Laboratory Information Management System Records

The LIMS Record Problem

Any organization setting up a LIMS struggles with the Laboratory Information Management System Records problem. Understanding the different types of records going into a LIMS is more challenging than one would think. LIMS applications are designed to be generic enough. This requires the use of generic terms that can create confusion in a particular context. For instance, many synthetic biology laboratories use plasmids on a daily basis. Should plasmids be recorded as sequences, bacterial strains, or samples? Chances are that each member of your lab will have a different perspective on this issue. It is also possible that their perspective will change over time. The consequence of this situation is that the plasmids used by your lab will be found in different areas of your LIMS or that they won’t be recorded because the users are not sure how to record them.

In this tutorial, we propose convention directly applicable to the LabCollector LIMS. Similar conventions can be adapted to other LIMS systems. The LabCollector home page includes multiple modules. The proper use of the sequence, plasmid, strain & cell lines, and samples is the most common source of confusion.

Laboratory Information Management System Records

Categories of Laboratory Information Management System Records

Sequences

Sequences are just that. Sequences are data. They are not physically available.

In a synthetic biology context, sequences can be regarded as the objective of a vector assembly workflow. The sequence module can be used to keep track of what we want to make rather than what we have already made. As a reminder, you will notice that sequences do not have storage area associated with them.

Plasmids

Plasmids can mean different to very different objects. It can mean the sequence of a circular DNA molecule. It can also refer to a solution of the DNA molecule itself that can be used for a transformation. Finally, some people would refer to a bacterial strain carrying a plasmid as the plasmid itself.

We recommend recording using the Plasmid module to record samples containing the physical plasmid in some long-term storage format. Plasmids correspond to tubes that you have somewhere in your lab. If you can transform bacteria with the content of this tube it’s probably a plasmid. We also recommend using the Plasmid module only to record verified plasmids or plasmids of known sequences. Plasmids generated as part of a workflow like unsequenced plasmids are best recorded as Samples.

Cells and Strains

Records in the Cells and Strains module should be reserved for biological material that has been extensively characterized and sequenced. As a rule of thumb, if you want to keep it in a -80C freezer, then it should probably be recorded in the Cells and Strains module.

What you do not want to record in this module are cell cultures. We recommend recording them as samples.

Samples

Samples are everything else. And we really mean everything. The natural tendancy of first-time users of LIMS is to only record the sample intended for long term storage. There is an innate reluctance to record working samples.

The sample module should be used to record all the working samples that are not intended for long term storage. This module allows users to define different categories of sample types. This feature should be taken advantage to distinguish different categories of samples like cell culture or PCR products.