Difference between revisions of "CSB Assignment Week 5"
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| − | Assignments for Week 5 | + | Assignments for Week 5<br/> |
| + | <span style="font-size: 70%">Graphs !</span> | ||
</div> | </div> | ||
| + | <table style="width:100%;"><tr> | ||
| + | <td style="height:30px; vertical-align:middle; text-align:left; font-size:80%;">[[CSB_Assignment_Week_4|< Assignment 4]]</td> | ||
| + | <td style="height:30px; vertical-align:middle; text-align:right; font-size:80%;">[[CSB_Assignment_Week_6|Assignment 6 >]]</td> | ||
| + | </tr></table> | ||
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__NOTOC__ | __NOTOC__ | ||
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==Pre-reading== | ==Pre-reading== | ||
| − | This paper is a good crash-course in concepts of graph theory and their application to biology. It contains a lot of definitions that I don't expect you to learn by heart. But do familiarize yourself with the concepts | + | This paper is a good crash-course in concepts of graph theory and their application to biology. It contains a lot of definitions that I don't expect you to learn by heart. But do familiarize yourself with the concepts - they are important to properly work with the '''R''' graph tutorial. |
{{#lst:Graph_theory|reading}} | {{#lst:Graph_theory|reading}} | ||
| + | {{Vspace}} | ||
| + | |||
| + | ==An '''R''' tutorial on biological graphs== | ||
| + | |||
| + | {{task|1= | ||
| + | |||
| + | Graph theory has so many applications in computational systems biology that being able to compute with graphs in '''R''' is a phantastic asset. This brief tutorial reviews the basics and then covers the igraph package in some detail. It concludes with an exploration of the graph of functional relationships of human proteins from the STRING database. | ||
| + | |||
| + | |||
| + | * Open RStudio | ||
| + | * Select '''File → New Project ...''' | ||
| + | * Choose '''Version control → Git ''' | ||
| + | * Enter the repository URL for the tutorial: https://github.com/hyginn/R_Exercise-Graphs | ||
| + | * Click on '''Create Project'''. | ||
| + | * Start the tutorial by typing <code>init()</code> | ||
| + | |||
| + | }} | ||
| + | |||
| + | |||
| + | {{Vspace}} | ||
| + | |||
| + | {{#lst:CSB_Assignment_Week_1|assignment_footer}} | ||
| + | |||
| + | |||
| + | <table style="width:100%;"><tr> | ||
| + | <td style="height:30px; vertical-align:middle; text-align:left; font-size:80%;">[[CSB_Assignment_Week_4|< Assignment 4]]</td> | ||
| + | <td style="height:30px; vertical-align:middle; text-align:right; font-size:80%;">[[CSB_Assignment_Week_6|Assignment 6 >]]</td> | ||
| + | </tr></table> | ||
[[Category:Computational_Systems_Biology]] | [[Category:Computational_Systems_Biology]] | ||
</div> | </div> | ||
Revision as of 06:13, 29 February 2016
Assignments for Week 5
Graphs !
| < Assignment 4 | Assignment 6 > |
Note! This assignment is currently active. All significant changes will be announced on the mailing list.
Pre-reading
This paper is a good crash-course in concepts of graph theory and their application to biology. It contains a lot of definitions that I don't expect you to learn by heart. But do familiarize yourself with the concepts - they are important to properly work with the R graph tutorial.
| Pavlopoulos et al. (2011) Using graph theory to analyze biological networks. BioData Min 4:10. (pmid: 21527005) |
An R tutorial on biological graphs
Task:
Graph theory has so many applications in computational systems biology that being able to compute with graphs in R is a phantastic asset. This brief tutorial reviews the basics and then covers the igraph package in some detail. It concludes with an exploration of the graph of functional relationships of human proteins from the STRING database.
- Open RStudio
- Select File → New Project ...
- Choose Version control → Git
- Enter the repository URL for the tutorial: https://github.com/hyginn/R_Exercise-Graphs
- Click on Create Project.
- Start the tutorial by typing
init()
- That is all.
Footnotes 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. Success comes from joining the conversation.
- Do consider how to ask your questions so that a meaningful answer is possible. the following two links:
- How to create a Minimal, Complete, and Verifiable example on stackoverflow and ...
- How to make a great R reproducible example
- ... are required reading.
| < Assignment 4 | Assignment 6 > |
