There’s no question that one of the key drivers in lab-centric businesses today is connectivity – integrating all of the disparate instruments in the laboratory, such as chromatography and mass spec, with data management systems like LIMS (laboratory information management system) or CDS (chromatography data system). What’s needed further is complete integration of these laboratory sources of data with enterprise systems such as ERP, PIMS or MES. This type of integration now makes data available across the organization to anyone needing it, in real time, and this greatly enhances the ability of management at any level to make knowledgeable decisions that achieve key business metrics.

Today we’re going to talk about how this type of integration occurs because in reality, many organizations want the benefits of integrated systems but the perceived difficulties in implementing this type of connectivity have kept some from taking the steps necessary to actually do it. But the time to do it is now, because the amount of data being generated in your labs is only going to increase, and the complexity of managing that data and then making decisions based on that data is going to depend on a fully integrated laboratory – meaning connecting instruments with the LIMS – and also a fully connected enterprise.

Thermo Scientific Integration Manager moves data between two systems automatically, regardless of the original data sources or the output format required. Because the data is moved electronically, Integration Manager removes the error-prone human data entry aspect of getting information into one or many systems. and it also unifies the many different integration solutions that previously existed.

Most laboratories have in place many different types of instruments that generate data locally. They require human intervention to access data from each of the instruments individually before preparing a report that makes use of the collected data. This collection of data is most often done through re-keying of report data, leading to human error in the time consuming transcription of data. With Integration Manager, the disparate instruments in the laboratory can be fully integrated, with LIMS, ERP and MES. This allows data to be collected electronically and stored in a central database, regardless of the individual output formats produced by each instrument.

To say Integration Manager moves data between two systems, while technically accurate, is a somewhat broad statement. So let’s start with a simple example of a common solution Integration Manager provides. All laboratories contain instruments which perform some analysis and output a data file that describes what’s analyzed in scientific terms. These data then need to be entered and stored in a Laboratory Information Management System (LIMS). In many cases, the instrument doesn’t talk directly to the LIMS system and worse yet, the format of the data coming from the instrument is foreign to the LIMS system. This is where Integration Manager is a game changer. Integration Manager will monitor a directory to which the instrument is outputting data, consume that file, parse it and translate it into something that the LIMS system can understand so the analysis can be tracked and that data used by anyone who needs it.

Lims integration


To understand how Integration Manager does this one needs to understand its underlying architecture. Integration Manager works by utilizing the concept of an Agent. An Integration Manager Agent is simply a Microsoft Windows Service that performs a specific task. File, Remote, SampleManager, Watson, ERP, SQL, COM Port, Forms and Web Service are just some of the Agents. For example, the SampleManager Agent talks to the Thermo Scientific SampleManager LIMS product and the Watson Agent talks to our Watson LIMS and our File Agent works with, you guessed it, files. To get any two Agents to work together a connection (called Interfaces in Integration Manager IM) needs to be defined.

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Let’s use a typical lab scenario of an instrument generating data and needing to share that data with a LIMS; a scientist will want to perform an analysis on some samples. The scientist creates a sequence (a set instructions for the instrument to perform) in the LIMS and sends it to the Instrument via Integration Manager. After the instrument performs the analysis, Integration Manager will send the results back to the LIMS. To do this a File Agent is installed on a machine and configured to write to the instrument input directory and also monitor the directory where the instrument is outputting files. For the sake of an example, let’s say a SampleManager Agent is installed on a machine and configured to talk to Thermo Scientific SampleManager LIMS. An Interface is then defined such that the File Agent knows about the Sample Manager Agent. The sequence is sent from SampleManager LIMS to the SampleManager Agent. Integration Manager converts this request into something the instrument will understand and then writes these instructions into the instrument’s input directory. After the instrument performs the analysis it writes a file with the results. The File Agent will pick up that file, process it and send the necessary information to the SampleManager Agent. The SampleManager Agent then handles putting the information into SampleManager LIMS. The same scenario could take place across multiple instruments in the lab, and across multiple, and changing, daily workflows.

As laboratories look to streamline the flow of information, having multiple disparate systems with minimal to no connectivity is no longer an option. The shift to a laboratory fully integrated with the enterprise yields a greatly enriched user experience that allows individuals and organizations to not only manage and capture their data more efficiently and securely, but also to simplify their daily workflow.

You can learn more about Integration Manager and other integration solutions by reading about CONNECTS for the Paperless Lab or emailing us at

There’s a lot of technical detail that’s been glossed over here. In upcoming articles I’ll discuss some of the tools Integration Manager uses to install and configure the Agents, including specific Agents like the ERP and Forms Agent and how Integration Manager translates data from one format to another.

Technical content for this blog post was provided by William Frati, Software Development Manager, Informatics Business, Thermo Fisher Scientific.


We hope this information was valuable to you. Your comments are most welcome and appreciated.