constellation-js

Latest stable version available at ConstellationCAD

Usage

Requirements

Local UI

git clone [email protected]:hicsail/constellation-js.git
npm run build && npm run start

Then open http://localhost:8082/ on browser

NPM Package

The package can be installed in the following way.

npm install constellation-js

It is possible to generate a collection of designs that match a specification using graph construction and traversals.

const constellation = require('constellation-js');
let goldbar = '{PT7_a then galK}';
let categories = {
	"PT7_a":{
	  "promoter": [
	    "PT7_WTa",
	    "PT7_3a",
	    "PT7_1a"
	    ]
      },
	"galK":{
	  "cds": [
	    "galK"
	    ]
      }
}
let result = constellation.goldbar(goldbar, categories, {designName: 'my-first-design'});
// result.stateGraph, result.designs, result.sbol, result.messages

Optional parameters	Description
designName	Name of design space for SBOL output, defaults is "constellation-design"
numDesigns	Max number of designs to enumerate, default is 20
maxCycles	Cycle depth for -orMore operators, default is 0
representation	Choose between EDGE or NODE based graph, default is EDGE

Output	Description
stateGraph	See Graph Data Structure
designs	List of enumerated designs
sbol	See Synthetic Biology Open Language
messages	Errors or warnings, if applicable

It is also possible to generate a collection of designs that match a specification using a purely symbolic approach (note that this approach supports only a tolerance of 0 for the AND operator and does not support the MERGE operator).

let result = constellation.symbolic(
               "(one-or-more a) then (one-or-more x)", 
               {"a": {"b": ["c"]}, "x":{"y": ["z1", "z2", "z3"]}}, 
               {"numDesigns": 'all', "maxCycles":7});

Case Studies

GOLDBAR syntax for the case studies described in the manuscript are available here and can be demoed on Constellation's UI via the drop down menu.

Design Space Representations

Genetic design spaces in Constellation are represented in three ways:

1. GOLDBAR
2. Directed cyclic graph
3. SBOL

GOLDBAR Syntax

The supported GOLDBAR concrete syntax for genetic design spaces is presented below using extended BNF notation. Notice that then and . are equivalent, and the delimiters (...) and {...} are equivalent.

 <seq> ::= <exp> then <seq>
        |  <exp> . <seq>
        |  <exp>

 <exp> ::= <term> or <exp>
        |  <term> and0 <exp>
        |  <term> and1 <exp>
        |  <term> and2 <exp>
        |  <term> merge <exp>
        |  <term>

<term> ::= one-or-more <term>
        |  zero-or-more <term>
        |  zero-or-one <term>
        |  reverse-comp <term>
        |  ( <seq> )
        |  { <seq> }
        |  <atom>

<atom> ::= ([A-Za-z0-9]|-|_)+

The JSON schema for the GOLDBAR abstract syntax tree representation (parsed from the concrete syntax presented above) can be found in schemas/ast.schema.json.

Graph Data Structure

Constellation supports both NODE and EDGE based versions of a design space. Below are examples equivalent to the GOLDBAR specification promoter then one-or-more CDS then terminator

Visualization of node-based graph	Visualization of edge-based graph

The JSON schema for a design space graph can be found in schemas/graph.schema.json. Below is an example of a node-based graph within a single node in JSON format.

{
  "604571a7-9e38-4647-afd0-9546399480b5": {
    "id": "604571a7-9e38-4647-afd0-9546399480b5",
    "text": "root",
    "type": "root",
    "edges": [
      "b79407eb-95f0-4b78-99da-779f2c9cad46",
      "7f6ca2fb-ef67-4687-924c-4285de896877"
    ],
    "operator": ["One"]
  }
}

Synthetic Biology Open Language

SBOL is an open standard for the representation of in silico biological designs, and the icons used in this tool are provided by SBOL Visual. Design spaces are expressed in SBOL via the CombinatorialDerivation extension and can be exported and stored in Knox. This third form of design space representation allows Constellation to be easily integrated in the synthetic biology community.

Manuscript

Nicholas Roehner, James Roberts, Andrei Lapets, Dany Gould, Vidya Akavoor, Lucy Qin, D. Benjamin Gordon, Christopher Voigt, and Douglas Densmore. GOLDBAR: A Framework for Combinatorial Biological Design. ACS Synthetic Biology Article ASAP (2024).

DOI: https://pubs.acs.org/doi/full/10.1021/acssynbio.4c00296