GenMAPP User - Revision history

Kmeilak: /* Guild Members */

2013-11-19T18:29:49Z

‎Guild Members

Kdahlquist: /* Milestone 1 */ deleted correspondence item because it's found in milestone 2

2013-11-06T18:42:35Z

‎Milestone 1: deleted correspondence item because it's found in milestone 2

Kdahlquist: /* Milestone 1 */ added create table for correspondence between data and samples

2013-11-06T18:41:52Z

‎Milestone 1: added create table for correspondence between data and samples

Kdahlquist: /* Guild Members */ added guild members

2013-11-05T18:26:24Z

‎Guild Members: added guild members

Kdahlquist: /* Future Milestones */ note that outline useful for final presentation also

2013-10-18T19:43:02Z

‎Future Milestones: note that outline useful for final presentation also

Kdahlquist: /* Milestone 1 */ note about citation and copyright

2013-10-18T19:42:20Z

‎Milestone 1: note about citation and copyright

Kdahlquist: added category for group projects

2013-10-18T19:16:06Z

added category for group projects

Dondi: Initial transcription of this page.

2013-07-02T18:14:48Z

Initial transcription of this page.

New page

* [[Gene Database Project]]
* [[Gene Database Project Report Guidelines]]

==Guild Members==

* ''To be determined.''

== Milestones ==

The milestones do not necessarily correspond to particular weeks, instead they are sets of tasks grouped together.

==== Milestone 1 ====
# Find and acquire the microarray paper for your team (done [[Week 10]]).
#* Link to the online version of the paper on the journal web site
#* Upload the pdf version of the paper to the wiki
# Download microarray data in it's "rawest" form that you can find. (Consult with Dr. Dahlquist about this.)
# Verify that the gene IDs in the microarray data match the chosen species and '''''strain''''' that is being used to create the .gdb.
#* This last task needs to be done in conjunction with the Quality Assurance person and Coder.
# File management: on your team's home page
#* Link to the source of the microarray data
#* Upload the microarray data files to the wiki

==== Milestone 2 ====

# Read the microarray paper to understand the experiment.
# Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
# Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
# Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
# Consult with Dr. Dahlquist on how to process the data (normalization, statistics).

==== Future Milestones ====

# Perform the statistical analysis in Excel
# Format the gene expression data for import into GenMAPP.
# Import data into GenMAPP, create ColorSets, and run MAPPFinder.
# Document and take notes on test runs with GenMAPP.
#* Use the EX.txt file to help the Coders/ID Minders to validate the .gdb
# Do a journal club outline of the paper so that you can use it in the Discussion section of your group report.
# Create a .mapp file showing one pathway that is changed in your data.

@@ Line 5: / Line 5: @@
 * Dillon
-* Kevin Meilek
+* Kevin Meilak
 * Kevin McGee and Viktoria
 * Lauren and Miles

← Older revision		Revision as of 19:16, 18 October 2013
Line 38:		Line 38:
	# Do a journal club outline of the paper so that you can use it in the Discussion section of your group report.		# Do a journal club outline of the paper so that you can use it in the Discussion section of your group report.
	# Create a .mapp file showing one pathway that is changed in your data.		# Create a .mapp file showing one pathway that is changed in your data.
		+
		+	[[Category:Group Projects]]

@@ Line 21: / Line 21: @@
 # Verify that the gene IDs in the microarray data match the chosen species and '''''strain''''' that is being used to create the .gdb.
 #* This last task needs to be done in conjunction with the Quality Assurance person and Coder.
 # File management: on your team's home page
 #* Link to the source of the microarray data

@@ Line 16: / Line 16: @@
 # Find and acquire the microarray paper for your team (done [[Week 10]]).
 #* Provide the proper bibliographic reference for your paper
-#* Link to the online version of the paper on the journal web site
+#* Link to the HTML version of the paper on the journal web site
-#* Upload the pdf version of the paper to the wiki ''(if no copyright restrictions)''
+#* Upload the pdf version of the paper to the wiki ''(if no copyright restrictions)''; otherwise provide a download link to the publisher site.
 # Download microarray data in it's "rawest" form that you can find.  (Consult with Dr. Dahlquist about this.)
 # Verify that the gene IDs in the microarray data match the chosen species and '''''strain''''' that is being used to create the .gdb.
 #* This last task needs to be done in conjunction with the Quality Assurance person and Coder.
 # File management: on your team's home page
 #* Link to the source of the microarray data

@@ Line 4: / Line 4: @@
 ==Guild Members==
-* ''To be determined.''
+* Dillon
 == Milestones ==

@@ Line 37: / Line 37: @@
 # Document and take notes on test runs with GenMAPP.
 #* Use the EX.txt file to help the Coders/ID Minders to validate the .gdb
-# Do a journal club outline of the paper so that you can use it in the Discussion section of your group report.
+# Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
 # Create a .mapp file showing one pathway that is changed in your data.
 [[Category:Group Projects]]