cello - Genetic circuit design automation

  •        33

The Cello input is a high-level logic specification written in Verilog, a hardware description language. The code is parsed to generate a truth table, and logic synthesis produces a circuit diagram with the genetically available gate types to implement the truth table. The gates in the circuit are assigned using experimentally characterized genetic gates. In assignment, a predicted circuit score guides a breadth-first search, or a Monte Carlo simulated annealing search. The assignment with the highest score is chosen, and this assignment can be physically implemented in a combinatorial number of different genetic layouts. The Eugene language is used for rule-based constrained combinatorial design of one or more final DNA sequence(s) for the designed circuit. Verilog programs start with a module keyword, followed by the module name, followed by the list of output and input wire names. Within a module definition, Cello currently parses three forms of Verilog: case statements, assign statements, and structural elements (examples below). Verilog code can be entered using a text editor and saved with a .v extension.

http://www.cellocad.org/
https://github.com/CIDARLAB/cello


Dependencies:

org.springframework.boot:spring-boot-starter-web:null
org.springframework.boot:spring-boot-starter:null
org.springframework.boot:spring-boot-starter-log4j:null
commons-fileupload:commons-fileupload:1.3.1
org.antlr:antlr4-maven-plugin:4.3
com.amazonaws:aws-java-sdk:1.9.22
org.sbolstandard:libSBOLj:2.2.1
org.cellocad:netsynth:1.0
org:eugene:2.0.1-SNAPSHOT
org.apache.derby:derby:10.11.1.1
org.eclipse.persistence:javax.persistence:2.1.0
org.eclipse.persistence:eclipselink:2.5.2
mysql:mysql-connector-java:5.1.25
org.projectlombok:lombok:1.16.6
log4j:log4j:1.2.17
org.apache.ant:ant:1.9.4
org.apache.commons:commons-math3:3.5
commons-io:commons-io:1.3.2
org.json:json:20090211
com.googlecode.json-simple:json-simple:1.1
com.google.code.gson:gson:2.3.1
com.google.guava:guava:17.0
org.codehaus.jackson:jackson-mapper-asl:1.9.13
org.zeroturnaround:zt-zip:1.8
org.apache.maven.plugins:maven-resources-plugin:3.0.2

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