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2013-03-19In the process of trying to use Nick's pylmmKinship.py code toZachary Sloan
precompute the kinship matrix for the human datasets we have plink .bed genotype data for
2013-03-19Added Nick's input.py file which uses plink .ped files as inputZachary Sloan
for his pylmm code
2013-03-19Searches work for the full access human datasets with mRNA assayZachary Sloan
searches, and the trait page can be loaded Need to get marker regression page working with human data now
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 filesZachary Sloan
The script was created to regenerate a bad file for Evan
2013-03-12Highlighting points works in Firefox but still doesn't work in chromeZachary Sloan
Also noticed issue with chromosome ordering in Firefox
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 workingZachary Sloan
Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code
2013-03-07Have first 45% of progress bar workingZachary Sloan
Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work
2013-03-07Created file temp_data to store data related to progressZachary 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
2013-03-06Stored percent of calculate_kinship function completion inZachary Sloan
variable
2013-03-06Improved positioning/size of copy/print/save buttons forZachary Sloan
marker regression table
2013-03-05Implemented DataTables; there are now options to download the markerZachary Sloan
regression result table in various formats
2013-03-02Created generate_probesetfreeze_file to create theZachary Sloan
"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-28Updated benchmark.py to aggregate run times when you run theZachary Sloan
operation(s) multiple times
2013-02-28Added benchmark.py that compares the time of various operationsZachary Sloan
and gives a report with the percent of total computation time each takes
2013-02-28Chromosome labels on marker regression plot are centeredZachary Sloan
Tick marks are now correct and in intervals of 25 for each chromosome
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 issueZachary Sloan
with the location of points on the x-axis
2013-02-20Created y-axisZachary Sloan
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
2013-02-19Manhattan plot and chromosome lines are all correct nowZachary Sloan
Hovering over a point automatically searches for its corresponding marker in the data table Added headers for the plot and table
2013-02-19Made lines for manhattan plot proportional to chromosome lengthsZachary Sloan
2013-02-15Points are labeled with marker names and hovering causes the LRSZachary Sloan
value to appear above the plot
2013-02-15Made it to where hovering over a point in the manhattan plot changesZachary Sloan
its style
2013-02-15Created lines in marker regression scatter plot separatingZachary Sloan
chromosomes
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)Zachary Sloan
using d3.js
2013-02-13Got results displaying for BXD and fixed genofile_parser.py to workZachary Sloan
for all of our genofiles
2013-02-13Got results for marker regression page displaying in tableZachary Sloan
2013-02-13Fixed some bugs related to getting the marker regression page workingZachary Sloan
with Nick's code
2013-02-12Edited marker_regression.py and data_set.py to store the p-valuesZachary Sloan
and their corresponding markers to be used in the table of qtl results and other figures
2013-02-08Converted .geno files to json files and wrote code in marker_regression.pyZachary Sloan
that loads the json files, converts them into the relevant numpy arrays, and passes them into Nick's code (which is returning results that may or may not be correct, but is at least running)
2013-02-07Added code to marker_regression.py that creates the numpy arrays toZachary 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
2013-02-06Edited genofile_parser.py to go through all genofiles and convertZachary Sloan
them to the format used by nick's code
2013-02-06Added changes to example.py and prep_data.py that lets nick's code read inZachary Sloan
our data
2013-02-06Small change to search_results.py to get search results page to workZachary Sloan
2013-01-31Added wqflask-nginx.confZachary Sloan
2013-01-31Copied over nginx.conf from /etc/nginxZachary Sloan
2013-01-31Merge branch 'flask' of https://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Changed reference to 'dataset_name' in keywords to 'dataset' to getZachary 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