genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-06-13	Merge /home/sam/gene into flask	Zachary Sloan
	Conflicts: wqflask/wqflask/templates/index_page.html Merging the code on Sam's branch onto my own
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
2013-06-13	Put the template html for the quick search page when all trait types	Zachary Sloan
	are displayed in a separate file that is included in quick_search.html
2013-06-13	Small changes	Sam

2013-06-12	Fixed a couple issues with the template that caused the	Zachary Sloan
	regular search results and show trait page to not display
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
2013-05-31	Fixed the location column for the quick search page	Zachary Sloan
	Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet)
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

2013-05-23	Added a template	Sam

2013-05-23	Lots of changes around users	Sam

2013-05-21	Added caching to the search page (for both regular and quick searckes)	Zachary Sloan

2013-05-17	Did a little work with quick search page	Zachary Sloan

2013-05-17	Simplification of modal code	Sam
	Created css file to hold modal padding
2013-05-17	Modal windows now working better	Sam
	Going to simplify the code next
2013-05-17	Added flask_security locally	Sam

2013-05-17	More working on security templates	Sam

2013-05-16	Switching between login and register working pretty well	Sam

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)
2013-05-16	Before trying a new modal window	Sam

2013-05-10	Sign in template looking even better	Sam

2013-05-10	Sign in template looking pretty good	Sam

2013-05-10	More security changes	Sam

2013-05-10	Have the beginnings of a user_manager working	Sam

2013-05-09	Just added some print statements so I can show matrix/vector	Zachary Sloan
	shapes to Tony
2013-05-09	Added original security templates (so we can change them)	Sam

2013-05-09	Working on user registration	Sam

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