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ODBC connectivity for LIMS to Oracle for demanding laboratory informatics and automation

ODBC connectivity for LIMS to Oracle for demanding laboratory informatics and automation

September 13, 2012 0 Comments

One of the best gauges for increasing data volumes from Laboratory Information Management Systems (LIMS) is whether your lab is exceeding the scalability of a native ODBC driver. From recent engagements, I am seeing a growing trend with pharmaceutical companies running LIMS software on Oracle. These environments are increasing their data access loads that require DataDirect Connect for ODBC Oracle Wire Protocol drivers.

More specifically, integrating LIMS and Chromotography Data Systems (CDS) can exceed the capabilities of native ODBC drivers. The wire protocol architecture of DataDirect Oracle Wire Protocol drivers is designed for these environments (i.e. StarLims or Labware interfaces to Empower), and it is exciting to consult on data access for systems that are constantly adapting to advancements in scientific innovation and instrumentation.

Common use cases for DataDirect ODBC drivers for use with LIMS

  • From working with laboratories and clinical research organizations, I've learned that the instant data access performance boost provided by DataDirect Connect for ODBC Wire Protocol drivers for Oracle, Sybase, and DB2 enables LIMS to scale with increasing loads while maintaining an efficient footprint suitable for virtualized environments, including citrix technology.
  • DataDirect ODBC drivers integrate LIMS with lab data warehouses that store historical data including Hadoop Hive for analyzing big data sets. This is done through data federation technologies such as Oracle Database Gateway for ODBC, Sybase ECDA for ODBC, or SQL Server Linked Server.
  • DataDirect Bulk Load can be used for LIMS data integration projects from the primary storage database to the LIMS data warehouse for analysis, reporting and process management.
  • Achieve high availability through codeless DataDirect failover capabilities without having to invest in expensive HA technologies.

Interview: Data Access focus on LIMS

Below is an interview focused around data connectivity with an end user PhD Biologist from a multinational pharmaceutical company in Research Triangle Park (RTP), NC. The DataDirect office in RTP is conveniently surounded by thousands of professionals using LIMS software (45% of tenants in the park are in Life Sciences).

What kind of data is stored in the LIMS systems?

As a biologist, the type of data we store is derived from biological experiments. This includes multiple fields starting from dates and unique experiment identifiers to type of cell lines, numbers of cells used, specific compounds tested, and the end results such as cytotoxicity concentrations or inhibitory concentrations.

What are the sources of the data?

The source is biological experiments in my set

Do you know the vendors of the LIMS application?

I have used generic applications such as ActivityBase and also home grown software that is specific (and integral) to each company.

How does performance of the system impact your daily work, and work done in the lab?

The system needs to be up and running consistently so that we can document any results produced in the lab on a regular basis for two reasons: IP purposes and the ability to share data in a time-sensitive manner.

What changes have you observed over time in these systems?

We are doing most of these things to ease accessibility and accommodate large data volumes. All of our systems are also integrated so that different data sets are linked based on a unique identifier. We use multiple software add-ons (mostly for Excel) that tailor to our specific needs, but there are biostatistic-specific software available for more involved data analysis.

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Sumit Sakar

Sumit Sarkar

Sumit Sarkar is a Chief Data Evangelist at Progress, with over 10 years experience working in the data connectivity field. The world's leading consultant on open data standards connectivity with cloud data, Sumit's interests include performance tuning of the data access layer for which he has developed a patent pending technology for its analysis; business intelligence and data warehousing for SaaS platforms; and data connectivity for aPaaS environments, with a focus on standards such as ODBC, JDBC, ADO.NET and ODATA. He is an IBM Certified Consultant for IBM Cognos Business Intelligence and TDWI member. He has presented sessions on data connectivity at various conferences including Dreamforce, Oracle OpenWorld, Strata Hadoop, MongoDB World and SAP Analytics and Business Objects Conference, among many others. 

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