genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2015-05-12	Add info to warning	pjotrp

2015-05-12	More elaborate handling of finding pylmm	Pjotr Prins

2015-05-12	Move path search into tools.py	pjotrp

2015-05-11	Moving pylmm out of the tree	pjotrp

2014-08-12	Fixed the scrollable data tables for the show trait page	Zachary Sloan
	Added the option to display the rqtl results (and soon other mapping results) as either a manhattan plot or "interval map" style curve chart Removed a couple unnecessary javascript imports Changed the function in helper_functions.py that creates the trait and dataset objects, making it to where the trait object also gets qtl info Fixed color by trait after it was broken by the "scatterplot matrix" function
2014-07-18	Added outlier highlighting	Zachary Sloan
	Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-05-05	Committing a bunch of changes related to integrating GEMMA and	Zachary Sloan
	adding the correlation matrix page
2014-02-27	Began working on a TraitCollection.py file that will contain both the	Zachary Sloan
	object for logged in user collections and collections created by anonymous users.
2013-10-17	Sample objects are now passed to js_data for drawing the correlation	Lei Yan
	scatter plot
2013-10-11	Merge /home/sam/gene	Lei Yan

2013-10-07	Worked on logins, session_ids, flash messages, etc.	Sam

2013-09-13	Merge https://github.com/zsloan/genenetwork	Lei Yan
	Resolved conflicts: wqflask/base/trait.py wqflask/wqflask/correlation/correlationFunction.py wqflask/wqflask/correlation/correlation_function.py wqflask/wqflask/correlation/correlation_functions.py wqflask/wqflask/correlation/show_corr_results.py
2013-07-19	Finished integrating code that reads sample list from geno files	Zachary Sloan
	withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-12	Rewrote code related to getting the tissue correlation column to display	Lei Yan
	Created new files for mrna assay tissue data and commonly used db query related functions
2013-06-20	Added file corr_result_helpers.py that includes the function that	Zachary Sloan
	normalizes the lists of sample values
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	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
2013-05-23	Lots of changes around users	Sam

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
2013-04-18	The plink_input is split into chunks that are stored in temp_data, but	Zachary Sloan
	we might decide to store it differently
2013-04-17	Created file with pickled SNPIterator (from input.py) data	Zachary Sloan
	for HLC datasets Still need to read in file
2013-04-05	Loading bar now correctly shows the time to completion	Zachary Sloan
	and the code seems to run correctly
2013-03-12	Got cashing working with pickle	Zachary Sloan

2013-03-07	Have first 45% of progress bar working	Zachary Sloan
	Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work
2013-03-07	Created file temp_data to store data related to progress	Zachary Sloan
	of the marker regression calculations Storing progress of kinship matrix calculation in variable as portion of 45 (the rough percent of total marker regression calculation time
2013-02-28	Updated benchmark.py to aggregate run times when you run the	Zachary Sloan
	operation(s) multiple times
2013-02-28	Added benchmark.py that compares the time of various operations	Zachary Sloan
	and gives a report with the percent of total computation time each takes
2013-02-19	Made lines for manhattan plot proportional to chromosome lengths	Zachary Sloan

2013-01-31	Changed reference to 'dataset_name' in keywords to 'dataset' to get	Zachary Sloan
	page to work, but will change all references to the dataset name to 'dataset_name' in future to avoid confusion between the dataset name and the actual dataset object
2013-01-22	Pushed through a few errors in getting the correlation page running	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
2012-09-27	Worked on getting attributes in the SampleList object to display data ↵	Zachary Sloan
	properly, changed SampleList from an object list to object
2012-09-26	Worked on implementing the extra attributes feature on the trait data page	Zachary Sloan

2012-08-29	Fixed so that outliers are now correctly highlighted	Zachary Sloan

2012-08-28	Various changes related to the webqtlCaseData object and the way ↵	Zachary Sloan
	values/variances/num_cases are called in DataEditingPage.py
2012-06-22	Working my way through getting the review and edit data dynamically ↵	Sam Ockman
	generated in Jinja2
2012-06-05	Ran reindent.py recursively on wqflask directory	Sam Ockman

2012-06-02	Coming along in trying to get trait page working	Sam Ockman

2012-05-24	Trying to get stuff working under new structure	Sam Ockman