genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-06-19	:Merge git://github.com/zsloan/genenetwork into flask	Lei Yan
	Conflicts: wqflask/requirements.txt
2013-06-19	Changed QTL parameter name to "get_qtl_info" on trait.py and	Lei Yan
	other places it's called, like search_results.py Added other trait info fields to correlation results page
2013-06-13	Fixed issue where too much memory was used as a result of creating a	Lei Yan
	dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-11	Put trait info for correlation results page into a dictionary instead	Lei Yan
	of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-30	Rewrote some code in get_trait_info in dataset.py	Lei Yan
	Added spearman correlation to show_corr_results and template
2013-05-28	Have correlation values appearing in a table in the template	Lei Yan
	Use scipy to calculate pearson correlation instead of old GN code
2013-05-23	Worked on rewriting the function in data_set.py that gets the sample	Lei Yan
	values for each trait
2013-05-23	Changed the way the query that gets sample ids is generated	Lei Yan

2013-05-23	Now calculates correlation values for traits, but not yet in template	Lei Yan

2013-05-08	Worked on correlation page	Lei Yan
	Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-04-30	Changed path to log file	Lei Yan
	Added server port to configuration file
2013-04-23	Created file correlation_plot.py for the correlation scatterplot	Zachary Sloan
	Reverted temp_data.py to previous version that doesn't include the "part" input (for chunks) Made change to lmm related to splitting main iterator into chunks Deleted a bunch of unnecessary commented out code from show_trait.py
2013-04-19	Fixed the issue with the x-axis coordinates for marker regression plot	Zachary Sloan

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