News
- 09/22/2008
- Login and password have been sent to Registered Students to access the lectures.
Greetings Students!
Welcome to SBIO228 Computational Structural Biology course
Login and password is sent to each student's STANFORD email address.
If you have registered for the class either through Axess or SCPD and have not yet received a login name and password to access the lectures. Please contact us right away.
Course outline
New lectures will usually be available on Mondays and Fridays.
A syllabus is available here in PDF format.
Assignment Zero will be posted Sep. 22nd
Lecture #1 (Introduction) and Multiple-Choice #1 will be posted Sep. 22nd
Assignment Zero is due Sep. 29th
Assignment #1 will be posted Sep. 29th
Lecture #2 (Molecular Architecture I) and Multiple-Choice #2 will be posted Sep. 29th
Lecture #3 (Molecular Architecture II) and Multiple-Choice #3 will be posted Oct. 6th
Assignment #1 is due Oct. 13th
Assignment #2 will be posted Oct. 13th
Lecture #4 (Bioinformatics I) and Multiple-Choice #4 will be posted Oct. 13th
Lecture #5 (Bioinformatics II) and Multiple-Choice #5 will be posted Oct. 20th
Assignment #2 is due Oct. 27th
Assignment #3 will be posted Oct. 27th
Lecture #6 (Molecular Simulation I) and Multiple-Choice #6 will be posted Oct. 27th
Lecture #7 (Molecular Simulation II) and Multiple-Choice #7 will be posted Nov. 3rd
Lecture #8 (Structure Prediction I) and Multiple-Choice #8 will be posted Nov. 17th
Assignment #3 is due Nov. 17th
Assignment #4 (FINAL PROJECT) will be posted Nov. 17th
Lecture #9 (Structure Prediction II) and Multiple-Choice #9 will be posted Nov. 17th
Assignment #4 (FINAL PROJECT) is due Dec. 10th
The assignments are due at midnight - late day policy appears below.
Note that Assignment Zero is fairly easy. Also, note that there is a little more time to complete Assignments 3 & 4, the final two assignments which are worth quite a bit of the grade (i.e. start early).
NO LATE DAYS ARE PERMITTED FOR THE FINAL PROJECT
At the end of each assignment page (you'll see when we post them) there is a link for you to submit the url of your submitted answer.
We wish to emphasize this last point:
All assignments should be submitted as web pages, not sent as attachments to emails.
Overview
SB228 has been completely over-hauled and specially designed for web-based
instruction. There will be 10 Lectures each consisting of 6 to 8 Concepts. Each Concept will involve about 10 "Talklets". A Talklet is a slide that includes
animation, mouse movements and voice commentary. For an example of a talklet,
click on this link.
SB228 course is a 3-Unit graduate class and you will need to register to get a password to the teaching material.
Links to SSH clients
Sick of Samson? Why not try SSH instead? Check out our SSH page.
- This course consists of online lectures (provided in Talklet format on this site), short, multiple-choice quizzes on each lecture (submitted via a web form), and five
homework assignments to be submitted as web pages.
- The grade you get on the course is based on the multiple-choice questions (25%),
assignment Zero (5%), assignment 1 (10%), assignment 2 (15%), assignment 3 (20%) and assignment 4 (final project) (25%).
- Research in computational structural biology is heavily dependent on computers
and the Internet, so it is essential to have prior exposure to personal computers,
e-mail, and the World Wide Web. The course does NOT require any significant (if any)
Unix skills. A Macintosh or PC based personal computer is perfect.
Assignments are handed in as web pages. Although no prior knowledge of web design is required, we do expect you to create web pages that are navigatable and easy to read for the TA's. A portion of the grade in each assigment will be dedicated to the organization of the page.
- Each student is allowed 3 late days to use during the quarter when submitting the
homework assignments and/or final project. You can use them one at a time, or all at
once, but once they are gone, further late assignments will be penalized (-10% per day).
- The homework assignments will be based on many resources available on the web.
It is very important that web pages, servers, research papers, textbooks, etc. used
for homework assignments and the final project are cited properly in a reference
section. We will not tolerate plagiarism of any kind.
There are tons of structural biology information and software available on the internet - just use Google to search for any of the
terms mentioned in the lectures. We have prepared a couple of the most useful resources for you here:
Dr. Levitt is unavailable for any office hours during the course due to his extremely busy schedule and the online nature of the course. Office
hours are available with the TA by appointment, if you happen to live locally; just send us an email.
Please also include the topic of any questions that you might want answered so that I can prepare myself ahead of time.
About a fourth of your grade on the course is based on these relatively easy multiple-choice questions for each lecture. Note that you will have to login with your username and password to answer them, and you can only submit an answer once. You can submit your answers anytime you want, but the final deadline for all multiple-choice questions is Wednesday, Dec. 10th, 2008 by midnight PST. We recommend that you submit your multiple-choice questions for each lecture as soon as you are done with the respective lecture and not wait until the last day to submit the Final Project and the multiple-choice questions together.
There will be no extensions past Dec. 10th 2008.
There will be a total of five assignments in the course. The last assignment will be
slightly bigger and doubles as a final project. The assignments should be handed
in/presented as web pages written in HTML. You don't have to be a whiz at coding
HTML, you should use the web to convey information. There is no need to fuss with
fancy layouts, etc. The assignment zero will get you started with "How to make a webpage?". There are several options for making a web page:
- Use an HTML editor like Netscape Composer, or even Microsoft Word (NOT highly recommended). Web sites like geocities or yahoo often provide similar tools for free.
- Learn to hand-code HTML. We have an online web page design primer to help you do this.
- Find someplace to "host" your page. If you are a Stanford student, put your pages in the WWW directory of your Leland account. If you don't have access to a website you can use any of the many free online services (like Yahoo, http://geocities.yahoo.com.)
- Please don't use any special plugins (like Flash), use only compressed images like jpegs or gifs, and don't write 25-page presentations :-). The TA's will be viewing your pages from many different browsers and machine architectures, so try to keep your page as "vanilla" as possible to make grading easier. We have had particular trouble with pages generated from Microsoft Powerpoint, so avoid that if possible.
- Assignments are due by Midnight PST on the due date i.e. if the assignment due date is Monday, Oct. 2nd 2006, it should be submitted by 11:59 PM on Monday Oct. 2nd, 2006.
Problems? Questions about the Page or the Class? Contact The TAs
