| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2013-04-16 | Wrote functions that divide a list into a specified number of chunks | Zachary Sloan | |
| (to be used on the list of snps for the LMM code) | |||
| 2013-04-16 | Checking in before making some changes | Zachary Sloan | |
| 2013-04-16 | Put most of the code calculating human association statistics in | Zachary Sloan | |
| lmm.py into a separate function | |||
| 2013-04-11 | Fixed a bug with quick_search_table.py | Zachary Sloan | |
| Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines | |||
| 2013-04-10 | Created template for quick search page | Zachary Sloan | |
| Fixed a couple bugs with quick_search_table.py | |||
| 2013-04-09 | Have quick search working for phenotypes | Zachary Sloan | |
| 2013-04-09 | Nick's code works fine with human data | Zachary Sloan | |
| Added option to limit results based on lod score (which also changes the y-axis of the plot) | |||
| 2013-04-05 | Loading bar now correctly shows the time to completion | Zachary Sloan | |
| and the code seems to run correctly | |||
| 2013-04-05 | Made change to nginx config file that seems to have fixed the | Zachary Sloan | |
| 504 gateway timeout issue with the human datasets | |||
| 2013-04-05 | Got Nick's code working with the MDP datasets under the BXD group, | Zachary Sloan | |
| but with only BXD strains | |||
| 2013-04-05 | Made changes to get pylmm code working with HMDP datasets | Zachary Sloan | |
| 2013-04-02 | Finished adding code that uses the plink genotype data if | Zachary Sloan | |
| a human dataset and json data if any other species | |||
| 2013-04-02 | Committing before splitting code that runs pylmm with plink files | Zachary Sloan | |
| and code that runs it with json | |||
| 2013-04-02 | pylmm code is running for human data (plink .bed genotype files) | Zachary Sloan | |
| 2013-03-28 | quick_search_table.py seems to be running OK for the PublishXRef | Zachary Sloan | |
| table, but will need to check later to make sure | |||
| 2013-03-28 | quick_search_table.py now seems to run correctly for ProbeSetXRef | Zachary Sloan | |
| rows | |||
| 2013-03-28 | Committing before putting quick_search_table code in classes | Zachary Sloan | |
| 2013-03-27 | Got quick_search_table.py to a point where it runs; will | Zachary Sloan | |
| know tomorrow whether it ran correctly or not | |||
| 2013-03-27 | Worked on trying to get results for quick search to display | Zachary Sloan | |
| 2013-03-26 | Continued working on quick_search_table.py, which now gets | Zachary Sloan | |
| all of the terms from the ProbeSet table to be included in the quick search | |||
| 2013-03-26 | Created quick_search_table.py to create table with all of the | Zachary Sloan | |
| information needed for the the quick search features (which searches across all datasets) | |||
| 2013-03-26 | Just checking in code while in the process of trying to get | Zachary Sloan | |
| the quick search working properly | |||
| 2013-03-22 | Began creating templates for login/registration | Zachary Sloan | |
| 2013-03-22 | Added secure_server.py | Zachary Sloan | |
| Updated notes.txt | |||
| 2013-03-22 | Removed zach_settings.py from git tracking | Zachary Sloan | |
| Changed mysql password as a result of it being up on git before | |||
| 2013-03-21 | Did some work towards getting Nick's code working with our plink | Zachary Sloan | |
| human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot | |||
| 2013-03-19 | In the process of trying to use Nick's pylmmKinship.py code to | Zachary Sloan | |
| precompute the kinship matrix for the human datasets we have plink .bed genotype data for | |||
| 2013-03-19 | Added Nick's input.py file which uses plink .ped files as input | Zachary Sloan | |
| for his pylmm code | |||
| 2013-03-19 | Searches work for the full access human datasets with mRNA assay | Zachary Sloan | |
| searches, and the trait page can be loaded Need to get marker regression page working with human data now | |||
| 2013-03-15 | Began work with implementing general search | Zachary Sloan | |
| 2013-03-15 | Changes related to searching for selected points in marker regression plot | Zachary Sloan | |
| 2013-03-13 | Merge branch 'flask' of http://github.com/zsloan/genenetwork into flask | Zachary Sloan | |
| 2013-03-13 | Added some to notes | Zachary Sloan | |
| 2013-03-12 | Added the script generating probesetfreeze data matrix files | Zachary Sloan | |
| The script was created to regenerate a bad file for Evan | |||
| 2013-03-12 | Highlighting points works in Firefox but still doesn't work in chrome | Zachary Sloan | |
| Also noticed issue with chromosome ordering in Firefox | |||
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan | |
| 2013-03-09 | Trying to get caching working with pickle now | Zachary Sloan | |
| 2013-03-08 | Caching is working for marker regression but really slowly | Zachary Sloan | |
| 2013-03-08 | Refactored GWAS function in lmm.py | Zachary Sloan | |
| 2013-03-07 | Progress bar is now completely working | Zachary Sloan | |
| Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | |||
| 2013-03-07 | Have first 45% of progress bar working | Zachary Sloan | |
| Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work | |||
| 2013-03-07 | Created file temp_data to store data related to progress | Zachary 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 | |||
| 2013-03-06 | Stored percent of calculate_kinship function completion in | Zachary Sloan | |
| variable | |||
| 2013-03-06 | Improved positioning/size of copy/print/save buttons for | Zachary Sloan | |
| marker regression table | |||
| 2013-03-05 | Implemented DataTables; there are now options to download the marker | Zachary Sloan | |
| regression result table in various formats | |||
| 2013-03-02 | Created generate_probesetfreeze_file to create the | Zachary Sloan | |
| "probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with | |||
| 2013-02-28 | Updated benchmark.py to aggregate run times when you run the | Zachary Sloan | |
| operation(s) multiple times | |||
| 2013-02-28 | Added benchmark.py that compares the time of various operations | Zachary Sloan | |
| and gives a report with the percent of total computation time each takes | |||
| 2013-02-28 | Chromosome labels on marker regression plot are centered | Zachary Sloan | |
| Tick marks are now correct and in intervals of 25 for each chromosome | |||
| 2013-02-23 | A static progress bar now displays when loading the marker regression results | Zachary Sloan | |
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |