SMDC
Small Molecule Discovery Center
Data Analysis

We request that user labs comply with our Data Sharing Agreement (under development) and read our policy on intellectual property before starting a screen.

The most common data text file outputs we receive are from either plate readers that detect fluorescence or luminescence signals, or from high content imagers. When raw assay data is in a standard text file format, we can rapidly upload the data and calculate standard values such as % inhibition or % activation relative to reference controls on each plate. In addition, each assay plate is bar-coded with the parent ID from the parent stock plate from which the sample compound aliquots were withdrawn and transferred into the assay plate.

All compound information including chemical properties, well and plate locations are mapped and registered in our database. The assay plate barcodes are concurrently processed with the assay text file raw data in Pipeline Pilot, in order to retrieve stored information about each compound and create records to match each compound structure and associated properties to its corresponding raw data value from the assay text file.

If there are any specialized pre-processing calculations required by the user lab such as background subtraction or normalization of values relative to transfection controls, we ask that the user lab perform these calculations and document them in the automation protocol before submitting the final assay text file to the SMDC for database upload.

The dataset is processed within Pipeline Pilot. Currently, a summary data report is provided to user labs in HTML formats where tables, heat maps and scatter plots display concise representations of the screening results. Standard assay metrics such as Z prime are calculated for each plate. Structures of each compound screened are linked to its activity (usually % inhibition or % activation), and in cases where hits are obtained from portions of the collection that exist as a series of structurally related compounds, preliminary SAR can be obtained from the primary screen.

For a summary of the steps involved and the distribution of tasks between SMDC personnel and the user lab, please see the Data Analysis and Cherry Pick section of the HTS Screening Workflow Outline in the documents section.