Printouts, spreadsheets and a lot of careful typing
The instrument finishes its run and produces a report. Some are exported as CSV, some only as PDF or a printout. The analyst opens the Excel sheet your lab uses for that method, types in the readings, the sheet calculates results with dilution factors, and the analyst then types the final results into the LIMS against each sample ID. A colleague checks the transcription.
Across a lab with several instruments, older ones in particular, this is a large part of an analyst's day.
Why instruments are still not connected
- Full LIMS interfaces are expensive and each instrument is different.
- Older instruments only export files or print reports.
- Calculations live in Excel sheets built over years.
- Sample sequences on the instrument use different IDs from the LIMS.
- Validation of any change feels daunting, so the manual process stays.
The spreadsheets themselves are a hidden risk. They were built by capable people years ago, have been copied and adjusted since, and often nobody is quite sure which copy is the approved one. A formula that was changed for a one-off job and never changed back can sit unnoticed for months.
What transcription costs
Analyst time goes into typing and double checking instead of analysis. Transcription errors still slip through and lead to amended reports. Calculation spreadsheets are hard to control and can be changed without anyone noticing. Results reach the LIMS later than they could, adding to turnaround.
| Step | Manual | With data capture |
|---|---|---|
| Instrument output | Printed or exported | File picked up from a watched folder |
| Parsing | Read by eye | Parsed by a tested routine for that instrument |
| Calculation | Uncontrolled Excel sheet | Approved calculation with version control |
| Sample matching | Analyst matches by hand | Sequence IDs matched to LIMS IDs, mismatches flagged |
| LIMS entry | Typed | Loaded for analyst review |
| Audit | Printout filed | Raw file stored with the result |
Peak periods make it worse. When sample numbers rise, instruments can run overnight, but results still wait for someone to type them in the morning. Transcription becomes the ceiling on how much the lab can report in a day.
How we build it
- For each instrument, we write a parser for its output format, tested against real files from your lab.
- Output files are saved to a watched folder, or collected from the instrument PC, and parsed automatically.
- Calculations from your spreadsheets are rebuilt as controlled, versioned routines, and checked against the spreadsheet results before use.
- Sequence positions and instrument sample names are matched to LIMS sample IDs. Anything that does not match is shown to the analyst.
- Results are loaded into the LIMS in a 'for review' state, never as authorised, through its API or import.
- The raw file and the calculation version are stored with each result.
- We provide documentation to support your validation of each parser and calculation.
Your lab validates and approves the routines before use, following your quality procedures. Analysts review every result as they do now.
What changes for analysts
Results arrive in the LIMS ready to review instead of waiting to be typed. Transcription checks become checks of the data, not of typing. Calculation spreadsheets are replaced by controlled routines. Results move faster, and the audit trail is better than before.
Retiring an old instrument or adding a new one also becomes more manageable, because each parser is a separate, documented piece. Adding a new instrument means writing and validating one parser, not reworking the whole process.
Is transcription eating your analysts' time?
- Instrument results are typed into Excel or the LIMS.
- Calculation spreadsheets are used for key methods.
- Transcription checks take a colleague's time.
- Amended reports come from typing errors.
- Older instruments have no LIMS interface.