BIO Assignment Week 1

Assignment for Week 1
Wiki editing, Chimera and R

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

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:

• familiarize yourself with basic Wiki editing on the Student Wiki;
• install the statistics workbench R, and work through selected parts of an introductory tutorial.

Caution: this is a lengthy assignment and can't be done in one day. Work on it every day, or better every morning and evening. A lot of this has to do with learning the R programming language and you need constant repetition to bring this material into active memory. Cramming everything in a single, desperate effort makes you forget things quickly and is a waste of your time.

 

Wiki

Collaboration is a common theme for modern lab work and a Wiki is a great way to share and seamlessly update information in groups - or just for yourself. Probably the most sophisticated Wiki software is MediaWiki, a set of PHP scripts that is under continuous development by the Wikimedia foundation; it is the same software that runs Wikipedia. This is open source, free software that is easy to install, is well documented and requires very little resources other than a machine that runs a MySQL database server and an Apache Webserver. Numerous extensions exist (and extensions are not hard to write); they enhance the already rich functionality. But let's start with small steps. I will create an account for you on the Student Wiki, and I have configured the Wiki so that

• only logged in users can view the pages;
• all logged in users can create and edit pages at will.

This means you could edit pages that don't "belong" to you. Respect the "House Rules" and don't edit other's things without permission, even if you can think of a particularly witty comment or hilarious prank. If you want to comment on a page: every page has an associated "Discussion" page that you can freely edit. Remember to "sign your name" to discussion entries.

Task:
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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.

Programming in R is a main focus of the course.

Task:

• Access the R tutorial on this site.
• Work carefully through the following sections:
  • The environment;
  • Simple commands;
  • Scalar data;
  • Vectors;
  • Matrices;
  • Scalar data;
  • Lists;
  • Data frames; and
  • Subsetting;

.

If any of this material is confusing, discuss it on the mailing list. At the end of this assignment you should be competent to read expressions in basic R syntax, able to predict their result and spot syntax errors, familiar with the concepts in the tutorial, and able to write your own expressions.

 

Links and resources

• Student Wiki
• R tutorial

 

 

Notes and references

 

Ask, if things don't work for you!

If anything about the assignment is not clear to you, please ask on the mailing list. You can be certain that others will have had similar problems. Please remember that "participation" is a significant part of your course mark.