This glossary will help you with the main concepts and vocabulary used within various TeselaGen modules. This vocabulary is mainly based on biological experimentation’s nomenclature and the canonical language from LIMS (Laboratory Information Management System) software.
Is a division of a sample or another aliquot. The first aliquot of a defined sample is a sample-aliquot. Any further aliquots of that sample (made by dividing the sample-aliquot) is a replicate-aliquot. Aliquots are held within plates/containers and they have physical information such as volume, concentration, and mass.
Are used to group up material in the app and link them to the job that they are associated with. Once the batch is active, only inventory items (plates/tubes) that are associated with the batch will be viewable. All plates and tubes that are created while a batch is active will be assigned to that batch. This helps users filter inventory so that they can easily access what they need for a specific user request/job.
An eCommerce interface that allows you to order DNA sequences (from Twist, IDT and GenScript). This continually developing tool is intended to enable you to make your purchases without leaving the platform and to be able to trace each of the ordered sequences back to the corresponding assembly report in an efficient manner.
It holds different items from inventory. You can access it from the top menu: Inventory > Container, and create a new one, export an existent (as CSV file) or see the following details of the existing ones: “Name”, “Type”, “Label”, “Location”, “Position”, “Path”, “Added By”, “Created” and “Modified”.
A Data map stores lists of json values.
A collection of Data Tables, files, j5 reports, etc. than can be grouped by its type.
A Data Table stores a table of Data Rows which each points store a reference to an inventory item or j5 item.
A list of the items that are cataloged and inventoried in a lab. You can have access to it from the top menu bar as Inventory and see the different categories: Samples, Aliquots, Reagent Lots, Plates, Tubes, Locations, Equipment, Containers and Placement Strategies.
An Inventory List is a data table of aliquots. This can be useful for a "cherry-picking" operation where the user needs to be able to pick multiple aliquots from a host of different plates or tubes.
Subservient to "Requests", privileged internal users (admins) create "Jobs" in order to satisfy "Requests". Actually, a User Request (see below) can have one or more jobs. So, a job is just a way to micro-manage the work from a user request. Each job can have one or more batches/workflow runs.
It can be a Building, Lab, Floor, Room, etc. It is at a site and can be nested. You can access it from the top menu: Inventory > Locations, and create a new Location, export an existent (as CSV file) or see the following details of the existing ones: “Name”, “Type”, “Path”, “Site”, “Added By”, “Created”, “Modified”.
Is a definition of either a piece of DNA, or a strain (which could hold DNA). There can be many instances of the material -- these are tracked using the sample and aliquot data models. Material includes (from the menu’s option): “DNA sequences”, “Coding Sequences”, “Sequences features”, “Functional Protein Units”, “Aminoacid Sequences”, “Region Annotations”, “DNA materials”, “Microbial Materials”, “Protein Materials”, “Reagents”.
Plate (container array)
Is a type of container with NxM matrix of wells or NxM rack of tubes.
A list of wells that can be used to describe operations on a plate.
Is a type of container with a NxM matrix rack of tubes.
N to 1 mapping of aliquots of particular materials into a new aliquot of a possibly new material.
Set of reactions grouped together as a matter of course when executing a task or tool.
BUILD module entry point. Usually, users start by creating "Requests". Although they can create workflows independently of that step, so it is not mandatory (however, is good to know that a Workflow is subordinated to a Request from a hierarchical point of view).
A sample is the first instance of a new batch of a material. A sample is either a formulated-sample or a registered-sample. A formulated-sample is a sample which was created by containing two other samples together (for example as the result of a worklist execution). When a formulated-sample is created we also create sample formulation entries in the database which tracks the inputs and their quantities.
Atomic level unit of work. Also referred to as Task in the context of the workflows. Each Tool can be run from the Tool Library as an independent action, but also can be chained in a workflow that runs multiple Tools..
A library with the predetermined tools that you can have access from the top menu bar.
Tubes are used in the lab to contain single aliquots.
A user request is generated to keep track of a bulk of work that a user has to do for one of their clients.
Well contain single aliquots in the context of a plate.