Instrument Interface should be considered an essential part of a laboratories on-going goal of increasing compliance and efficiency. No longer will there be the thought of transcription errors, fears of data manipulation, and the time spent printing report and pasting them into notebooks. Understanding the demands of instrument interface are important, and as the benefits far exceed the effort, lab personnel will want to know how to navigate through the process of using their data repository (ELN/LIMS) to interface with instruments.

Are you or the scientists in your lab currently printing instrument reports and then pasting them into paper laboratory notebooks? Is the protocol to save the instrument report to pdf and then send it to ELN? Or, is the method to manually copy instrument data into your workbook?

These kinds of processes can be improved by switching to an ELN/LIMS, which offers a number of benefits:

  • Direct Access – eliminate searches for instrument reports through shared folders or, worse, file cabinets.
  • Instrument Data Repository – consolidate all instrument data in a single repository
  • Eliminate Transcriptions – instrument results are often copied for reporting or analysis
  • Context – associate a complete description of the context surrounding an instrument file or printout to assist understanding and facilitate searches
  • Communicate with Stakeholders – share instrument data with customers to enable informed decisions

Bring inhalation results to SciCord ELN

Bring all your instruments and documents into SciCord
  • An Electronic Repository Application – many products on the market can replace a paper notebook and support instrument interface including ELN, LIMS, LES. SciCord is built as a hybrid solution, offering the combined advantages of the other major data management schemes.
  • Instrument Data Repository – consolidate all instrument data in a single repository.
  • Connected – a means of porting the instrument output to the electronic repository, often a network connection but can be accomplished via “sneaker net” using a USB card to extract the instrument output from an unconnected device.

There are obstacles with creating an instrument interface, but when managed appropriately, the benefits become indispensable. SciCord is prepared to adapt to any instrument interface scenario, such as:

  • Instrument Variation – the sheer number of interface variations introduced by vendors, instrument models, and even firmware releases.


  • Technical Specifications – obtaining quality interface information from instrument vendors can be challenging and may require reverse engineering if the original company can’t provide documentation.
  • Software Supplier Support – If new instruments are being added that can’t be interfaced through the default SciCord resource configuration, SciCord has offices in America and Europe to ensure assistance can be provided regardless of your location or time-zone.
  • Coordinating Context – the context for a measurement must be seamlessly communicated between context source (the “notebook”) and the instrument. SciCord can produce custom templates or more generic modules to provide this context where needed.
  • Compliance – SciCord is fully validated for GxP environments (if needed), allowing instruments to retain compliance when interfaced through SciCord.

Instruments such as balances or pH meters often produce discrete measurements without automated sample introduction. This requires scientists to introduce the measurement target and instruct the instrument to obtain a measurement. SciCord can facilitate this process with pre-configured instrument resources and data extraction to link results to samples.

Instruments requiring a real-time connection can be handled in any of the following ways:

  • The Notebook application prescriptively defines a series of measurements. The scientist is prompted to “feed” the instrument in the prescribed order. Each measurement is then recorded with context.
  • The Notebook application is programmed to look for a scanned sample label and then associate the next instrument measurement with the scanned context object.
  • The Notebook application listens and displays the instrument measurement in real-time. The scientist records the displayed measurement into the context. This means the scientist can operate in any order and with complete flexibility.



Older, simpler instruments may require being connected to a networked printer to produce any output. SciCord can act as a “virtual printer” to obtain this output and record it appropriately.

  • The instrument generates a report which includes the measurements of interest and optionally the run time parameters and sample context.
  • Instrument reports are “printed” to a SciCord supplied printer driver. The printed report output is translated to pdf format and recorded as a file by the Notebook application. The context of the file can be supplied by the scientist.
  • Optionally, in addition to the pdf file, the printer driver may translate the printer output into a textual format to support parsing. The parsed data can then be utilized for summarizations or statistical analysis.

Application controlled, relatively high throughput instruments such as Moisture Meters or Chromatography often require manufacturer or third party software to run (such as Empower™). SciCord can then interface with this third party software to retrieve the data and further process it or link it to samples.

  • Individual instruments are managed by centralized software which facilitates analysis and storing the instrument output. The centralized software often exposes the instrument data through API (application programming interface), database connection, or web services. Managed instruments provide a single point of interface and eliminate the need to interface with individual instruments.
  • SciCord is the source of the sample context for a single sample or an entire run sequence. The sample context or sequence is uploaded to the centralized software to define a prescribed sequence/process. The centralized software incorporates the sample context with operational parameters and instructs an instrument to run. This step may be fully automated or may include manual steps.
  • The instrument executes and uploads the measurement information to the centralized software. SciCord communicates with the centralized software to obtain sample context and measurements which are in turn recorded in the notebook.




Many instruments are capable of generating an electronic file documenting either a single measurement or a sequence of measurements. The files often contain instrument parameters and may also contain the context of the measurement.

  • Files generated by networked instruments may be maintained on shared network drives which are readily available for use in SciCord.
  • In most cases, files are selected by the scientist for attachment to a SciCord document. A combination of file contents/name and context provided by the scientist at the time the file is inserted provide the context for the data.
  • Alternatively, instrument files may be directed to a shared directory which is monitored by SciCord. Files recorded to the shared directory are “picked up” and recorded. SciCord is often configured to expect certain types of files in specific directories and in some cases with prescribed nomenclature.
  • Specific information can be extracted from attached files using parsing techniques (see Parsing topic). The extracted information can provide sample context, distinct measurements, and instrument parameters.

Some instruments can regularly report one or measurements over time.

  • Similar to Real-Time instrumentation, these can be connected to the network directly with wireless, ethernet, or indirectly from RS232 output through an RS232 to IP converter.
  • Measurements are transmitted at intervals and collected in a database or other storage facility. Queries provide regular reports and results that break defined limits are flagged.



Instrument output can be parsed from an output string or file.

  • The outputs from laboratory instruments are not standardized. There are initiatives to generate standards across instrument vendors and models (Allotrope) but at this time, it can be assumed each instrument vendor will output data and reports in a proprietary format. The output format can differ between models and even firmware releases from the same vendor.
  • Because of the wide disparity in formats, there is no one “right” parsing application, methodology, or language. SciCord will adapt the parsing method as needed to include simple C# data matching or more complex regular expressions in order to ensure data is reliably extracted from the instrument output.