Databases at the HTS @ The Nucleus

We work with three main databases; A cloud based cheminformatics database  from  Dotmatics, and two locally managed databases; an image storage and analysis database from Molecular Devices (ORACLE 19c), and a HTS analysis database running Genedata Screener (ORACLE 19c).

Cheminformatics Database

1. The Cheminformatics Database stores all the information from the compound libraries and links this information together with the results from screening. The cheminformatics system we use is from a cloud based system from Dotmatics and contains the following products:

(A) Browser for viewing structures and associated data including assay/HTS data and inventory.

(B) Register which is used to register new compounds and batches.

(C) Inventory which stores the compound inventory and plate inventory including the concentrations, volume and location of all compounds in our screening library.

(D) Studies which contains the HTS data and other assasy data. For HTS data we import the out put from Genedata Screener and also imported historic data from our old MDL Cheminformatics system. Studies also incorporates Electronic Notebook (ELN) capabilities.

(E)  Vortex  which is intuitive data visualization & analysis for chemistry decision support.

(F)  Elemental Draw for drawing chemicals, and other tools for medicinal chemistry support.

High-Content Image Storage and Image Analysis Database

2. The Molecular Devices MetaXpress image acquisition software captures and stores image files from the ImageXpress Micro CONFOCAL during high-content screens. The images are stored in the MDCStore database which uses an Oracle database. MetaXpress is used for image analysis, through the use of custom scripts or analysis application modules. Thus, these combined applications not only store the image files, but also the image analysis results. We also have an API from Genedata that links the MetaXpress image analysis to Screener to allow for simplyfied linking of images and image analysis data to HTS data linking the images to the compounds that were tested.

High-Throughput Screening Analysis Database

3. For High-Throughput Screening data analysis, we use Genedata Screener.  Besides the High-Throughput Screening Module, we have the High Content Analysis Module to link to our MetaXpress Database. 

Servers

Other than the Cheminformatics data which is stored on the cloud, our HTS and Image data is stored on 5 Dell PowerEdge Database/File Servers. Three are Dell PowerEdge R740 Servers. The two High-Content image servers run Windows Server 2019. One is an ORACLE 19c Database server and the other is connected to a MD1420 External RAID with 42 TB of storage.  The Genedata Screener Server runs on RedHat Linux 8.2. Two olderPowerEdge R810 servers running Windows Server 2016 are mostly used as file servers to store data for tape backup. These servers are attached to external Powervault MD1220 RAID6 arrays (one with >10 TB of RAID6 SAS storage for high-content image files). A Dell Powervault TL1000 LTO-8 automated Tape Backup with 9 slots for 12/30TB LTO-8 tapes is utilized to backup all data and image files with Veritas Backup Exec 22.

The HTS labs are located in the Sarafan ChEM-H Building Room W008 and CCSR, Room 0133-North Wing, between the Transgenic Research Center and the Stanford Genomics Facility.

For Directions to the HTS labs, see our Contact page.

HTS iLAB Page for HTS registration, room access, and to see equipment Calendars.