Doug Brutlag, Rhiju Das, Gavin Sherlock, Mike Snyder, and Peter Karp
Spring Quarter 2013-2014
Computational Molecular Biology (Biochem 218) is a practical, hands-on approach to the field of computational molecular biology. The course is recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning analysis of genomes, sequences and structures. Various existing methods will be critically described and the strengths and limitations of each will be discussed. There will be practical assignments utilizing the tools described. All homework and coursework will be submitted electronically. Prerequisites include an introductory molecular biology course at the level of Biology 41 or permission of the instructor. Students who have not had a course in molecular biology may acquire the necessary background by reading either Stryer's Biochemistry (5th edition by Berg, Tymoczko and Stryer) or Lewin's Genes IX.There will be several homework assignments utilizing the tools described in the lectures. All homework and final projects will be submitted in electronic form, as e-mail or e-mail attachments to firstname.lastname@example.org. A final paper will be required for the course that critically and constructively analyzes any area of computational molecular biology, bioinformatics or genomics. The final project may also present a novel application of existing tools or the development of some new or improved method. The final projects will be due Friday evening June 11, 2014, at midnight. There will be no extensions of this deadline.
The course will be available online only in the Spring Quarter.On campus students must register with the registrar via AXESS. Off campus students must register with the Stanford Center for Professional Development.Students receiving a grade of B or better in this course may use this grade as partial completion towards the Stanford Bioinformatics Certificate program.
Dan Davison (email@example.com) is the teaching assistant for the course and will answer questions about the homework and course content. Doug Brutlag (firstname.lastname@example.org) is the Administrator for the course. You should contact him for all administrative needs such as registration priority, web page problems, student status, etc. It is much prefered if you send all mail about the class to the staff mailing list: email@example.com rather than to either of us personally. This permits us to repond faster to your questions.
Also we have set up a mailing list that includes just other students in the class. If you would like to send a message to other registered students you may send to the address: firstname.lastname@example.org. None of the instructors or the TA participate in this mailing list so if you want us to see your message as well, you must send to both the staff and student mailing lists.
Genomics, Bioinformatics & Molecular Biology
Systematic Literature Search
Human Genome Project
Genome and Sequence Databases
Protein Sequence and Motif Databases
Sequence Similarity Search
Multiple Sequence Alignment
Distance based Phylogenies
Building Protein Motifs and Models
Ab initio Protein Structure Prediction
Clustering Coordinately Regulated Genes
Discovering Gene Regulatory Signals
Gene Regulatory Modules and Networks
MicroRNA Regulatory Networks
Simple Nucleotide Polymorphisms (SNPs)
Genome-Wide Association Studies
Metabolic Pathways and Analyses I
Metabolic Pathways and Analyses II
The video links in this table let you download quicktime videos of the lectures. Please right click on Video link and dowload the videos before viewing. You should also download the PDF file containing the slides by right clicking on the Slides link. You should have both files (Video and Slides) open when you watch the class video. The Video presents the video and audio, the Slide PDF gives you a high resolution version of the slides which are sometimes difficult to see in the video. Also, the URL links on the PDF file are all active so you can follow along the lecture more easily.
If you have a fast Intenet connection you may watch streaming videos from the SCPD site given below. This site requires a Stanford ID. Again, it is very useful to have the Slide PDF open in a separate window while you watch.
The directions for the homework assignments are given in this table and they take precedence over any directions given in the lectures or lecture slides. Changes in the web sites and algorithms that have occured since the lectures were recorded are reflected in the instructions below. Please click on the title of each homework assignment to see the specific directions.
|Introduction and short resumé||April 10|
|Human Gene Analysis||April 17|
|Protein Functional Analysis||April 24|
|Sequence Alignment and Search||May 1|
|UPGMA and Neighbor Joining Phylogenies||May 8|
|BLAST, PSI-BLAST and HMM Protein Families||May 15|
|Final Project for course (see Course Requirements above)||Jun 11|
The homework must be submitted as an attachment to an email addressed to email@example.com by midnight (Pacific Time) of the evening of the due date in order to get full credit. If you are late, you will lose 1 point (10%) for each day late. If you have a valid reason for being late (illness, conference, death in family etc.) and let us know ahead of time we can arrange a later due date for you. Please submit your homework in any of the following formats: Word, text, PDF, postscript or HTML document. Please put all copied material in quotes with a full URL or bibliographic reference to the source. Failure to quote and reference copied material is considered plagiarism and is a violation of the Stanford Honor Code. If you do not get 100% correct on an assignment you will given a description of what you did wrong and you will then have one week to submit a revised homework for full credit.
** Last Updated March 30, 2014**