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:

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 followign 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.

Claimed Stories
 Modified yeast produce
opiates from sugar
 ancient African skeleton shows widespread mixing
with Eurasians
5300-year-old Helicobacter pylori genome of the Iceman MicroRNAs silence
the noisy genome
DNA of ‘an entire
nation’ assessed
gene expression changes in wild vs. domestic chickens schizophrenia genomics Genome-wide Inactivation of Porcine Endogenous Retroviruses
 single neuron genomes artemisinin resistance in the malaria The Indispensable Genome history of Native Americans
 proteomics of jelly fish sting 45,000 year old human genome origins of Europeans predictive medicine from healthy people's genomes
 transcriptome reveals APOE4 effectors Principles of Chromatin Looping pig genome cleaning for xenotransplanting origins of dogs
 octopus genome head/nick cancer genomic variability Protein-RNA networks  

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):


Second Web Assignment

Your second project is to choose one paper from a short list I provide, and summarize 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 at a time to summarize what each figure says. You do not have to comment on every single part of these figures, 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


Genomics Overview

Genomics Reading Schedule

Biology Home Page


Copyright 2016 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu