BIO Assignment Week 1

Assignment for Week 1
Wiki editing, Chimera 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:

• familiarize yourself with basic Wiki editing on the Student Wiki;
• install the molecular graphics viewer UCSF Chimera on your own computer, work through a tutorial on its use and begin practicing the skill of viewing split-screen stereographic scenes without aids;
• install the statistics workbench R, and work through selected parts of an introductory tutorial.

 

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. You should have created an account 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:

• Access the Student Wiki;
• log in and navigate to your user page;
• open the "Help" link in the left-hand sidebar in a separate tab;
• follow the link to the "Editing" page on the Student Wiki;
• try and learn basic editing syntax by editing your User Page:
  • enter your name,
  • your major(s), specialist program, year of study - or your lab and thesis theme if you are a graduate student;
  • and your eMail address.
  • Add a category tag to your User page for this year's BCH441 course. All pages with this tag are accessible via the link in the sidebar.

Feel free to look at my User Page for code examples: clicking on the edit link will show you the source text. How do you find my User Page? Good question ...

• Create a subpage to your User Page; call it "Resources" or something similar. Note: the link MUST be in your "User space". If you don't add the prefix User:yourname/... before your page name, the new page will end up in the main "namespace". I'll then have to delete it. That's not good because you have then failed this part of the assignment. Make sure you know what you are doing, for example by looking at the code on my User Page, asking someone who knows, or asking on the mailing list.
• Put some text on your new page - perhaps a link to a Wikipedia article, or to PubMed, or to the NCBI. Make sure you understand the difference between an internal link and an external link (they have slightly different formats), and you understand the concept of namespace and categories. Also add a category link to that page.
• Play around some more. Feel free to ask how to go about achieving a particular effect that you may have seen elsewhere.

Before you are done, you should be comfortable with the following mark-up conventions and concepts:

• Login and accessing your user page;
• viewing a page's history;
• basic text formatting;
• "signing" your name;
• creating internal and external links;
• creating sections headers on a page on multiple levels;
• reverting a changed page to an earlier version;
• creating a new page (as a subpage of an existing page);
• the concept of namespaces - especially the default ("main") and User: namespace;
• the concept of categories.

I expect that there may be aspects of the Wiki you find puzzling, it is after all a complex piece of software that supports the world's largest collaborative project and one of the busiest sites on the Internet. Do ask about these things on the mailing list. My first encounter with Wikis is a while back and I can't remember everything I was initially confused about.

 

Molecular graphics

A molecular viewer is a program that takes protein structure data and allows you to display and explore it. For a number of reasons, I chose to use the UCSF Chimera viewer for this course.

UCSF Chimera

Task:

• Access the Chimera page.
• Install the program as per the instructions in the section: "Installing Chimera".
• Access the Chimera User's Guide tutorial section. The "Getting Started" tutorial is offered in two versions: one for work with the graphical user interface (GUI), i.e. the usual system of windows and drop-down menu selections. The other is a command-line version for the same. What is the difference? In general, GUI interfaces (Menu version) are well suited for beginners who are not yet familiar with all the options. Having the commands and alternatives presented on a menu makes first steps very easy through simple selection of keywords. On the other hand work from command line interfaces is much faster and more flexible if you know what you are doing and thus much better suited for the experienced user. It is also quite straightforward to execute series of commands in stored scripts, allowing you to automate tasks. For now, we will stay with the menu version but we will use commands later in the course and you are of course welcome to explore.
• Work through the Chimera tutorial Getting Started - Menu version, Part 1.

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.

 

Links and resources

• Student Wiki
• Chimera page
• Stereo vision tutorial
• R tutorial

 

• Molecular Graphics Software Links– a collection of links at the PDB

 

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.