To do list for dissertation 8-16-13

2015-01-13

To do list for dissertation 8-16-13

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

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"

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