Difference between revisions of "Week 3"
From LMU BioDB 2015
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The purpose of this assignment is: | The purpose of this assignment is: | ||
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| + | # To give you some hands-on practice time with a command-line interface. | ||
| + | # To show you an example of how a manual task can be automated. | ||
| + | # To reinforce the material from the previous week. | ||
== Individual Journal Assignment == | == Individual Journal Assignment == | ||
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**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.''''' | **'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.''''' | ||
* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual wiki page. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook. | * For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual wiki page. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook. | ||
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| + | === Homework Partners === | ||
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| + | ''Not yet assigned.'' | ||
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| + | === The Genetic Code, by Computer === | ||
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| + | Connect to the ''my.cs.lmu.edu'' workstation as shown in class and do the following exercises from there. | ||
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| + | For these exercises, two files are available in the Keck lab system for practice; of course, you can always make your own sequences up. The practice files are ''~dondi/xmlpipedb/data/prokaryote.txt'' and ''~dondi/xmlpipedb/data/infA-E.coli-K12.txt''. | ||
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| + | ==== Complement of a Strand ==== | ||
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| + | Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand. In other words, fill in the question marks: | ||
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| + | cat ''sequence_file'' | ????? | ||
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| + | For example, if ''sequence_file'' contains: | ||
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| + | agcggtatac | ||
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| + | Then your text processing commands should display: | ||
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| + | tcgccatatg | ||
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| + | ==== Reading Frames ==== | ||
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| + | === XMLPipeDB Match Practice === | ||
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== Shared Journal Assignment == | == Shared Journal Assignment == | ||
Revision as of 21:55, 6 September 2015
This journal entry is due on Tuesday, September 22, at midnight PDT. (Thursday night/Friday morning)
Contents
Overview
The purpose of this assignment is:
- To give you some hands-on practice time with a command-line interface.
- To show you an example of how a manual task can be automated.
- To reinforce the material from the previous week.
Individual Journal Assignment
- Store this journal entry as "username Week 3" (i.e., this is the text to place between the square brackets when you link to this page).
- Link from your user page to this Assignment page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
- Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
- For your assignment this week, you will keep an electronic laboratory notebook on your individual wiki page. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
Homework Partners
Not yet assigned.
The Genetic Code, by Computer
Connect to the my.cs.lmu.edu workstation as shown in class and do the following exercises from there.
For these exercises, two files are available in the Keck lab system for practice; of course, you can always make your own sequences up. The practice files are ~dondi/xmlpipedb/data/prokaryote.txt and ~dondi/xmlpipedb/data/infA-E.coli-K12.txt.
Complement of a Strand
Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand. In other words, fill in the question marks:
cat sequence_file | ?????
For example, if sequence_file contains:
agcggtatac
Then your text processing commands should display:
tcgccatatg
Reading Frames
XMLPipeDB Match Practice
- Store your journal entry in the shared Class Journal Week 3 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
- Link to your journal entry from your user page.
- Link back from the journal entry to your user page.
- NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
