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 basis. 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 guidance.

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., 2016) 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 have at least 3 web pages. To make it easier for everyone to read your pages, you should have a "home page" that you must call "home.html". I will create a template home page and a link to your front page and it will be easier for me if all of you use the same file name. From this home page, you can gradually add relative links to your web pages as you produce them. This home 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.

Two notes about your web assignments:
Some of you may know about Bloom's taxonomy of learning. His seminal work helped us identify 6 different types of learning from lowest to highest:

1. knowledge
2. comprehension
3. application
4. analysis
5. synthesis
6. evaluation

By this point in your college career, you should be moving beyond 1-3 and reaching 4-6 more often. In particular, these web assignments call upon you to synthesize and evaluate. These two levels of knowledge are the hardest to accomplish. By having you summarize key points, you must synthesize what you already know as well as what the authors have provided. By asking for your opinion, I am pushing you to evaluate the work. Did the authors convince you with data that their interpretations are valid? Did they make statements you are not sure are true? Did they provide equally compelling alternative interpretations? I hope you will continue to push yourselves to the highest levels of knowing.

First Web Assignment

Your first project is to summarize a research project in genomics. You may use a popular press source, but you must find its original scientific source. Or, you can use a scientific summary as found in Nature, Science, PLoS, eBiology, etc. I do not want you to evaluate the science. Instead, I want you to answer the following questions:

1) What was the research project?
2) Were they testing a hypothesis or doing discovery science?
3) What genomic technology was used in the project?
4) What was the take home message?
5) What is your evaluation of the project?

Your target audience is a biology major at Davidson who has completed Bio113/111. What do you think a biology major should know about your chosen area? Once you have selected your topic, send me an email with this information (story topic and your source) so others will know the project has been claimed. I will fill in the table below in the order the emails are received.

There are two main goals of this web page assignment. First, I want to make sure everyone can build an html web page. Second, I want you to understand the difference between old-school genetics and genomics.

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.
• You must create a relative link back to your genomics home page which I will make for you.

Second Web Assignment

Your second project is to choose one paper from a short list I provide, and review the paper you have chosen. To begin, summarize the paper (main point and conclusions) and tell me your opinion of the paper. Then go through one figure or table at a time to summarize what each figure says - be sure to address every panel in the figure. You do not have to comment on every single aspect within each penel, but you should summarize the question they were asking, what method they used, and the main take home messages. No draft necessary. Just post the final version by the deadline.

This should not be a super detailed review of the paper, but I want you to demonstrate your facility (i.e. #4 - 6 of Bloom's taxonomy) with the material and the big picture addressed in the paper.

Web-Related Resources

• How to evaluate a WWW site
• A WWW Template for you to use
• How to use Dreamweaver
  • "Advanced" HTML (rollover images, image maps, invisible tables to align text)
    • Download entire folder (Zipped)
• How to make Greek Letters
• How to make Greek letters in html
• How to add sounds to your web pages (thanks to Pratt Institute, NYC)
• How to Access your Folder on the Web Server
• Uploading Web Pages to the Bio Server Using Dreamweaver (8)
• How to Create Relative Links for your Web Pages
• Student web pages for Genomics