Difference between revisions of "CSB Assignment Week 2"

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<section end=warm-up />
 
<section end=warm-up />
  
==Exercises==
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==Towards systems discovery==
  
Similarly to BCH441, in which we pursued the annotation and study of a single protein, we will focus on one system in this course. I have decided to take the human Sox2 gene as the protein from which we will bootstrap our explorations. Sox2 is a transcription factor that is of interest both for its role in inducing and maintaining stem cells, as well as playing multiple roles in cancer. As such, it takes centre-stage in a number of recent high-profile papers. I myself know very little about regulatory pathways, and I am not sure at all that the role of this protein in the context of its "system" is well defined. This makes the consideration of this gene and its collaborators particularly interesting for me, and I hope for you too.
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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.
  
In this assignment we will focus on Gene Ontology annotation.
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{{task|
 
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;Existing databases and strategies
 
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# Study the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_2015_Data_Sources '''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.
{{#lst:CSB_Ontologies|exercises}}
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# For one of the databases, fill in the data access information.
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# Study the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_2015_Systems_Discovery_Strategies '''System Discovery Strategies'''] page on the student Wiki.  
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##Think about the listed strategies.
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##See if you can add information.
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##See if you can add a strategy.
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##See if you add a comment.
  
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&nbsp;
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;New workflows
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I have put a [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_2015_Workflow_Collection '''Workflow Collection'''] page on the student Wiki.
  
&nbsp;
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# Create a "Project" subpage on your User page (follow the instructions from [[CSB_Assignment_Week_1#Student_Wiki|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.
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# '''Transclude''' your paragraph to the Workflow Collection (instructions are there).
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}}
  
 
==Pre-reading==
 
==Pre-reading==

Revision as of 01:06, 15 January 2015

Assignments for Week 2


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

 
 

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...]


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:

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. For one of the databases, fill in the data access information.
  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 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).

Pre-reading

In week 3, we will discuss various aspects of working with genome-scale data sets. For many experimental approaches, the ultimate outcome is a list of genes and the challenge is how to infer information from what such lists have in common:

Kim (2012) Chapter 8: Biological knowledge assembly and interpretation. PLoS Comput Biol 8:e1002858. (pmid: 23300429)

PubMed ] [ DOI ]