genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-04-18	The plink_input is split into chunks that are stored in temp_data, but	Zachary Sloan
	we might decide to store it differently
2013-04-18	LMM code now reads in gzipped pickled plink snp iterator object	Zachary Sloan

2013-04-18	input file is now loaded by pickle	Zachary Sloan

2013-04-17	Created file with pickled SNPIterator (from input.py) data	Zachary Sloan
	for HLC datasets Still need to read in file
2013-04-17	Added a benchmark for running the chunks code on the list of snps	Zachary Sloan

2013-04-17	Renamed chunk_test.py to chunks.py	Zachary Sloan

2013-04-17	Updated chunk_test.py	Zachary Sloan

2013-04-17	Added chunk_test.py which compared my/ and sam's split into	Zachary Sloan
	chunks algorithms' accuracy/speed
2013-04-17	Wrote code that tests the effectiveness of the function that divides a	Zachary Sloan
	list into a given number of chunks
2013-04-17	Fixed small issue with the divide_into_chunks function	Zachary Sloan
	that caused one too many chunks to be created
2013-04-16	Wrote functions that divide a list into a specified number of chunks	Zachary Sloan
	(to be used on the list of snps for the LMM code)
2013-04-16	Checking in before making some changes	Zachary Sloan

2013-04-16	Put most of the code calculating human association statistics in	Zachary Sloan
	lmm.py into a separate function
2013-04-11	Fixed a bug with quick_search_table.py	Zachary Sloan
	Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines
2013-04-10	Created template for quick search page	Zachary Sloan
	Fixed a couple bugs with quick_search_table.py
2013-04-09	Have quick search working for phenotypes	Zachary Sloan

2013-04-09	Nick's code works fine with human data	Zachary Sloan
	Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05	Loading bar now correctly shows the time to completion	Zachary Sloan
	and the code seems to run correctly
2013-04-05	Made change to nginx config file that seems to have fixed the	Zachary Sloan
	504 gateway timeout issue with the human datasets
2013-04-05	Got Nick's code working with the MDP datasets under the BXD group,	Zachary Sloan
	but with only BXD strains
2013-04-05	Made changes to get pylmm code working with HMDP datasets	Zachary Sloan

2013-04-02	Finished adding code that uses the plink genotype data if	Zachary Sloan
	a human dataset and json data if any other species
2013-04-02	Committing before splitting code that runs pylmm with plink files	Zachary Sloan
	and code that runs it with json
2013-04-02	pylmm code is running for human data (plink .bed genotype files)	Zachary Sloan

2013-03-28	quick_search_table.py seems to be running OK for the PublishXRef	Zachary Sloan
	table, but will need to check later to make sure
2013-03-28	quick_search_table.py now seems to run correctly for ProbeSetXRef	Zachary Sloan
	rows
2013-03-28	Committing before putting quick_search_table code in classes	Zachary Sloan

2013-03-27	Got quick_search_table.py to a point where it runs; will	Zachary Sloan
	know tomorrow whether it ran correctly or not
2013-03-27	Worked on trying to get results for quick search to display	Zachary Sloan

2013-03-26	Continued working on quick_search_table.py, which now gets	Zachary Sloan
	all of the terms from the ProbeSet table to be included in the quick search
2013-03-26	Created quick_search_table.py to create table with all of the	Zachary Sloan
	information needed for the the quick search features (which searches across all datasets)
2013-03-26	Just checking in code while in the process of trying to get	Zachary Sloan
	the quick search working properly
2013-03-22	Began creating templates for login/registration	Zachary Sloan

2013-03-22	Added secure_server.py	Zachary Sloan
	Updated notes.txt
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