Laboratory Information Management System (LIMS)

Overview of a custom LIMS system.  The central SQL Server database is accessed using several mechanisms: customs Windows application, web-based forms, and data analysis packages such as Excel and Spotfire.
 overview of LIMS system

The company by whom I (T. Flak) was employed needed a system to organize several types of data.  These included information about the many gene targets on which we worked; the different assays that were developed for these gene targets; the different projects for clients; and gene experession information collected by TaqMan real-time PCR (see details about that sub-system on the example TaqMan Real-time PCR data system).

At the center of this system is a SQL Server database, with more than 150 tables.  The schema design allowed linkage of one or more genes to each project; and one or more projects to each gene.  It also incorporated linkages to public databases (e.g. Entrez Gene).

The primary client is a Windows application, written in Microsoft Visual Basic.NET (VB.NET).  This application allows a user to navigate all of the data, and create new projects.  It includes the TaqMan real-time PCR data, detailed here.

Between the database and the LIMS client application, we created a "data library" database interface layer.  This was linked directly into the VB.NET  application.  In addition, specific data were exposed as an XML-SOAP Web Service; these web service functions were used by other applications, including some web-based reports, and several Excel-based tools.  In addition, several Microsoft Access database used ODBC connections to the LIMS database.

We also used Spotfire DecisionSite, by means of a feature called Information Interaction Server.  This allowed specialized Information Links to be built to facilitate simple data retrieval for specific purposes.

The LIMS Client VB.NET application (a few different screenshots)

Gene info

Gene Expression

Tissue Histolgy
LIMS Client interface screen shot
Some applications accessed the database by means of a XML-SOAP Web Service.  This figure shows the web service test page, which allows testing of each of the functions and examples of SOAP interface syntax.
TaqMan database processing flow
An example of some of the data relations in the LIMS database.  This view is from the ComponentOne data library that is used to abstract the underlying data tables for the LIMS Client.database relationship diagram