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2013-04-02pylmm code is running for human data (plink .bed genotype files)Zachary Sloan
2013-03-28quick_search_table.py seems to be running OK for the PublishXRef...table, but will need to check later to make sure Zachary Sloan
2013-03-28quick_search_table.py now seems to run correctly for ProbeSetXRef...rows Zachary Sloan
2013-03-28Committing before putting quick_search_table code in classesZachary Sloan
2013-03-27Got quick_search_table.py to a point where it runs; will...know tomorrow whether it ran correctly or not Zachary Sloan
2013-03-27Worked on trying to get results for quick search to displayZachary Sloan
2013-03-26Continued working on quick_search_table.py, which now gets...all of the terms from the ProbeSet table to be included in the quick search Zachary Sloan
2013-03-26Created quick_search_table.py to create table with all of the...information needed for the the quick search features (which searches across all datasets) Zachary Sloan
2013-03-26Just checking in code while in the process of trying to get...the quick search working properly Zachary Sloan
2013-03-22Began creating templates for login/registrationZachary Sloan
2013-03-22Added secure_server.py...Updated notes.txt Zachary Sloan
2013-03-22Removed zach_settings.py from git tracking...Changed mysql password as a result of it being up on git before Zachary Sloan
2013-03-21Did some work towards getting Nick's code working with our plink...human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot Zachary Sloan
2013-03-19In the process of trying to use Nick's pylmmKinship.py code to...precompute the kinship matrix for the human datasets we have plink .bed genotype data for Zachary Sloan
2013-03-19Added Nick's input.py file which uses plink .ped files as input...for his pylmm code Zachary Sloan
2013-03-19Searches work for the full access human datasets with mRNA assay...searches, and the trait page can be loaded Need to get marker regression page working with human data now Zachary Sloan
2013-03-15Began work with implementing general searchZachary Sloan
2013-03-15Changes related to searching for selected points in marker regression plotZachary Sloan
2013-03-13Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-03-13Added some to notesZachary Sloan
2013-03-12Added the script generating probesetfreeze data matrix files...The script was created to regenerate a bad file for Evan Zachary Sloan
2013-03-12Highlighting points works in Firefox but still doesn't work in chrome...Also noticed issue with chromosome ordering in Firefox Zachary Sloan
2013-03-12Got cashing working with pickleZachary Sloan
2013-03-09Trying to get caching working with pickle nowZachary Sloan
2013-03-08Caching is working for marker regression but really slowlyZachary Sloan
2013-03-08Refactored GWAS function in lmm.pyZachary Sloan
2013-03-07Progress bar is now completely working...Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code Zachary Sloan
2013-03-07Have first 45% of progress bar working...Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work Zachary Sloan
2013-03-07Created file temp_data to store data related to progress...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 Zachary Sloan
2013-03-06Stored percent of calculate_kinship function completion in...variable Zachary Sloan
2013-03-06Improved positioning/size of copy/print/save buttons for...marker regression table Zachary Sloan
2013-03-05Implemented DataTables; there are now options to download the marker...regression result table in various formats Zachary Sloan
2013-03-02Created generate_probesetfreeze_file to create the..."probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with Zachary Sloan
2013-02-28Updated benchmark.py to aggregate run times when you run the...operation(s) multiple times Zachary Sloan
2013-02-28Added benchmark.py that compares the time of various operations...and gives a report with the percent of total computation time each takes Zachary Sloan
2013-02-28Chromosome labels on marker regression plot are centered...Tick marks are now correct and in intervals of 25 for each chromosome Zachary Sloan
2013-02-23A static progress bar now displays when loading the marker regression resultsZachary Sloan
2013-02-22Added some to notesZachary Sloan
2013-02-21Added underscore.jsZachary Sloan
2013-02-21Add my_pylmm packageZachary Sloan
2013-02-21Plot points and chromosome lines are now correctZachary Sloan
2013-02-20Did more work with manhattan plot, trying to fix a small issue...with the location of points on the x-axis Zachary Sloan
2013-02-20Created y-axis...Split create_graph into many functions Added a buffer to the x and y dimensions in order to add tick labels for the x and y axis Zachary Sloan
2013-02-19Manhattan plot and chromosome lines are all correct now...Hovering over a point automatically searches for its corresponding marker in the data table Added headers for the plot and table Zachary Sloan
2013-02-19Made lines for manhattan plot proportional to chromosome lengthsZachary Sloan
2013-02-15Points are labeled with marker names and hovering causes the LRS...value to appear above the plot Zachary Sloan
2013-02-15Made it to where hovering over a point in the manhattan plot changes...its style Zachary Sloan
2013-02-15Created lines in marker regression scatter plot separating...chromosomes Zachary Sloan
2013-02-14Put coffeescript code for manhattan plot into a class/functionsZachary Sloan
2013-02-14Have marker regression results displaying as a scatterplot (just the points)...using d3.js Zachary Sloan
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