BIO Assignment Week 1

Assignment for Week 1
Introduction, VMD and R

Note! This assignment is currently inactive. Major and minor unannounced changes may be made at any time.

 
 

Concepts and activities (and reading, if applicable) for this assignment will be topics on next week's quiz.

 

The Assignment

In this assignment you will install the molecular graphics viewer VMD on your own computer, work through a tutorial on its use and begin practicing the skill of viewing split-screen stereographic scenes without aids. You will also install the statistics workbench R, and work through selected parts of an introductory tutorial.

Molecular graphics

VMD

Task:

• Access the VMD page.
• Install the program as per the instructions in the section: "Installing VMD".
• In the tutorial section work through
  • Part 1 (Introduction), and
  • Part 2 (Working with a single molecule).

Stereo vision

Task:

Access the Stereo Vision tutorial and practice viewing molecular structures in stereo.

Practice at least ...

• two times daily,
• for 3-5 minutes each session,

Keep up your practice throughout the course. Stereo viewing will be required in the final exam, but more importantly, it is a wonderful skill that will greatly support any activity of yours related to structural molecular biology. Practice with different molecules and try out different colours and renderings.

Note: do not go through your practice sessions mechanically. If you are not making any progress with stereo vision, contact me so we can help you on the right track.

R

The R statistics environment and programming language is an exceptionally well engineered, free (as in free speech) and free (as in free beer) platform for data manipulation and analysis. The number of functions that are included by default is large, there is a very large number of additional, community-generated analysis modules that can be simply imported from dedicated sites (e.g. the Bioconductor project for molecular biology data), or via the CRAN network, and whatever function is not available can be easily programmed. The ability to filter and manipulate data to prepare it for analysis is an absolute requirement in research-centric fields such as ours, where the strategies for analysis are constantly shifting and prepackaged solutions become obsolete almost faster than they can be developed. Besides numerical analysis, R has very powerful and flexible functions for plotting graphical output.

R is not a main focus of the course, but an important tool I would like you to pick up "on the side".

Task:

• Access the R tutorial on this site.
• Work through the sections Installation, User interface, and Packages.