Implementing profiling workflows

• We will use this dataset to work on the data analysis pipeline http://www.broadinstitute.org/bbbc/BBBC021/. The webpage describes the data and associated metadata.
• If you would like to work directly on the images, you can download them here: http://www.broadinstitute.org/bbbc/BBBC021/.
• The features at the single cell level are available either as
• tab-separated files: http://www.broadinstitute.org/pubs/ljosa_jbiomolscreen_2013/ (Supplemental Data S2). More instructions to work with this data are at https://gist.github.com/shntnu/63d1b1a80964c7301044, or
• sqlite database: http://www.broadinstitute.org/~shsingh/BBBC021.sqlite
• Create this view to get metadata for each image

CREATE view supplement_Image_withmoa 
AS 
  SELECT TableNumber, 
         ImageNumber, 
         Image_Metadata_Plate_DAPI, 
         Image_Metadata_Well_DAPI, 
         Image_Metadata_Compound, 
         Image_Metadata_Concentration, 
         moa AS Image_Metadata_MOA 
  FROM   supplement_Image AS image 
         JOIN `supplement_GroundTruth` AS ground 
           ON image.`Image_Metadata_Compound` = ground.`compound` and 
           image.`Image_Metadata_Concentration` = ground.`concentration`

• Create this view to data at the per-cell level along with metadata

CREATE view supplement_Object_withmoa 
AS 
  SELECT * 
  FROM   supplement_Object AS object 
         JOIN `supplement_Image_withmoa` AS image 
           ON image.`TableNumber` = object.`TableNumber` and 
           image.`ImageNumber` = object.`ImageNumber` 

• The features at the per well and per treatment level are available here:
• Download http://www.broadinstitute.org/pubs/singh_jmicroscopy_2014/reproduce.zip. Go to the directory analysis_multivariate/AZ_Median500M/outputs. The file mean.well.profiles.txt is per-well, and mean.treatment.profiles.txt is per treatment