TeselaGen's Materials and Inventory Management Toolkit uses hierarchy levels with your abstract and physical entities. This organizes your data on different layers or information levels, allowing a better control organization for your Lab Inventory Management System.

At the topmost level of the organization, we find an abstract entity (that may be a molecule's sequence). Those entities can be found under the "Molecules" and "Cells and Genomes" libraries of the Molecular Biology Toolkit. On your libraries, the entries you add represent a piece of information that is not necessarily linked to any particular physical molecule, so we call it "Reference Information"

For example, Functional Protein Units are an abstraction helpful in focusing one's attention on regions of a protein of particular interest for protein engineers. At this level, our schema looks something like this:

At the next level, we have the notion of "Materials". A material is tied tightly to its corresponding reference information and is used as a bridge to the real world of samples and aliquots. You can think of materials as the somewhat abstract idea of a biological entity, while it's still an abstract piece of information, it is actually linked to a physical entry. With this information, our schema looks like this:

Materials available in the system are found under the "Materials" libraries from the Materials and Inventory Management Toolkit.

Under the "Materials" level, we get actual samples and aliquots. Samples make the connection between various types of materials and their physical presence in the lab as an aliquot with a volume, concentration, plate/well, location, etc. Think of the hierarchy like this: an abstract entity (Reference Information) is just a theoretical entry, and a Material contains the theoretical information belonging to a physical sample. On the Materials libraries, you can see and edit information on the molecule itself, while on the Samples Inventory, you can see and edit information on the concentration, availability, physical location in the lab, etc.

From Samples, you can create as many aliquots as you want/need (as long as the total volume of aliquots doesn't surpass the total volume of the sample). Many samples can be associated with a material and many aliquots can be associated with an originating sample.

The need for these three levels of abstraction becomes clear in more complex workflows such as hit picking, say for sequencing QC purposes, where you may take several distinct "samples" in the form of colonies all of which point to the same reference information, but from which will be derived separate aliquots in later steps, eventually leading to sequencing data (measured sequence) which we want to keep distinct and unique to the sample/hit for comparison to the original reference sequence. Volume tracking is also a necessary feature for full-tracking systems like TeselaGen, but often volume needs to be adjusted, so the system allows you to modify or add to volumes and adjust concentrations as needed. With this next level of tracking our set of relationships might look something like this:

Tracking in the real world adds a good deal of complexity. Here we show a simplified workflow for what might be a microbial transformation followed at some point by protein extraction and purification. We are leaving out steps to focus on how tracking is done at the sample/aliquot level.

In this example, 100 µL from microbial material "Sample A, Tube C, Aliquot 15" is pooled with 100 µL from DNA material "Sample B, Tube B, Aliquot 14". This "(Pooled) Sample C, Tube D, Aliquot 16" constitutes a "Formulation" that brought two distinct samples/aliquots together.

Next, a reaction between the two samples is recorded via a 'Reaction Map' whereby the 'Two Material Pooled Sample C' is transformed into a 'New Material Sample C, Tube D, Aliquot 16'. Note that the reaction vessel 'Tube D' and the aliquot 'Aliquot 16' stay the same in this example.

In the final step, a 30 µL aliquot is taken from "Sample C, Tube D Aliquot 16" into "Sample C, Tube E, Aliquot 17", then put through a "protein purification" step that is captured by another reaction map and worklist, yielding a final product "Sample D, Tube F, Aliquot 18". Note that in a process like protein purification that may use intermediate tubes and plates that are not saved, the most important entities to track are those that are input to a procedure and those that emerge at the end.

Note that the final purified protein is automatically tied back to the material definition and reference information for the protein.