Week 8 - Revision history

Kdahlquist: clarification about electronic lab notebook

2013-10-08T22:32:55Z

clarification about electronic lab notebook

Kdahlquist: /* Reflection */ raised the heading level by one

2013-10-08T21:05:32Z

‎Reflection: raised the heading level by one

Kdahlquist: removed under construction notice from assignment

2013-10-08T21:05:00Z

removed under construction notice from assignment

Kdahlquist: /* Downloading and installing the GenMAPP and MAPPFinder Software */ instructions to download vibrio databases

2013-10-08T19:15:25Z

‎Downloading and installing the GenMAPP and MAPPFinder Software: instructions to download vibrio databases

Kdahlquist: /* Reflection */ fixed date on Merrell paper

2013-10-08T19:03:00Z

‎Reflection: fixed date on Merrell paper

Kdahlquist: /* MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2) */ started new section on how to install GenMAPP/MAPPFinder

2013-10-08T19:02:40Z

‎MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2): started new section on how to install GenMAPP/MAPPFinder

Kdahlquist: /* Overview of Microarray Data Analysis */ designated parts 1 and 2

2013-10-08T19:01:39Z

‎Overview of Microarray Data Analysis: designated parts 1 and 2

Kdahlquist: /* Overview of Microarray Data Analysis */ note to which steps we are doing

2013-10-08T19:01:17Z

‎Overview of Microarray Data Analysis: note to which steps we are doing

Kdahlquist: removed extra blank line

2013-10-08T18:59:36Z

removed extra blank line

Kdahlquist: copied overview of microarray data analysis from openwetware

2013-10-08T18:59:14Z

copied overview of microarray data analysis from openwetware

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 * Keep an "electronic lab notebook", containing your methods, results, and interpretations of the ''Vibrio cholerae'' microarray analysis [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2] in your "''username'' Week 8" journal page. Although you will have assigned partner(s), you will need to fill out your own individual journal page.
 ** Be sure to answer any questions embedded in the protocol in your journal page.
 * Upload the requested files from [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae part 1] and [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols part 2] to this wiki and link to them on your individual journal page.

@@ Line 86: / Line 86: @@
 * Optional: for more information on the Duke saga, see the web site put together by Baggerly and Coombes [http://bioinformatics.mdanderson.org/Supplements/ReproRsch-All/Modified/StarterSet/ here].
-==== Reflection ====
+=== Reflection ===
 * What were the main issues with the data and analysis identified by Baggerly and Coombs?  What best practices enumerated by DataONE were violated?  Which of these did Dr. Baggerly claim were common issues?

← Older revision		Revision as of 21:05, 8 October 2013
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−	~~{{Under Construction}}~~
−
	'''This journal entry is due on Friday, October 18, at midnight PDT.''' ''(Thursday night/Friday morning)'' Note that there is an interim deadline for uploading your files from part 1 by midnight, Monday, October 14. ''(Sunday night/Monday morning)''		'''This journal entry is due on Friday, October 18, at midnight PDT.''' ''(Thursday night/Friday morning)'' Note that there is an interim deadline for uploading your files from part 1 by midnight, Monday, October 14. ''(Sunday night/Monday morning)''

← Older revision		Revision as of 19:15, 8 October 2013
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	==== Downloading and installing the GenMAPP and MAPPFinder Software ====		==== Downloading and installing the GenMAPP and MAPPFinder Software ====
		+
		+	* We will be using GenMAPP and MAPPFinder version 2.1 (http://genmapp.org). This software is already installed on the Windows machines in the Keck lab annex and in the Seaver 120 computer lab.
		+	** This version is now called "GenMAPP Classic" and can be downloaded [http://www.genmapp.org/download_v2.1.php from this page].
		+	** Follow the instructions in the installer.
		+	** During installation, the installer will open a window called the GenMAPP Data Acquisition Tool. It will not function because it cannot connect to the server. This is OK, you will download your ''Vibrio cholerae'' Gene Database from the XMLPipeDB project at SourceForge.org.
		+	*** Half of the class will use the Vc-Std_External_20090622.gdb Gene Database that was created by the Fall 2008 Biological Databases class.
		+	**** To download this Gene Database, [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020090622/Vc-Std_External_20090622.zip/download follow '''''this link''''' to the XMLPipeDB SourceForge Download page].
		+	*** Half of the class will use a more recent Vc-Std_External_20101022.gdb Gene Database that was created by Drs. Dahlquist and Dionisio in 2010.
		+	**** To download this Gene Database, [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download follow '''''this link''''' to the XMLPipeDB SourceForge Download page].
		+	*** The members of a pair should each choose a different gene database.
		+	* Click on the link for the Gene Database to which you have been assigned, download the file, and save it into the folder C:\GenMAPP 2 Data\Gene Databases (if you accepted the default folders during the installation), and extract it.

	=== Groups ===		=== Groups ===

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 * What recommendations does Dr. Baggerly recommend for reproducible research?  How do these correspond to what DataONE recommends?
 * Do you have any further reaction to this case after viewing Dr. Baggerly's talk?
-* Look at the methods and results described in the [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2020)] paper.  Do you think there is sufficient information there to reproduce their data analysis?  Why or why not?
+* Look at the methods and results described in the [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002)] paper.  Do you think there is sufficient information there to reproduce their data analysis?  Why or why not?
 <!--

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 * We will begin this analysis in class on Tuesday, October 15.
 * The detailed instructions can be found on the [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols GenMAPP and MAPPFinder Protocols page] hosted by [http://www.openwetware.org OpenWetWare.org].
 === Groups ===

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 # Map onto biological pathways (we will use GenMAPP for this)
-In this week's exercise, we will do steps 5-7 (in Microsoft Excel) and 9 (using GenMAPP & MAPPFinder).
+In this week's exercise, we will do steps 5-7 (part 1, using Microsoft Excel) and 9 (part 2, using GenMAPP & MAPPFinder).
 === Statistical Analysis of ''Vibrio cholerae'' Microarray Data (Part 1) ===

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 * [http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.(2000) Gene Ontology: tool for the unification of biology.  ''Nature Genetics''  25: 25-29.]
 *  [http://genomebiology.com/content/4/1/R7 Doniger, S.W., Salomonis, N., Dahlquist, K.D., Vranizan, K., Lawlor, S.C., Conklin, B.R. (2003) MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data.  ''Genome Biology'' 4:R7.]
 === Statistical Analysis of ''Vibrio cholerae'' Microarray Data (Part 1) ===