics so that as much as possible, they are driven by the problems students are confronting in the lab.

Syllabus for Biology 3830, Bioinformatics, St. John's University, Spring, 2013


BIOINFORMATICS
BIOLOGY 3830/3831L
Department of Biological Sciences, St. John’s University

Lectures: Mon & Thurs 10:40-12:05, Rm 215 St. Albert Hall
Instructed Lab: Thursday, 1:50-4:50 PM, Rm 215

Course Description: Students will be introduced to modern genomic analysis in a research project-driven course in which computational tools are used to finish and annotate genome assemblies from various Drosophila species. Lecture/discussion sections will focus on the molecular biology required to understand basic genomics, including gene structure, replication, transcription, splicing, and translation, the conceptual basis of computational tools used in genomic analysis, and chromatin structure and function, especially as it relates to epigenetics.

TEXTS

Required: Michael Agostino, Practical Bioinformatics A. Garland Science, New York, 2013. ISBN 978-0-8153-4456-8
pdf files of other readings will be uploaded to the course Blackboard site, some from the texts below, others obtained online. I will mention each of them as they are posted
Other Books that you may find helpful/interesting:
-Malcolm Campbell and Laurie J. Heyer, Discovering Genomics, Proteomics, and Bioinformatics, 2nd Ed. Pearson Benjamin Cummings, 2007. ISBN 0-8053-8219-4. We used this text for a number of years prior to this one, very readable and generally useful, if a little scattered.
-Steven Haddock and Casey Dunn, Practical Computing for Biologists. Sinauer Associates, 2011. ISBN 978-0-87893-391-4. An excellent introduction to command-line computing, including the BASH shell, file reformatting with regular expressions, intro to Python programming, MYSQL, LINUX, basic principles for digital manipulation/editing of graphics files, and basic electronics for experimental biologists..
-A genetics text; an inexpensive one is: Genetics: A Beginner's Guide, by B. Guttman, A. Griffiths, D. Suzuki, and T. Cullis. 2003, Oneworld Publications (ISBN 978-1851683048) If you have a genetics text already, yours may be better; alternatively, borrow one from a friend.
-Shuba Gopal, A. Haake, R. P. Jones, T. Tymann (2012) Bioinformatics: a Computing Perspective. A computational perspective on biology, meant as an introduction to computer science students taking up bioinformatics. Interesting and useful perspective on biological systems as information processing systems.
How this course works: Some things are best understood by doing rather than thinking about them on a theoretical basis. We think this is true of bioinformatics. What is bioinformatics? Depends on who you ask. It’s a catchall term that refers to the increasingly broad overlap between computation and biology, and within which many biologists of the 21st century will labor. Our focus in this course will be on basic genomics—how the genome of an organism is sequenced, assembled, and annotated. In this course, what we discuss in “lecture” will be motivated primarily by what we are doing in the lab, where we will be participating, with other college and university groups, in the finishing and annotation (we'll discuss what those are at some detail....) of the “Muller F Element”.
Calculation of Final Grades will be by the formula: Quality of Lab work: 50%; Quizzes: 15%; Midterm Exam, 10%; Final Exam: 20%; Class participation: 5%. I do not have a rigid formula for grades. I expect that the average grade in this course (judging from past experience) will be in the B range. However, a high quality group of students that works together and participates positively and constructively could do better than this.
Lab: Labs will meet on Thursdays from 1:50-4:50, starting January 24. Most labs will begin with a short quiz on discussion topics from the previous several meetings of the class. In labs, you will, with your teaching assistant (Paromita Gupta) and I, build a Linux computer system, then use it to annotate and finish ~40 kB segments of Drosophila genome. Students who complete their projects will be eligible for coauthorship on any papers including the data they have generated.
Readings: Readings will be specified in lecture/discussion sessions and posted on the Blackboard site as we progress through the semester.
MAJOR ONLINE RESOURCE: The GEP (Genomics Education Project), Washington University, is the source of our research materials. EXTENSIVE resources in the form of tutorials, videos explaining sequencing technology, and expert advice available through the Wash U. course wiki, are available there. Your liberal use of them is essential for your success in the course. The site is at: http://gep.wustl.edu/

Office Hours (Rm 246C St. Albert Hall:
Tuesdays 1-3
Wednesdays 10:30-12
Or by appointment:
bazinetc@stjohns.edu
718-990-1419 (office)