genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-05-08	Worked on correlation page	Lei Yan
	Wrote function in dataset.py that gets all the traits in a dataset and their sample values
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	Made changes to get pylmm code working with HMDP datasets	Zachary Sloan

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

2013-03-19	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
2013-03-12	Got cashing working with pickle	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
2013-03-02	Created generate_probesetfreeze_file to create the	Zachary Sloan
	"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with
2013-02-14	Have marker regression results displaying as a scatterplot (just the points)	Zachary Sloan
	using d3.js
2013-02-13	Fixed some bugs related to getting the marker regression page working	Zachary Sloan
	with Nick's code
2013-02-12	Edited marker_regression.py and data_set.py to store the p-values	Zachary Sloan
	and their corresponding markers to be used in the table of qtl results and other figures
2013-01-31	Changed fd to kw in search_results.py, commented out some lines	Zachary Sloan
	related to fd
2013-01-18	Renamed CorrelationPage.py to show_corr_results.py	Zachary 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
2013-01-03	Began working on marker_regression.py and created Chromosomes class	Zachary Sloan
	in species.py
2013-01-03	Created template for marek regression page and made the compute button direct	Zachary Sloan
	to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-18	Created new file species.py and species class object TheSpecies	Zachary Sloan
	Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
2012-12-06	Added minimum/maximum to basic statistics table	Zachary Sloan
	Continued bug-shooting related to getting show_trait running with phenotype traits
2012-12-06	Got show_trait running again for MrnaAssay traits	Zachary Sloan

2012-12-06	Made many small changes to show_trait/data_set/search_results/trait to	Zachary Sloan
	remove use of the formData object and cursor
2012-12-05	Renamed webqtlTrait.py to trait.py	Zachary 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)
2012-12-05	Continued to make changes related to getting rid of cursor/db_conn	Zachary Sloan
	and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again
2012-12-04	Changed parser to allow quotes (i.e. name="rw williams")	Zachary Sloan
	Renamed webqtlTrait to GeneralTrait and began rewriting parts Changed database code in many places to use simple sqlalchemy
2012-12-04	Began changing references to cursor/db_conn to use sqlalchemy	Zachary Sloan
	Wrote function for phenotype author searches
2012-11-30	Added example of escaping strings now that trasitioning to simple SQLAlchemy	Zachary Sloan

2012-11-30	Started switching to using basic sqlalchemy to handle db connection/queries	Zachary Sloan
	Began fixing bugs related to this fix, still in progress
2012-11-29	Changed a number of variables (riset to group, db to dataset)	Zachary Sloan
	Put most of the code for cisLRS and transLRS searches into the class CisTransLrsSearch (might change this name to something else later) Simplified escape code for searches in do_search.py Got search_results working again after some changes
2012-11-28	Made some small changes to get code working for genotype searches	Zachary Sloan

2012-11-27	Created subclass for each main data set type and moved the code	Zachary Sloan
	for getting trait info that was in search_results.py into its respective class Renamed webqtlDataset to DataSet/create_dataset in webqtlTrait.py, webqtlDatabaseFunction.py, and CorrelationPage.py Got search page running again for mRNA assay data sets with these changes
2012-11-27	Renamed webqtlDataSet.py to data_set.py	Zachary Sloan
	Renamed the class webqtlDataset to DataSet Finished cisLRS and transLRS search types in d_search.py Fixed parent/f1 issue in show_trait.py