genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-03-22	Removed zach_settings.py from git tracking	Zachary Sloan
	Changed mysql password as a result of it being up on git before
2013-03-21	Did some work towards getting Nick's code working with our plink	Zachary Sloan
	human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot
2013-03-19	In the process of trying to use Nick's pylmmKinship.py code to	Zachary Sloan
	precompute the kinship matrix for the human datasets we have plink .bed genotype data for
2013-03-19	Added Nick's input.py file which uses plink .ped files as input	Zachary Sloan
	for his pylmm code
2013-03-19	Searches work for the full access human datasets with mRNA assay	Zachary Sloan
	searches, and the trait page can be loaded Need to get marker regression page working with human data now
2013-03-15	Began work with implementing general search	Zachary Sloan

2013-03-15	Changes related to searching for selected points in marker regression plot	Zachary Sloan

2013-03-13	Merge branch 'flask' of http://github.com/zsloan/genenetwork into flask	Zachary Sloan

2013-03-13	Added some to notes	Zachary Sloan

2013-03-12	Added the script generating probesetfreeze data matrix files	Zachary Sloan
	The script was created to regenerate a bad file for Evan
2013-03-12	Highlighting points works in Firefox but still doesn't work in chrome	Zachary Sloan
	Also noticed issue with chromosome ordering in Firefox
2013-03-12	Got cashing working with pickle	Zachary Sloan

2013-03-09	Trying to get caching working with pickle now	Zachary Sloan

2013-03-08	Caching is working for marker regression but really slowly	Zachary Sloan

2013-03-08	Refactored GWAS function in lmm.py	Zachary Sloan

2013-03-07	Progress bar is now completely working	Zachary Sloan
	Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code
2013-03-07	Have first 45% of progress bar working	Zachary Sloan
	Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work
2013-03-07	Created file temp_data to store data related to progress	Zachary 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
2013-03-06	Stored percent of calculate_kinship function completion in	Zachary Sloan
	variable
2013-03-06	Improved positioning/size of copy/print/save buttons for	Zachary Sloan
	marker regression table
2013-03-05	Implemented DataTables; there are now options to download the marker	Zachary Sloan
	regression result table in various formats
2013-03-02	Created generate_probesetfreeze_file to create the	Zachary Sloan
	"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-28	Updated benchmark.py to aggregate run times when you run the	Zachary Sloan
	operation(s) multiple times
2013-02-28	Added benchmark.py that compares the time of various operations	Zachary Sloan
	and gives a report with the percent of total computation time each takes
2013-02-28	Chromosome labels on marker regression plot are centered	Zachary Sloan
	Tick marks are now correct and in intervals of 25 for each chromosome
2013-02-23	A static progress bar now displays when loading the marker regression results	Zachary Sloan

2013-02-22	Added some to notes	Zachary Sloan

2013-02-21	Added underscore.js	Zachary Sloan

2013-02-21	Adding genotypes and new_genotypes (json files) directories to git	Zachary Sloan
	so they can be pulled to the new EC2 server
2013-02-21	Add my_pylmm package	Zachary Sloan

2013-02-21	Plot points and chromosome lines are now correct	Zachary Sloan

2013-02-20	Did more work with manhattan plot, trying to fix a small issue	Zachary Sloan
	with the location of points on the x-axis
2013-02-20	Created y-axis	Zachary Sloan
	Split create_graph into many functions Added a buffer to the x and y dimensions in order to add tick labels for the x and y axis
2013-02-19	Manhattan plot and chromosome lines are all correct now	Zachary Sloan
	Hovering over a point automatically searches for its corresponding marker in the data table Added headers for the plot and table
2013-02-19	Made lines for manhattan plot proportional to chromosome lengths	Zachary Sloan

2013-02-15	Points are labeled with marker names and hovering causes the LRS	Zachary Sloan
	value to appear above the plot
2013-02-15	Made it to where hovering over a point in the manhattan plot changes	Zachary Sloan
	its style
2013-02-15	Created lines in marker regression scatter plot separating	Zachary Sloan
	chromosomes
2013-02-14	Put coffeescript code for manhattan plot into a class/functions	Zachary Sloan

2013-02-14	Have marker regression results displaying as a scatterplot (just the points)	Zachary Sloan
	using d3.js
2013-02-13	Got results displaying for BXD and fixed genofile_parser.py to work	Zachary Sloan
	for all of our genofiles
2013-02-13	Got results for marker regression page displaying in table	Zachary Sloan

2013-02-13	Fixed some bugs related to getting the marker regression page working	Zachary Sloan
	with Nick's code
2013-02-12	Edited marker_regression.py and data_set.py to store the p-values	Zachary Sloan
	and their corresponding markers to be used in the table of qtl results and other figures
2013-02-08	Converted .geno files to json files and wrote code in marker_regression.py	Zachary Sloan
	that loads the json files, converts them into the relevant numpy arrays, and passes them into Nick's code (which is returning results that may or may not be correct, but is at least running)
2013-02-07	Added code to marker_regression.py that creates the numpy arrays to	Zachary Sloan
	pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited
2013-02-06	Edited genofile_parser.py to go through all genofiles and convert	Zachary Sloan
	them to the format used by nick's code
2013-02-06	Added changes to example.py and prep_data.py that lets nick's code read in	Zachary Sloan
	our data
2013-02-06	Small change to search_results.py to get search results page to work	Zachary Sloan

2013-01-31	Added wqflask-nginx.conf	Zachary Sloan