Where sample management meets electronic lab notebook


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What is sample management?

 

Three conceptions of sample managment

Sample management seems like a pretty simple concept — managing your samples for goodness sake!  But in the context of a lab things get a bit more complicated.  I’ve commented below on the three different conceptions of sample management, the perspectives and objectives they imply, and the kinds of tools available for managing samples in each of them.

Samples management as part of a LIMS

Strangely wikipedia does not have a separate entry on sample management.  Instead sample management is covered under section 2.1.1 of the LIMS entry!  There it says, “the core function of LIMS has traditionally been management of samples.”  The entry goes on to point out, however, that over the past 20 years  the focus (or at least the focus of people who look at sample management from a LIMS perspective!) has shifted from managing samples to managing information.  For clinical research and other kinds of research in heavily regulated environments samples have been reduced to a subsidiary role; they are just one of many kinds of  ‘information’ whose history needs to be recorded and tracked, and to the extent possible integrated with other kinds of information about relevant things taking place in the lab.  In these regulated environments the key drivers are accountability and reproducibility:  everything needs to be tracked, recorded, analyzed and prepared for subsequent review and attack.

Sample management as sample tracking

A second perspective puts the focus back on the samples themselves.  Perhaps partly as a corrective to the relegation of samples  in heavily regulated environments to just another form of information, ‘sample tracking’ has developed as a distinct activity in its own right.  A prime example is biobanking. A biobank is defined by Wikipedia as a cryogenic storage facility used to archive biological samples for use in research and experiments.  In biobanking the focus is firmly back on the samples themselves, and as such it is important to track everything that happens to them:  their provenance, when they enter the bank, what happens to them after that, etc. Samples are used in research and experiments, but the focus of the management is on the samples themselves, not the research or experiments or, as when LIMS are involved, the entire information history of the research environment.  Biobanking applications, both generic systems and bespoke systems created or commissioned by biobanks, have developed to carrying out the tracking functions needed by the biobanks.

Putting sample management back into the experimental process

‘Originally’, or back before LIMS and then biobanks anyway, samples were created and collected primarily to be used in experiments and research.  As can be seen from the brief look into LIMS and biobanking above, somewhat ironically one consequence of the scaling up of research that is both cause and consequence of increased regulation and mass collection and storage (biobanking) is that sample management has become divorced from research and experimentation.  Most labs in universities and government research institutions, which operate in a relatively unregulated environment and manage their own samples, view sample management and documenting research as distinct activities.  In line with this, they use different tools to manage samples — typically spreadsheets — and to document experiments — typically lab notebooks.

Since samples are at the heart of a wide range of biomedical experiments, this separation does not make a great deal of sense.   It is likely to persist, however, until affordable and easy to use tools become available that enable labs to manage samples and document experiments in an integrated environment.  That is exactly what we have tried to do with version 4.0 of the electronic lab notebook eCAT, which will be launched on May 11.  eCAT 4.0 has full sample management capabilities including support for barcoding, and these are integrated with the existing notebook functionality so that it is easy to make links and references between samples and the experiments they are used in.

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