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2013-05-09Added original security templates (so we can change them)Sam
2013-05-09Working on user registrationSam
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
2013-05-07Made some progress adding species/group tabs to the quick search result page toZachary Sloan
make the results easier to navigate
2013-05-02Got quick search code running (but not displaying properly)Zachary Sloan
Code that processes subset of snps works, in process of putting into a class
2013-04-30Merge branch 'flask' of git://github.com/leiyan/genenetwork into flaskZachary Sloan
2013-04-30Changed path to log fileLei Yan
Added server port to configuration file
2013-04-30Did a little with correlation_plot.pyZachary Sloan
2013-04-26Added file that checks how much time is added to a loop's runtime by print ↵Zachary Sloan
statements Continued work on file that processes each individual chunk of the snp iterator/plink input
2013-04-24Began writing code that writes some objects used in LMM to redisZachary Sloan
and writes/reads eachitem in the plink_input
2013-04-24Added original pylintrcZachary Sloan
2013-04-24Checking in quick_search_table.py before using pylinZachary Sloan
2013-04-24Fixed issue with the part of quick_search_table.py that loads phenotype traitsZachary Sloan
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
2013-04-19Fixed the issue with the x-axis coordinates for marker regression plotZachary Sloan
2013-04-18The plink_input is split into chunks that are stored in temp_data, butZachary Sloan
we might decide to store it differently
2013-04-18LMM code now reads in gzipped pickled plink snp iterator objectZachary Sloan
2013-04-18input file is now loaded by pickleZachary Sloan
2013-04-17Created file with pickled SNPIterator (from input.py) dataZachary Sloan
for HLC datasets Still need to read in file
2013-04-17Added a benchmark for running the chunks code on the list of snpsZachary Sloan
2013-04-17Renamed chunk_test.py to chunks.pyZachary Sloan
2013-04-17Updated chunk_test.pyZachary Sloan
2013-04-17Added chunk_test.py which compared my/ and sam's split intoZachary Sloan
chunks algorithms' accuracy/speed
2013-04-17Wrote code that tests the effectiveness of the function that divides aZachary Sloan
list into a given number of chunks
2013-04-17Fixed small issue with the divide_into_chunks functionZachary Sloan
that caused one too many chunks to be created
2013-04-16Wrote functions that divide a list into a specified number of chunksZachary Sloan
(to be used on the list of snps for the LMM code)
2013-04-16Checking in before making some changesZachary Sloan
2013-04-16Put most of the code calculating human association statistics inZachary Sloan
lmm.py into a separate function
2013-04-11Fixed a bug with quick_search_table.pyZachary Sloan
Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines
2013-04-10Created template for quick search pageZachary Sloan
Fixed a couple bugs with quick_search_table.py
2013-04-09Have quick search working for phenotypesZachary Sloan
2013-04-09Nick's code works fine with human dataZachary Sloan
Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05Loading bar now correctly shows the time to completionZachary Sloan
and the code seems to run correctly
2013-04-05Made change to nginx config file that seems to have fixed theZachary Sloan
504 gateway timeout issue with the human datasets
2013-04-05Got Nick's code working with the MDP datasets under the BXD group,Zachary Sloan
but with only BXD strains
2013-04-05Made changes to get pylmm code working with HMDP datasetsZachary Sloan
2013-04-02Finished adding code that uses the plink genotype data ifZachary Sloan
a human dataset and json data if any other species
2013-04-02Committing before splitting code that runs pylmm with plink filesZachary Sloan
and code that runs it with json
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 PublishXRefZachary Sloan
table, but will need to check later to make sure
2013-03-28quick_search_table.py now seems to run correctly for ProbeSetXRefZachary Sloan
rows
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; willZachary Sloan
know tomorrow whether it ran correctly or not
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 getsZachary Sloan
all of the terms from the ProbeSet table to be included in the quick search
2013-03-26Created quick_search_table.py to create table with all of theZachary Sloan
information needed for the the quick search features (which searches across all datasets)
2013-03-26Just checking in code while in the process of trying to getZachary Sloan
the quick search working properly
2013-03-22Began creating templates for login/registrationZachary Sloan
2013-03-22Added secure_server.pyZachary Sloan
Updated notes.txt