Standards and Assignments for Student Web Pages in
Genomics, Proteomics and Systems Biology

These web page assignments are designed to let you practice what you have learned during the semester. They are open-ended so you can experience the same uncertainty researchers do when initiating research. To maximize the educational value of these assignments, you may work in groups on the process of your in silico research, but the writing must be done on an individual baiss. This work is covered by the Honor Code and if you have any doubts, please ask me. See the Department's plagiarism policy for further guidence.

There are certain guidelines I want you to follow for all your web pages for this course:

At the top of every page, add this line; "This web page was produced as an assignment for an undergraduate course at Davidson College."
Do not have any fancy backgrounds on any page other than your first page. In general, it is better to keep web pages simple.
Do not have any animations on any page other than your first page, unless it is a part of your presentation (e.g. no moving eyeballs, or dancing bears).
The color of text should be black on a light-colored background, for easy reading (see how bad this is?).
All references (e.g. Campbell et al., 2002) to WWW resources must be written in the proper format (as described online) and must be hyperlinks if they are web references. You must use the (Name, Year) form of CBE style citations. Do put a comma between the name and the year, and do not say "and others" but rather I want you to use "et al. ". Do not use the style (Campbell, page 1000). Full citations should be located at the bottom of each page and not on a separate reference page.
All figures must have figure legends and in these figure legends, you must cite your sources, and provide hyperlinks when appropriate. You must seek permission to reproduce any figures not your own.
At the bottom of each page, you must put your contact information and a link back to the genomics web page <www.bio.davidson.edu/genomics> and the college (see the bottom of this page as an example).
Use relative links for all the pages you create rather than absolute links. This will prevent problems in the future if the BioServer is reorganized again.
Finally, you should know that I grade content and not presentation. If you spend time making fancy graphics, that is OK as long as it enhances your ability to communicate to the reader. The text is the most important part of your web page so concentrate on that rather than whizbang layout.

Before you produce your first web assignment, you should take a few minutes to think about your overall web site. You are going to produce at least 4 web pages. To make it easier for everyone to read your pages, you should have a "front page" that you must call "home.html". I will create a link to your front page and it will be easier for me if all of you use the same file name. From this front page, you can gradually add relative links to your web pages as you produce them. This front page is where you may put any bells and whistles that you want to have fun with your web page. I will only grade its functionality (i.e. do all the links work, are all the images visible, etc.)

I have provided a list of web resources that may help you with some aspects of creating web pages. If you have never created a web page before, tell me ASAP.

First Web Assignment

Your first project is to select a trait that the popular press has dubbed a genomics issue. You may not use any of the traits from previous classes. The trait may be "a disease gene" but it does not have to be. You may choose any genomics story from any species as long as it has been published. You should find both a popular press citation and a scientific publication when choosing your genomics story.

The purpose of this web page is to explore the commonalities and differences between popular press and scientific literature. In your description, you should tell your readers about biology being described. Your writing should target Bio111 students.

Before you write your web page, you must read this paper that describes what a good popular press science story should do:

Eunice Kua, Michael Reder, and Martha J. Grossel. 2004. Science in the News: A Study of Reporting Genomics. Public Understanding of Science. 13: 309–322.

As a bare minimum, you must have the following features (in addition to the ones required on each of your web pages):

You must have at least one link to an appropriate site off campus.
You must have at least one figure on your page. If you can find a PDB for your protein, that would be beneficial.
You must create a relative link back to your front page.
You must utilize the recommendations in Kua et al.

Second Web Assignment

Your second project is to choose one of two papers and summarize the paper you have chosen. You should summarize what YOU learned in this paper and your opinion of it. Then, go through the paper one figure at a time to explain the main points of each figure. This should not be a super detailed review of the paper, but I want you to demonstrate you facility with the material and the big picture addressed in the paper.

Third Web Assignment

Your third project is to choose one of two papers and summarize the paper you have chosen. You should summarize what YOU learned in this paper and your opinion of it. Then, go through the paper one figure at a time to explain the main points of each figure. This should not be a super detailed review of the paper, but I want you to demonstrate you facility with the material and the big picture addressed in the paper.

Web-Related Resources

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Standards and Assignments for Student Web Pages in Genomics, Proteomics and Systems Biology

Standards and Assignments for Student Web Pages in
Genomics, Proteomics and Systems Biology