genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-05-16	Made the first level of quick search tabs species, followed by	Zachary Sloan
	trait type (was the opposite before Rob commented on it earlier today)
2013-05-09	Just added some print statements so I can show matrix/vector	Zachary Sloan
	shapes to Tony
2013-05-08	Merge branch 'flask' of git://github.com/leiyan/genenetwork into flask	Zachary Sloan

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
2013-05-07	Made some progress adding species/group tabs to the quick search result page to	Zachary Sloan
	make the results easier to navigate
2013-05-02	Got quick search code running (but not displaying properly)	Zachary Sloan
	Code that processes subset of snps works, in process of putting into a class
2013-04-30	Merge branch 'flask' of git://github.com/leiyan/genenetwork into flask	Zachary Sloan

2013-04-30	Changed path to log file	Lei Yan
	Added server port to configuration file
2013-04-30	Did a little with correlation_plot.py	Zachary Sloan

2013-04-26	Added file that checks how much time is added to a loop's runtime by print ↵	Zachary Sloan
	statements Continued work on file that processes each individual chunk of the snp iterator/plink input
2013-04-24	Began writing code that writes some objects used in LMM to redis	Zachary Sloan
	and writes/reads eachitem in the plink_input
2013-04-24	Added original pylintrc	Zachary Sloan

2013-04-24	Checking in quick_search_table.py before using pylin	Zachary Sloan

2013-04-24	Fixed issue with the part of quick_search_table.py that loads phenotype traits	Zachary Sloan

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