genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-06-27	Created a group manager page where user administrators can create	Zachary Sloan
	groups of datasets to give/add read privileges to
2013-06-26	Moved code creating DataSets object to a function in dataset.py	Zachary Sloan
	Added caching to creating DataSets object
2013-06-26	Got code that creates DataSets object running	Zachary Sloan
	Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases
2013-06-25	Added DataSets class to dataset.py that will be used to create list of	Zachary Sloan
	confidential datasets
2013-06-21	Fixed bug where cursor was still being used in query	Zachary Sloan

2013-06-20	Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask	Zachary Sloan
	Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py
2013-06-19	Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columns	Lei Yan
	in the correlation page weren't displaying
2013-06-19	Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask	Lei Yan
	Conflicts: wqflask/base/data_set.py
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
2013-06-19	Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask	Zachary Sloan
	Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page
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
2013-06-12	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

2013-05-09	Just added some print statements so I can show matrix/vector	Zachary Sloan
	shapes to Tony
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
2013-04-17	Created file with pickled SNPIterator (from input.py) data	Zachary Sloan
	for HLC datasets Still need to read in file
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	Made changes to get pylmm code working with HMDP datasets	Zachary Sloan

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

2013-03-19	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
2013-03-12	Added the script generating probesetfreeze data matrix files	Zachary Sloan
	The script was created to regenerate a bad file for Evan
2013-03-12	Got cashing working with pickle	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
2013-03-02	Created generate_probesetfreeze_file to create the	Zachary Sloan
	"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-22	Added some to notes	Zachary Sloan

2013-02-14	Have marker regression results displaying as a scatterplot (just the points)	Zachary Sloan
	using d3.js
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
2013-02-07	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
2013-01-31	Changed fd to kw in search_results.py, commented out some lines	Zachary Sloan
	related to fd
2013-01-25	Fixed a few bugs while trying to get the code running on the new server	Zachary Sloan

2013-01-18	Renamed CorrelationPage.py to show_corr_results.py	Zachary Sloan
	Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places
2013-01-08	Created IndChromosome class in species.py and wrote functions for	Zachary Sloan
	chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08	Deleted some unnecessary code in marker_regression.py and fixed some bugs	Zachary Sloan
	Added a couple utility functions to the Chromosomes class in species.py
2013-01-03	Began working on marker_regression.py and created Chromosomes class	Zachary Sloan
	in species.py
2013-01-03	Created template for marek regression page and made the compute button direct	Zachary Sloan
	to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-18	Created new file species.py and species class object TheSpecies	Zachary Sloan
	Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
2012-12-07	Got basic statistics in show_trait to display the correct number	Zachary Sloan
	of samples for each group Got show_trait page to display for genotype traits
2012-12-06	Added minimum/maximum to basic statistics table	Zachary Sloan
	Continued bug-shooting related to getting show_trait running with phenotype traits
2012-12-06	Got show_trait running again for MrnaAssay traits	Zachary Sloan

2012-12-06	Made many small changes to show_trait/data_set/search_results/trait to	Zachary Sloan
	remove use of the formData object and cursor
2012-12-05	Renamed webqtlTrait.py to trait.py	Zachary Sloan
	Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough)