To do list for dissertation 8-16-13

2015-01-13

-make a program that can automate analysis pipeline (AutomaticAbStatAnalysisPipeline)
--for sample classification. . randomly assign classes multiple times and record a standard deviation
--perform classification using peptides with an intensity less than 2,000
--maybe look at the same type of peptide removal analysis with another dataset
--I don't think I'll do this, and I have submitted my dissertation 04-26-2014d1120
-maybe look at comparing samples from different sources and see if the entropy is still the same (related to Bart's question)
--I don't think I'll do this, and I have submitted my dissertation 04-26-2014d1120

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Backlinks
"F:\kurt\storage\CIM Research Folder\DR\2013\8-10-13\azim58 wikispaces download as of 8-10-13\Dissertation Portal started 8-20-12.txt"

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Some finished to do list items (newest top to oldest bottom)

-finish getting immunosignaturing data for each section (especially the non-disease sections now)
--don't have background info for "3.2.3	6 day timecourse", "3.4	Reduction in antibody repertoire complexity with lymphoma"
---e-mail from Bart: https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/1448a2ee0f69d6e9
-possibly look at entropy of normal and cancer mice from my cDNA library (04-03-2014d1444)
-see which requirements from grad college format manual I am meeting (finished 4-1-14)
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-31-2014d1348\Requirements from grad college manual 03-31-2014d1452.xlsx"
--shorten acknowledgements section
---spreadsheet to keep track of shortening acknowledgements section
----C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\12-3-13\Acknowledgements for dissertation 12-03-2013d1103.xlsx
-add legends to every figure
{
count post 03-30-2014d1533
{
how many figures have figure legends 03-19-2014d2313 from ch 2 on
llllllllllllllllllllllllllllllllllllllllllllllllllllllllll
57

how many don't have

0
(Chapter 2 is done; Chapter 3 is done; Chapter 4 is done; Appendix A is done; Appendix B is done; Appendix C is done; Appendix E is done)
-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\03-31-2014d1348\Tracking table and figure legends 03-31-2014d1348.xlsx"
}
count pre 03-30-2014d1532
{
how many figures have figure legends 03-19-2014d2313 from ch 2 on
lllllllllllllllllllllllllllll
29

how many don't have
lllllllllllllllllllllllllllll
29
}
}
-address this issue: //I could put some information about troubleshooting the protein production in a 96 well plate here (finished)
-label figure near this phrase: antibody was applied to the three million component tumor library array demonstrated that the SMC1Afs containing lysate pools were selectively (this was actually already labeled, but I just didn't realize this when I added this to the to do list (03-30-2014d1113)
-remove the phrase "random peptide" 03-29-2014d1022
-continue making headers one more level down (start from "Reduction in antibody repertoire complexity. . ." 03-28-2014d1621
-remember to remove format advising tool page at the end of dissertation 03-28-2014d1621
-fix errors in figure cross references 03-19-2014d1939
-add details/description to every caption in dissertation 03-18-2014d2301
-maybe look at poly-specific antibodies from Rebecca.  I think I've decided not to use this data as of 03-06-2014d1641.
-maybe look into whether the trend between breast cancer and normal changed with the peptide removal graphs (finished 03-05-2014d1429)
-analyze intensity values as highest intensity features are removed 02-26-2014d1622
-analyze different bin sizes (and bin sizes that change according to the noise (I think I won't look at this part)). . also look at the amount of variation in different intensity regions 02-25-2014d1605
-add lowest intensity peptide data to dissertation
-send lung cancer analysis to Phil. . 02-17-2014d1634
-read through dissertation and plan out speech for presentation
-finish going through last few biological entropy type papers for review section (immunology paper part needs to be written)
-try a half training half test with AbStat for at least one of the experiments (maybe HT330K first chip disease dataset)
-make a better graph for aged and young samples
-add specific peptide age analysis to dissertation and presentation

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