Standards for Molecular Web Page Assignments


Minimal Standards for Producing a Home Page for Dr. Campbell's Courses

Guidelines I want you to follow when producing web pages for this course.

  1. At the top of every page, add this line; "This web page was produced as an assignment for an undergraduate course at Davidson College."
  2. Do not have any fancy backgrounds on any page other than your front page. In general, web pages work better if they are kept simple.
  3. Do not have any animations on any page other than your front page, unless it is a part of your presentation (e.g. no moving eyeballs, or dancing bears).
  4. The color of text should be black on a white background, for easy reading (see how bad this is?).
  5. All file names must conform to WWW standards which means no spaces in the file names. Text files must end with .htm or html and figures must end in .gif or .jpeg. Your home page for this course must be called "home.html".
  6. All references (e.g. Campbell et al., 2000) to WWW resources must be written in the proper format (as described in Online! chapter 8) 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. ".
  7. You may not use more than 50% of your references from the WWW. Therefore, you will have to use the library's collection, PDF reprints, or ILL papers for at least half of your references. Note that published research papers accessed via the web are not considered web resources since they first appeared in print.
  8. All figures must have figure legends and in these figure legends, you must cite your sources, and provide hyperlinks when appropriate.
  9. You should have at least one link to a different but appropriate site.
  10. At the bottom of each page, you must put contact information and a link back to the molecular web page (see example at the end of this page). <www.bio.davidson.edu/molecular>

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Molecular Biology Web Assignments

Your first home page assignment

Your task is to create a web page that describes a protein and its structure. I suggest you begin by searching Protein Data Bank, your favorite textbook, or PubMed. The key is to indentify a protein whose structure has been determined. I highly recommend that you NOT choose a structure/protein whose information is based on multiple NMR structures. You want to find a protein that has each amino acid identified. The second criteria will be gaining access to the paper that describes your chosen protein. Many papers are freely available, but some publishers never make papers freely available. Therefore, you will want to plan ahead enough to secure the papers via the library (either online or via Inter-Library Loan which can take 2 weeks).

The main point of this assignment is to link structure to function. Use the one paper that determine the protein's structure as you only journal source unless you want general background such as that found in textbooks.

You may start with the template I have created. As a part of this assignment, you must include the following:

I will be reading the content to look for accuracy and clarity. I will be looking at your references to make sure you have used proper CBE style citation. I will be testing your links (including the email link) to make sure they are all functional. I want you to target an audience that has completed Bio111 and Genetics. You can see previous pages, but they had different assignments.

To capture an image from the screen by holding down three keys simultaneously: command+shift+4, or save the image file from your browser.

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Your second home page assignment - Your Favorite Orthologs (YFO)

Your second assignment is to identify orthologs (genes evolved from a common ancestral gene) of your chosen protein. The best place to get this information is from a review paper, but you may want to consult sources such as BLAST, Entrez, OMIM, PDB, CLUSTALw, etc. to find these orthologs. I have created a help page for those of you new to DNA databases. If your original protein's structure was determined from a prokaryote, then your survey should include orthologs from metazoans. If your protein crystal was produced from a vertebrate, then be sure to survey other vertebrates but also prokaryotes. You should specifically look for orthologs in the "big seven" and any others species that prove helpful in understanding your proteins cellular roles. If you search for orthologs in the big seven but do not find any, be sure to state that clearly.

Big Seven Genomic Species
Human
Mouse
C. elegans
Drosophila
Arabidopsis
Yeast
E. coli
Others of interest


For Genomics alumni, this is not meant to be an all out genomics blockbuster assignment.

The main point is to provide sequences and information obained through orthologs of the species from which your structure was determined.

For this assignment, focus on phenotypes, mutations, diseases, drug binding sites, virus binding sites, similar proteins, etc. Since your first assignment focused on structure/function, this assignment should widen the circle of information about your chosen protein. Keep in mind you are trying to identify critical amino acids and evolution often retains those amino acids that are required for protein function.

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Your third web assignment - Your Favorite Jmol Structure (YFJS)

Your third assignment will no doubt stretch you into uncomfortable territory. The structure of a protein is becoming increasingly important and increasingly, biologists need to learn more about computer science. Therefore, it would would be good for you to create a Jmol tutorial for your chosen protein. You must use the same protein from assignment 1. A Jmol tutorial is one where you, the author, determine what you want the viewer to see. You write a script that creates buttons to provide viewers with the appropriate views. I will be looking for tutorials that tell me something functionally significant, not just secondary and quaternary structures. I created a page with links to examples and some commands you can use. Here is my refresher tutorial.

In order to run Jmol, I want you to use frames in html. We have created a template for you so all you need to do is modify it for your particular molecule. Jmol uses Java so it should work on all computers. You will need to work on this ahead of time and not save it to the last minute.

How do you create a link from a framed web page back to a non-framed page so the new page fills the entire browser and not just the tiny button frame? Highlight the text that will make the link and in the properties window (se below), find the place that says "Target". Click and hold and choose "parent". See the image below to see an example.

You have already seen some of my chime tuturials, like the one for dsDNA. Before Jmol, we used Chime. John Kogoy ('03) helped me write some direcitons on how to create Chime scripts that might still apply (see word file). Check out his tutorial on T7 RNA polymerase to get an idea of how fancy you can be. Remember, with all web pages you can view the source code to figure out how he coded this tutorial. In your folder on the BioServer, you will find all the files you need to modify the existing template of dsDNA. In addition, we will have an in-class workshop when you turn in your second exam.

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Your last home page assignment (due April 30; posted by class time) will be your review paper. The goals of this assignment are: 1) each student to choose a paper from the two I have selected; 2) summarize the results of the paper; 3) critique the paper (Do the results support the authors' claims? Are the figures adequate?); and 4) suggest future experiments to do to learn more about the topic. When you make suggestions about future work, indicate what question you want to ask, what method(s) you would use, and what kind of results might you expect.

For this assignment, you do not have to reproduce any figures (keeping in mind that figures from the original paper being reviewed will be copy right protected). However, it might be easier for you to explain the figures if you annotate parts with arrows, boxes, etc.

Here are your choices for 2010 (PDF Files):

I will grade your paper with the following weights:

You can see some papers from the past.


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Send comments, questions, and suggestions to: macampbell@davidson.edu