genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-12-17	Added the option to choose which method to use for the interval	Zachary Sloan
	mapping function (pyLMM or qtl reaper)
2013-12-12	Put the code that rebuilds the bar chart into a function	Zachary Sloan
	Still need to fix issue where attribute colors don't stay with their associated samples/strains
2013-12-11	Got sort by name/value buttons working and committing before trying	Zachary Sloan
	to put some of the d3 code into a function
2013-12-11	Got color by trait working, but still need to add a legend and make	Zachary Sloan
	some other small changes (like removing samples that don't overlap with the selected trait) Tentatively removed jquery-ui from base.html; I'm not sure if we're still using this anywhere, but removing it doesn't seem to have had an impact on the trait page
2013-12-05	Now trims selected trait's values by the samples of the primary trait and	Zachary Sloan
	gets their distinct values Created function that creates a dictionary of distinct values and their corresponding colors
2013-12-05	Interval map graph now works properly	Zachary Sloan
	Tried to export trait data for "color by trait" function
2013-11-27	Clicking a trait in "color by trait" now gets all of its sample values	Zachary Sloan
	that will be used to color the bar graph
2013-11-27	Can now view trait list of a collection after clicking the collection	Zachary Sloan
	in the modal that pops up after clicking "Color by Trait" above the bar chart
2013-11-26	Made some progress towards getting the traits inside a collection to display ↵	Zachary Sloan
	on hover
2013-11-25	Merge branch 'temp'	Zachary Sloan

2013-11-25	Got the interval mapping results into a table	Zachary Sloan

2013-11-22	Did some work towards getting the interval mapping page working	Zachary Sloan

2013-11-20	Merge /home/zas1024/gene	Lei Yan

2013-11-20	Created a box plot	Zachary Sloan
	Made the bar chart use a gradient if colored by something with more than 6 distinct values Put figures in tabs under the Charts/Figures part of the trait page
2013-11-14	Can change the parameters of Sample Correlation Scatterplot	Lei Yan

2013-11-05	Merge /home/zas1024/gene	Lei Yan
	Conflicts: wqflask/wqflask/templates/correlation_page.html
2013-11-05	Add Correlation Scatter plot	Lei Yan

2013-11-01	In the process of opening a modal with the collection page inside	Zachary Sloan

2013-11-01	In the process of adding the function to color bar chart by the	Zachary Sloan
	values of a trait in your collection
2013-11-01	Merge /home/sam/gene	Zachary Sloan

2013-11-01	Made the extra attribute bar chart coloring continue to work	Zachary Sloan
	when the user sorts and gave the option to revert to no coloring
2013-10-31	Refactored login code and got remember me working	Sam

2013-10-31	Implemented superuser and switching users for debugging purposes	Sam

2013-10-30	More work on collections	Sam

2013-10-30	Got coloring by attribute working for the bar chart	Zachary Sloan

2013-10-30	In process on view.html for user_collections	Sam

2013-10-30	Progress on user collections	Sam

2013-10-25	Began working on color coding bar chart by extra attributes	Zachary Sloan

2013-10-24	Added a dynamically resortable bar chart to the trait page	Zachary Sloan
	Improved the look/feel of the correlation page somewhat
2013-10-23	Adding new collections works	Sam

2013-10-22	Bunch of work on collections and user management	Sam

2013-10-17	Sample objects are now passed to js_data for drawing the correlation	Lei Yan
	scatter plot
2013-10-17	Merge /home/zas1024/gene	Lei Yan
	Conflicts: wqflask/wqflask/views.py
2013-10-17	Added file for the correlation scatterplot and added the @app	Lei Yan
	to views.py Added the link to the corr plot page to the correlation page template
2013-10-16	Added interval_mapping to views.py	Zachary Sloan
	Made some more changes to interval_mapping.py
2013-10-16	security code cleanup	Sam

2013-10-15	Merge /home/zas1024/gene	Sam

2013-10-15	Password reset now works...but needs some error checking still	Sam

2013-10-15	Before getting rid of query_string in DecodeUser	Sam

2013-10-15	Changed templates to call the header macro	Zachary Sloan
	Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-15	* Redid mail sending service to set a ping showing it's alive	Sam
	* Redid server so it wouldn't start unless mail service recently pinged * Wrote a bunch of forgot password code * Refactored sending email about verification and forgotten passwords
2013-10-11	Merge /home/sam/gene	Lei Yan

2013-10-11	Merge /home/sam/gene	Zachary Sloan

2013-10-11	Small changes around logging in	Sam

2013-10-11	Merge /home/lei/gene	Zachary Sloan
	Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10	Almost have correlation working for non-primary strain/group	Lei Yan
	There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work.
2013-10-09	Improved some of the code related to the correlation page	Lei Yan
	For example, changed the two functions getting gene symbols and ids for a dataset into one function that can take a column name as a parameter
2013-10-08	Literature correlation works when it is selected as the sorted	Lei Yan
	correlation type (that is, when it is run again all traits in a database) Added a function to data_set.py that gets all the gene_ids in the data set. Not sure if having a separate function for getting the gene_ids and another for getting the gene symbols makes sense.
2013-10-08	Did some work with interval mapping page; will use qtl reaper to do	Zachary Sloan
	the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl
2013-10-07	Worked on logins, session_ids, flash messages, etc.	Sam