genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-01-31	Added wqflask-nginx.conf	Zachary Sloan

2013-01-31	Copied over nginx.conf from /etc/nginx	Zachary Sloan

2013-01-31	Merge branch 'flask' of http://github.com/zsloan/genenetwork into flask	Zachary Sloan

2013-01-31	Deleted nginx.conf from the other_conf directory not in wqflask	Zachary Sloan

2013-01-31	Merge branch 'flask' of https://github.com/zsloan/genenetwork into flask	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
2013-01-31	Changed fd to kw in search_results.py, commented out some lines	Zachary Sloan
	related to fd
2013-01-25	Added a bunch of things to notes	Zachary Sloan

2013-01-25	Merge branch 'flask' of http://github.com/zsloan/genenetwork into flask	Zachary Sloan

2013-01-25	Fixed a few bugs while trying to get the code running on the new server	Zachary Sloan

2013-01-24	Added a lot to the notes in the process of setting up on the	Zachary Sloan
	new server
2013-01-23	Added a bunch to notes and created new notes file specifically	Zachary Sloan
	related to installing a new instance of GN
2013-01-22	Added a couple things to notes regarding installing mysql client	Zachary Sloan

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
2013-01-11	Commented out import of rpy2 in correlationFunction.py due to	Zachary Sloan
	problem with rpy2
2013-01-11	Upgraded packages requirements.txt but haven't tested	Zachary Sloan

2013-01-11	Overwrote requirements.txt	Zachary Sloan

2013-01-11	Trimmed a bunch of code off of marker_regression.py	Zachary Sloan

2013-01-10	Checking in before we try to write our own code for the manhattan	Zachary Sloan
	plot figure`
2013-01-10	Checking in before trying to put manhattan plot sections closer together	Zachary Sloan

2013-01-10	Normalized the y axis for each manhattan plot section	Zachary Sloan

2013-01-10	The plots now correctly appear above/below each other.	Zachary Sloan
	Committing before trying to combine all the manhattan plot segments
2013-01-10	Edited marker_regression.coffee to make every sub-manhattan plot	Zachary Sloan
	for each chromosome display Created css file for the marker_regression page Currently has display issue where the permutation histogram is overlapping with the manhattan plot
2013-01-10	Made Chromosome class in marker_regression.coffee; current	Zachary Sloan
	it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that.
2013-01-10	Made x-axis values into ints; committing before trying to add multiple graphs	Zachary Sloan
	for each chromosome
2013-01-10	Worked with the manhattan plot coffeescript to set x-axis and change	Zachary Sloan
	the plot point sizes and remove lines
2013-01-09	Manhattan plot results are appearing correctly for chromosome 1	Zachary Sloan

2013-01-09	The histogram coffeescript is now in its own class and the graph	Zachary Sloan
	still displays correctly
2013-01-09	Checking in before putting the histogram coffeescript into its own	Zachary Sloan
	class
2013-01-09	More or less finished the permutation histogram	Zachary Sloan

2013-01-09	Got the permutation plot working as a line plot; still need to make	Zachary Sloan
	it into a bar graph, though
2013-01-09	jqplot added	Zachary Sloan

2013-01-09	Got the marker regression page to display again	Zachary Sloan
	Passed lrs_array values as js_data for the permutation histogram
2013-01-08	js_data is being printed out (seemingly) correctly now for the	Zachary Sloan
	marker_regression page
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
2013-01-04	Continued rewriting marker_regression.py code	Zachary Sloan

2013-01-04	Correct results are being returned from reaper for the marker regression page	Zachary Sloan

2013-01-03	Began working on marker_regression.py and created Chromosomes class	Zachary Sloan
	in species.py
2013-01-03	marker_regression page is up again	Zachary Sloan

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
2012-12-20	Changed layout of marker regression options	Zachary Sloan

2012-12-20	The control locus field in the interval mapping settings is now disabled if	Zachary Sloan
	"choose closest control" is set to "yes"
2012-12-20	Made composite mapping options show/hide for the interval mapping section	Zachary Sloan

2012-12-20	More changes to the layout of interval mapping options	Zachary Sloan

2012-12-20	Continued to customize the interval mapping menu	Zachary Sloan

2012-12-20	Improved appearance/layout of the interval mapping tab using bootstrap	Zachary Sloan

2012-12-20	Form data passed via POST for marker regression	Zachary Sloan
	Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan
2012-12-18	Changed html for the marker regression tab	Zachary Sloan
	Created file show_trait_mapping_tools.coffee to handle submitting the form to the marker regression page Changed form name/id in show_trait.html to "trait_data_form"