• Eugene
• Spectacles
• Kepler
• Data Model

With the rise of partification in synthetic biology, there needs to be a formal specification to describe standard biological parts, especially when designing complex devices. The specification needs to be both human-writable and human-readable, a language that raises the level of abstraction where bioengineers can work. Eugene is such a language. Engineering at the part level requires both flexibility and rigidity. Eugene allows the user to mix custom parts with predefined parts from established databases. Parts can encapsulate an arbitrary amount of information, anything from a DNA sequence to experimental history. When designing a device in Eugene, parts can be freely stitched together on a whim, or strictly joined together based on rules. The design process is meant to be systematic yet intuitive. The user considers what information parts include, constructs parts to be used in the design, enforces restrictions on how parts can interact, and creates devices that are composites of the parts or other devices. Being a textual design, a device specified in Eugene is portable and easily lends itself to being translated into other formats, such as XML. In synthetic biology, the notion of part changes regularly and is debated tirelessly. Thus, Eugene tries to be adaptable and expressive in any climate. This page goes into the language specification in detail.

Language Definition

In this section we describe the elements in the language. These involve: primitive data types, properties, parts, devices, rules, and conditional execution. The relationships between these language elements are shown in Figure 2. Here you can see that each subsequent category is built upon the previous category.

Figure 2: Relationship between Eugene Categories

Primitives
The language supports five predefined primitives. These are txt, num, boolean, txt[], and num[]. Strings (sequences of characters) are represented through the data type “txt”, where the actual text is specified in double quotes. Real numbers and integers are supported by the data type “num” and logical values by the data type “boolean”. Ordered lists of num and txt values can be created and individual members inside a list accessed by specifying an integer in the range from 0 to |List| - 1.

Examples (1) and (2) are two real code snippets of how primitives can be specified in Eugene. “listOfSequences” is simply a list of 3 arbitrary DNA sequences. “specificSequence” is the last element of “listOfSequences” (i.e. “ATCG”). Examples (3) and (4) show how the data type “num” can support integers and decimals.

Properties
Properties represent characteristics of interest and are defined by primitives and associated with Parts. For example a user could define a property “Sequence” (the DNA sequence), ID (the uuid for a relational database which may hold the part), or Orientation (e.g. a forward or backward promoter). Examples 3-5 show how such properties would be defined. Property definitions must be defined by the five primitive types. In Part definitions properties will be bound to that Part as placeholders for the instantiation of values in Part declarations. Properties have to be defined before Parts can use them. The user can create new Property labels or use those created by other users and captured in “header files” . For example, the following Properties are predefined in the header file PropertyDefinition.h and do not need to be defined again if the header file is included in the main program: