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2013-04-17Wrote code that tests the effectiveness of the function that divides aZachary Sloan
list into a given number of chunks
2013-04-17Fixed small issue with the divide_into_chunks functionZachary Sloan
that caused one too many chunks to be created
2013-04-16Wrote functions that divide a list into a specified number of chunksZachary Sloan
(to be used on the list of snps for the LMM code)
2013-04-16Checking in before making some changesZachary Sloan
2013-04-16Put most of the code calculating human association statistics inZachary Sloan
lmm.py into a separate function
2013-04-11Fixed a bug with quick_search_table.pyZachary Sloan
Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines
2013-04-10Created template for quick search pageZachary Sloan
Fixed a couple bugs with quick_search_table.py
2013-04-09Have quick search working for phenotypesZachary Sloan
2013-04-09Nick's code works fine with human dataZachary Sloan
Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05Loading bar now correctly shows the time to completionZachary Sloan
and the code seems to run correctly
2013-04-05Made change to nginx config file that seems to have fixed theZachary Sloan
504 gateway timeout issue with the human datasets
2013-04-05Got Nick's code working with the MDP datasets under the BXD group,Zachary Sloan
but with only BXD strains
2013-04-05Made changes to get pylmm code working with HMDP datasetsZachary Sloan
2013-04-02Finished adding code that uses the plink genotype data ifZachary Sloan
a human dataset and json data if any other species
2013-04-02Committing before splitting code that runs pylmm with plink filesZachary Sloan
and code that runs it with json
2013-04-02pylmm code is running for human data (plink .bed genotype files)Zachary Sloan
2013-03-28quick_search_table.py seems to be running OK for the PublishXRefZachary Sloan
table, but will need to check later to make sure
2013-03-28quick_search_table.py now seems to run correctly for ProbeSetXRefZachary Sloan
rows
2013-03-28Committing before putting quick_search_table code in classesZachary Sloan
2013-03-27Got quick_search_table.py to a point where it runs; willZachary Sloan
know tomorrow whether it ran correctly or not
2013-03-27Worked on trying to get results for quick search to displayZachary Sloan
2013-03-26Continued working on quick_search_table.py, which now getsZachary Sloan
all of the terms from the ProbeSet table to be included in the quick search
2013-03-26Created quick_search_table.py to create table with all of theZachary Sloan
information needed for the the quick search features (which searches across all datasets)
2013-03-26Just checking in code while in the process of trying to getZachary Sloan
the quick search working properly
2013-03-22Began creating templates for login/registrationZachary Sloan
2013-03-22Added secure_server.pyZachary Sloan
Updated notes.txt
2013-03-22Removed zach_settings.py from git trackingZachary Sloan
Changed mysql password as a result of it being up on git before
2013-03-21Did some work towards getting Nick's code working with our plinkZachary Sloan
human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot
2013-03-19In the process of trying to use Nick's pylmmKinship.py code toZachary Sloan
precompute the kinship matrix for the human datasets we have plink .bed genotype data for
2013-03-19Added Nick's input.py file which uses plink .ped files as inputZachary Sloan
for his pylmm code
2013-03-19Searches work for the full access human datasets with mRNA assayZachary Sloan
searches, and the trait page can be loaded Need to get marker regression page working with human data now
2013-03-15Began work with implementing general searchZachary Sloan
2013-03-15Changes related to searching for selected points in marker regression plotZachary Sloan
2013-03-13Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-03-13Added some to notesZachary Sloan
2013-03-12Added the script generating probesetfreeze data matrix filesZachary Sloan
The script was created to regenerate a bad file for Evan
2013-03-12Highlighting points works in Firefox but still doesn't work in chromeZachary Sloan
Also noticed issue with chromosome ordering in Firefox
2013-03-12Got cashing working with pickleZachary Sloan
2013-03-09Trying to get caching working with pickle nowZachary Sloan
2013-03-08Caching is working for marker regression but really slowlyZachary Sloan
2013-03-08Refactored GWAS function in lmm.pyZachary Sloan
2013-03-07Progress bar is now completely workingZachary Sloan
Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code
2013-03-07Have first 45% of progress bar workingZachary Sloan
Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work
2013-03-07Created file temp_data to store data related to progressZachary Sloan
of the marker regression calculations Storing progress of kinship matrix calculation in variable as portion of 45 (the rough percent of total marker regression calculation time
2013-03-06Stored percent of calculate_kinship function completion inZachary Sloan
variable
2013-03-06Improved positioning/size of copy/print/save buttons forZachary Sloan
marker regression table
2013-03-05Implemented DataTables; there are now options to download the markerZachary Sloan
regression result table in various formats
2013-03-02Created generate_probesetfreeze_file to create theZachary Sloan
"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-28Updated benchmark.py to aggregate run times when you run theZachary Sloan
operation(s) multiple times
2013-02-28Added benchmark.py that compares the time of various operationsZachary Sloan
and gives a report with the percent of total computation time each takes
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