CSB Assignment Week 2

Assignments for Week 2

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

 
 

Assigned material will be reflected on next week's quiz. Please remember to contribute to quiz questions by Tuesday, 20:00.

Special dates

• Post your workflow sketch by Monday.
• Do the R tasks when they are announced.
• Post your quiz questions by Tuesday, 20:00.
• All other tasks are due by next week's class.

Warm up

You go to the Toronto Zoo. You see giraffes, ostriches and a green tree python. Altogether they have 30 eyes and 44 legs.

How many necks do these animals have? [I don't know...]

Seriously?
This may be easier than you think.
Maybe you are wondering whether snakes have necks? (TLDR; It's complicated. But: yes.)
Or do you need a hint? [Ok. A hint please...]

Maybe you are just confused by some irrelevant information.[No. I still don't get it...]

It's really quite simple. Thirty eyes are in fifteen heads. Fifteen heads are attached to fifteen necks. Fifteeeen. No more. No less.
How many of each? You could calculate this by substitution. Eight giraffes. Six ostriches. And one snake. But that wasn't the question.

Towards systems discovery

In class, we have discussed a number of data sources, the exemplar workflows of the papers you have posted, and some strategies to determine whether genes could be functionally interacting, or "collaborating" with each other. I have distilled the data sources and the strategies into tables that I have posted on the Student Wiki's project resource section.

Task:

In this task I would like you to review what we have discussed so far and attempt to synthesize your own approach.

Existing databases and strategies

1. Study the Data Sources page on the student Wiki. Navigate to the linked databases. Browse around. Get a sense of what data is available and how it can be accessed.
2. Choose one of the databases, edit the table to fill in the data access information and add any pertinent notes.
3. Study the System Discovery Strategies page on the student Wiki.
   1. Think about the listed strategies.
   2. See if you can add information.
   3. See if you can add a strategy.
   4. See if you can add a comment.

 

New workflows

I have put a Workflow Collection page on the student Wiki.

1. Create a "Project" subpage on your User page (follow the instructions from Assignment 1). On that page draft a workflow for data driven systems discovery using data/strategies of your choice. Keep this maximally brief (not more than three or four sentences). But be specific: make sure that the data you need is actually available, the algorithms are defined, and the computations are tractable. Discuss this on the list if you wish, or simply ask for feedback on your idea.
2. Transclude your paragraph to the Workflow Collection (instructions are there).

 

 

Software Development

Task:

• For an introduction to concepts of writing software, carefully read the Software Development page on this Wiki.
• Work through the knitr and RMarkdown tutorial.