Glossary: DESIGN Module

A list of the main concepts and terms used on the DESIGN module that may assist you at any moment.

Written by Eduardo Abeliuk
Updated over a week ago

Here is a glossary to assist you with the main concepts and the vocabulary used on the DESIGN module. You can also access it within the platform: click on your profile upper right hand corner and you’ll see a drop down menu with an option for ‘Glossary’. After hitting it the pop-up does not interfere with your actual screen and you can consult it whenever you want while you are in the module.

Assembly Report
A generated report containing instructions for combining parts into assembled constructs.

Assembly method
A strategy to create assembled constructs based on experimental approaches (MoClo, Golden Gate, Gibson) automated with j5 technology that optimizes the design process. 

A tool that allows you create new alignments from your sequences (Multiple Sequence Alignment, Pairwise Alignment and Map to Reference Sequence) and visualizes the alignments that you’ve already done.

Base Pairs
Type in base pairs of DNA that can be inserted into a design as a part without defining it first on a sequence.

A container for parts in the design editor that typically represents a functional group of the target construct. Each assembled construct contains one part from each bin in the design.

Seen in hierarchical views of the design editor, cards contain one or more bins and represent the sequence(s) resulting from the combination of the parts in the bins that they contain.

Combination Group
Used at the moment to “knock out” a subset of combinations in an hierarchical design so they won’t be submitted for assembly. The combination groups are displayed in the same combinatorial fashion as non-list layout designs (as much more compact way of displaying information that listing each combination of parts individually).

Design from an Alignment of Parallel Parts that Expose Regions of Diversity

Design Rule
Constraints that can be added to bins in a design editor that will throw warnings when their specifications aren’t met.

Regex Design Rule
Constraints that validate the bps of a part, e.g. throw warning if a CDS part does not start with ATG.

Tag Design Rule
Constraints that validate parts in design based on the presence or lack of presence of tags.

Design Rule Set
A grouping of Design Rules that can be applied to a bin in a design.

Design Template
Can be used to capture portions of designs that are reused from design to design, and can be applied within the design editor to quickly build out a design in an automated fashion.

Eugene Rule
Constraints for reducing the number of combinations produced by a design by linking together two parts with certain logical operators.

An annotation on a sequence (cannot be inserted into a design for assembly).

A high-level entity that multiple people can access (and thus a way to share data). Different entities can be moved into an  organized within them.

A special type of annotation on sequence that can be inserted into a design for assembly. 

Part Set
A grouping of parts that can be inserted into a design (once cell represents many parts).

Reactant Group
When adding a reaction the user starts with the assembly product and breaks it down into the inputs into the assembly reaction that produces it. The reactant group is what we call the input into the reaction which will be a grouping of bins (although a group can be just one bin).

Synthetic Biology Open Language which is an open standard for the representation of in silico biological designs. You can find it on the header of the design editor clicking “show SBOL”.

An abstract representation of a design that can be used to create a generic snapshot of a design or to kick off the design process at a higher level (they can be converted to designs).

Labels that can be added to tags and subsequently used for filtering and design rule validation.

Unmapped Part

A part that hasn’t yet been associated with any DNA.

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