Difference between revisions of "GenMAPP User"
From LMU BioDB 2013
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==Guild Members== | ==Guild Members== | ||
| − | * | + | * Dillon |
| + | * Kevin Meilak | ||
| + | * Kevin McGee and Viktoria | ||
| + | * Lauren and Miles | ||
== Milestones == | == Milestones == | ||
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==== Milestone 1 ==== | ==== Milestone 1 ==== | ||
# Find and acquire the microarray paper for your team (done [[Week 10]]). | # Find and acquire the microarray paper for your team (done [[Week 10]]). | ||
| − | #* Link to the | + | #* Provide the proper bibliographic reference for your paper |
| − | #* Upload the pdf version of the paper to the wiki | + | #* 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)''; 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.) | # 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. | # Verify that the gene IDs in the microarray data match the chosen species and '''''strain''''' that is being used to create the .gdb. | ||
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# Document and take notes on test runs with GenMAPP. | # Document and take notes on test runs with GenMAPP. | ||
#* Use the EX.txt file to help the Coders/ID Minders to validate the .gdb | #* 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. | # Create a .mapp file showing one pathway that is changed in your data. | ||
| + | |||
| + | [[Category:Group Projects]] | ||
Latest revision as of 18:29, 19 November 2013
Contents |
[edit] Guild Members
- Dillon
- Kevin Meilak
- Kevin McGee and Viktoria
- Lauren and Miles
[edit] Milestones
The milestones do not necessarily correspond to particular weeks, instead they are sets of tasks grouped together.
[edit] Milestone 1
- Find and acquire the microarray paper for your team (done Week 10).
- Provide the proper bibliographic reference for your paper
- 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); 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
- Upload the microarray data files to the wiki
[edit] 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).
[edit] 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 and your final presentation.
- Create a .mapp file showing one pathway that is changed in your data.
