For Want of a Nail

For Want of a Nail

For want of a nail the shoe was lost.
For want of a shoe the horse was lost.
For want of a horse the rider was lost.
For want of a rider the message was lost.
For want of a message the battle was lost.
For want of a battle the kingdom was lost.

Beyond a mild appreciation for the historical value of the 14th century proverb, how does the above text relate to life in the molecular biology lab?   An interesting case study follows that may shed some light on the subject.

A couple of weeks ago, SeqGen was hired to perform the annual preventative maintenance on a 3130 Genetic Analyzer.   The engineer completed the required service, but unfortunately discovered that the recently relocated machine had a broken right door sensor, that, at the time, was not affecting the operation of the instrument. The end user was alerted to the potential problem, the issue was notated on the report, and the engineer closed out the job.

Shortly thereafter, the end user reported that the machine had stopped while running the fifth plate in a series; the array had become misaligned and actually appeared bent. At first glance, it was not obvious how this could have happened so soon after a preventative maintenance, spectral calibration, and several successful sample runs. SeqGen’s Service Manager was consulted and he posed a potential explanation for what could have happened.

If the door sensor had malfunctioned during the running of the fifth plate, the machine would believe the sequencer door was open. This would trip the safety mechanism built into the machine to protect end users from exposure to the laser and the machine would shut down.   An unfortunate side affect of a sequencer shutting down mid-run, is that the data collection software can become “confused”. Life Technologies’ data collection software is a very complex database and is prone to some interesting “quirks” if interrupted. Stopping the database may result in lost data, lost hardware settings, or a lost database altogether.   As we can see – losing the “message” as a result of a lost “shoe” (or possibly a door sensor) can result in an unfortunate series of events.


If you find yourself in this situation, please follow these steps before you restart your machine. You may also want to give SeqGen a call if you suspect that your software has been corrupted.

  1. Close the data collection software
  2. Shut-down your instrument
  3. Shut-down or restart your computer
  4. Call SeqGen if you suspect any potential hardware or software issues. It may be necessary for a trained engineer to reinstall your software.

Conversely, the proper sequence to restart your sequencer is as follows:

  1. Turn on your computer
  2. Power up your sequencer
  3. Wait until your sequencer displays a green light
  4. Restart machine software

Careful attention to details can prevent thousands of dollars in potential damage. Even a door sensor, which only costs a few hundred dollars, may cause a battle (or array or data or….) to be lost!

Written by Susan Henry

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