Sample management
The majority of labs in the fields of biology, chemistry and medicine deal with samples in their research. These samples are of many kinds, e.g. blood, DNA, bacteria, etc., and fall into various categories, e.g. clinical and non-clinical. A lot is done to the samples, e.g. they are split into aliquots, shipped between facilities, checked in and out of freezers, counted, analyzed, and used in experiments.
Managing samples is a core function for these labs, and it is not be possible for the researchers who work in the labs to realize their core mission-carrying out experiments-without effective sample management. The physical side of sample management is highly standardized: samples are most often place in trays of standard configurations inside boxes, also of standard configurations, inside freezers, also of standard configurations. In many academic labs, keeping track of where a sample is, its history, whether it has been aliquoted, and other information about the sample is done by hand on a paper record, typically placed near the freezer and/or recorded in spreadsheets.
Depending on the size of the lab, the nature of the research, and where the lab falls on the spectrum of group-oriented to individual researcher-oriented, sample management may be handled by one or two people in the lab, or it may be something that many or most people do themselves from time to time. Thus one person or, more often, multiple people have access to the sample record and participate in its development.
In this environment, basic sample management needs include:
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To store all sample information, aliquot numbers, dates, web links and images
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To set alerts
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To generate reports
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To graphically display containers containing samples
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To name containers
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To assign roles-who can do what with which categories of samples
Experimental data management
For labs that use samples as an integral part of their research, managing samples is a vital task, but it is only a means to an end, conducting experiments. Samples, and analysis of samples, are used in experiments. Experiments are often carried out on the basis of protocols. They are usually documented with a mix of paper lab notebooks and things in electronic form like spreadsheets, Word documents, PDFs, and images in scientific formats. In addition to information specifically relating to experiments, labs also record general information like meeting notes. This general information, but not the data relating specifically to experiments, is increasingly created and shared within an online collaborative tool like a wiki.
With sample management a few well defined roles usually provides sufficient differentiation to reflect the differentiation of labor in the lab. When it comes to general information sharing and in particular management of experimental data, however, a finer grained controls system is needed, for example so that each individual in the lab can have their own completely private space, some records can be shared by specified groups or between the PI and a student, and some records can be seen by everyone in the lab.
Barriers to adoption of integrated management of samples and experimental data
The above picture of how labs in universities and government research institutions deal with experimental data and sample data reinforces the point that they have been slow to adopt electronic lab notebooks and sample management software. There are a variety of reasons for this, prominent among them inertia and the difficulty of making decisions in a consensual environment [5]. Other factors include price, the simplicity, flexibility, convenience and familiarity of paper notebooks and spreadsheets, conservatism on the part of PIs, and concerns about being tied in to proprietary file formats which might make data inaccessible in the future and/or how to ensure that records kept electronically enable compliance with regulations like 21 CFR part 11 [6].