Joint CMU-Pitt Ph.D. Program in Computational Biology

Robert F. Murphy and Ivet Bahar, Directors

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Curriculum - Core Course

02-760 Laboratory Methods for Computational Biologists

Spring 2007 course information

CMU Instructor: Elvira Garcia Osuna, Ph.D.
Office: 409A Mellon Institute
Phone: 412-268-7876
E-mail: elvira@cmu.edu
Office Hours: Monday 1:00-2:30 PM, Wednesday 1:00-4:00 PM, Friday 1-2:30 PM.
Other times by appointment.

Pitt Instructor: Judy Wieber, Ph.D., M.B.A.
Office: BST3 3053, Pitt
Phone: 412-648-8646
E-mail: jwieber@ccbb.pitt.edu
Office Hours: Monday, Wednesday, Friday 9:00-11:00 AM
Other times by appointment.

Class Times and Locations:
Lecture (all students will attend this lecture):
Monday, 3-3:55 PM, Room TBA

Lab Sections (each student will be assigned to one of these sections:
Tuesday, 1:30-3:55 PM, Lab TBA
Tuesday, 4:00-6:25 PM, Lab TBA
Thursday, 1:30-3:55 PM, Lab TBA
Thursday, 4:00-6:25 PM, Lab TBA

Lab Techniques Boot Camp: An introductory lab techniques boot camp will be held the first week of the semester. Attendance at boot camp is required unless Dr. Garcia Osuna or Dr. Wieber has issued an exemption. Exemptions will only be issued to students who have extensive lab experience. This will be determined by a Lab Skills Questionnaire, to be filled out by students at the end of the fall semester.

Alternative Laboratory Times: Several laboratories or laboratory tasks may have to be performed outside of the allocated classtime and days due to limited accessibility to key pieces of equipment and due to the nature of the lab (i.e. feeding cells every two to three days). This scheduling outside of the allocated class time will be kept to a minimum and will be performed with every effort to accomodate students' schedules.

Course Description and Objectives: Computational biologists frequently focus on analyzing large amounts of biological data, often from high-throughput assays or diverse sources. It is therefore critical that students training in computational biology be familiar with the paradigms and methods of experimentation and measurement that lead to the production of these data. This one-semester laboratory course has been developed to give students a deep appreciation of the principles and challenges of biological experimentation.

Touches upon a range of topics, including structural biology, genomics, prot eomics, and bioimaging

A different laboratory method is covered each week, in the lab of a host fac ulty member who uses that method

The theory and practical aspects of each method are covered during a lecture session prior to each lab session

Students are required to submit a short lab report each week, summarizing th e goals of the experiment, the critical steps and sources of error, and the anal ysis of the resulting data

With an empahasis on instrumentation and high-throughput data collection, this course is appropriate for students who have never taken a traditional undergraduate biology lab course, as well as those who have.

By the end of this course, the students should be able to do the following:

Understand and follow guidelines regarding chemical and biological safety

Maintain a laboratory notebook that follows the guidelines given in class

Prepare a laboratory report

Demonstrate experimental techniques as covered in class

Describe and demonstrate basic theoretical concepts of the methods covered in class

Perform literature search

Textbooks: The following textbooks are recommended, and will be placed on reserve at Falk Library (Pitt) and the Mellon Institute Library (CMU). They also will be available for purchase at the Health Book Center, University of Pittsburgh, 3527 Forbes Avenue.

At the Bench: A Laboratory Navigaotor, Updated Edition, Kathy Barker, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2005.

Biochemical Methods: A Concise Guide for Students and Researchers, A. Pingoud, C. Urbanke, J. Hoggett, A. Jeltsch, Wiley-VCH, Weinheim, 2002.

The following books will serve as reference material for the course, and will also be placed on reserve at Falk Library (Pitt) and the Mellon Institute Library (CMU). Students wishing to purchase personal copies of these books may do so through online booksellers.

Analyzing Microarray Gene Expression Data (Wiley Series in Probability and Statistics), Geofrey J. McLachlan, Kim-Anh Do, Christopeh Ambroise, John Wiley & Sons, Inc., Hoboken, NJ, 2004.

Basic Methods in Microscopy: Protocols and Concepts from Cells, a Laboratory Manual, David L. Spector and Robert D. Goldman, Eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2005.

Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, Third Edition, Gale Rhodes, Elsevier, New York, 2006.

Culture of Animal Cells: A Manual of Basic Technique, 5th Edition, R.I. Freshney, Wiley-Liss: Hoboken, NJ, 2005.

Data Analysis Tools for DNA Microarrays, Sorin Draghici, Chapman & Hall, CRC, Boca Raton, FL, 2003.

Flow Cytometry: First Principles, Alice Longobardi Givan, Wiley-Liss, Hoboken, NJ, 2001.

Handbook of Biological Confocal Microscopy, J.B. Pawley, Plenum Press, New York, 1995.

Introduction to Macromolecular Crystallography, Alexander McPherson, Wiley-Liss Inc., Hoboken, New Jersey, 2002.

Lab Ref, Volume 1: A Handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench, Jane Roskams and Linda Rodgers, Eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2002.

Lab Ref, Volume 2: A Handbook of Recipes and Other Reference Tools for Use at the Bench, Albert S. Mellick and Linda Rodgers, Eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2007.

Microarray Analysis, Mark Schena, John Wiley & Sons, Inc., Hoboken, New Jersey, 2003.

Proteomics in practice: a laboratory manual of proteome analysis, Reiner Westermeier and Tom Naven, Wiley-VCH, Weinheim, 2002.
http://www3.interscience.wiley.com/cgi-bin/booktoc?ID=93519285

Proteomics, Timothy Palzkill, Kluwer Academic Publishers, Norwell, Massachusets, 2001.
http://site.ebrary.com/lib/pitt/Doc?id=10051611

Class Website: All registered students will have access to the class website via Blackboard (http://www.cmu.edu/blackboard or http://courseweb.pitt.edu). Class announcements, course information, instructor and teaching assistant information, course documents, and assignments are contained on this website. This website will be constantly updated with relevant information throughout the semester.

Prerequisites: None.

Co-requisites: None.