Week 11

This journal entry is due on Tuesday, November 17, at midnight PST. (Monday night/Tuesday morning)

This page is under construction.

Overview

For this week, your team has two main tasks:

1. Prepare for journal club presentations in Weeks 12 and 13
   • You will deeply explore and perform a critical review of the genome paper (coder/QA) and microarray paper (GenMAPP users) for your team's species.
   • You will communicate your findings in an effective oral presentation.
2. Begin initial tasks on your research project
   • Coder/QA
     • Set up coding/testing environment
     • Determine the regular expression for the ordered locus ID for your species
     • Identify the appropriate model organism database for your species.
     • Perform an initial Gene Database export and Gene Database Testing Report
   • GenMAPP Users
     • Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
     • Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
     • Compile the raw data in preparation for normalization and statistical analysis.

Individual Journal Assignment

• Store this journal entry as "username Week 11" (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 journal entry page for this week. 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.

Team Journal Assignment

• Please make the requested changes to your team's wiki pages.
  • Please "comment out" the microarray papers that you won't be using for the project, just leaving the annotated bibliographic information for your genome paper and the microarray paper you will be using.
• Give a short executive summary of each person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
• Set up a system for managing team files, including a filename system that keeps track of versions of files.