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2016-02-08Renamed misc dir to docpjotrp
2014-01-30Most of the work is done towards running lmm.py from the command lineZachary Sloan
and storing the results in redis
2014-01-24Added natural sort to sort the index column for the sample data inZachary Sloan
the trait page Hid the Quick Search on the index page until it is working well. Started writing a file to run the pyLMM code in the background to avoid memory issues/timing out
2013-11-21Added apt-get dist-upgrade to notesZachary Sloan
2013-10-16Added interval_mapping to views.pyZachary Sloan
Made some more changes to interval_mapping.py
2013-08-21Fixed an issue where correlationFunction was being importedZachary Sloan
instead of its updated name correlation_function
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-07-23Fixed a couple issues with he quick_search_table.py scriptZachary Sloan
Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc)
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
2013-07-03Updated notes and created requirements.txt fileZachary Sloan
2013-06-21Fixed bug where cursor was still being used in queryZachary Sloan
2013-06-20Removed foobar from top of notes.txtZachary Sloan
2013-06-20Added fubar to the top of notes.txtZachary Sloan
2013-06-20Added explanation of pushing to github to notesZachary Sloan
2013-06-19Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flaskZachary 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
2013-06-11Put trait info for correlation results page into a dictionary insteadLei Yan
of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-08Merge branch 'flask' of git://github.com/leiyan/genenetwork into flaskZachary Sloan
2013-05-08Worked on correlation pageLei Yan
Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-04-24Began writing code that writes some objects used in LMM to redisZachary Sloan
and writes/reads eachitem in the plink_input
2013-04-23Created file correlation_plot.py for the correlation scatterplotZachary 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
2013-04-18LMM code now reads in gzipped pickled plink snp iterator objectZachary Sloan
2013-04-18input file is now loaded by pickleZachary Sloan
2013-03-22Added secure_server.pyZachary Sloan
Updated notes.txt
2013-03-22Removed zach_settings.py from git trackingZachary Sloan
Changed mysql password as a result of it being up on git before
2013-03-13Added some to notesZachary Sloan
2013-03-05Implemented DataTables; there are now options to download the markerZachary Sloan
regression result table in various formats
2013-02-22Added some to notesZachary Sloan
2013-02-21Adding genotypes and new_genotypes (json files) directories to gitZachary Sloan
so they can be pulled to the new EC2 server
2013-01-31Deleted nginx.conf from the other_conf directory not in wqflaskZachary Sloan
2013-01-25Added a bunch of things to notesZachary Sloan
2013-01-24Added a lot to the notes in the process of setting up on theZachary Sloan
new server
2013-01-23Added a bunch to notes and created new notes file specificallyZachary Sloan
related to installing a new instance of GN
2013-01-22Added a couple things to notes regarding installing mysql clientZachary Sloan
2013-01-18Renamed CorrelationPage.py to show_corr_results.pyZachary 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
2013-01-11Overwrote requirements.txtZachary Sloan
2013-01-04Correct results are being returned from reaper for the marker regression pageZachary Sloan
2012-12-05Renamed webqtlTrait.py to trait.pyZachary Sloan
Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough)
2012-11-21Changed parser to allow for bother square brackets and parenthesesZachary Sloan
Changed show_trait.coffee to get the stats table working again Still need to get stats table to work with changed values
2012-11-01Began integrating do_search.py's DoSearch object into search_results.py,Zachary Sloan
with simple searches returning correct results Still need to make results display in the table Sam also did some work with the bootstrap styling
2012-10-23Finished coffeescript that handles the home page dataset selection dropdownsZachary Sloan
2012-10-19Finished gen_select_dataset.py which generates the json file that defines theZachary Sloan
data structure used for the index page select dropdowns
2012-10-09Used tidyp to improve/beautify index_page.htmlZachary Sloan
2012-09-25Fixed issue with parent strains appearing twice and began replacing variable ↵Zachary Sloan
names (strain -> sample, for example)
2012-09-13Worked on improving readData and informativeStrains functions in ↵Zachary Sloan
webqtlFormData while trying to get correlation page running
2012-09-12Worked towards correctly passing form data to correlation page and addressed ↵Zachary Sloan
various bugs that arose while doing so
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