Violin

Instruction

Cello and Eugene requires users to learn Verilog or Eugene languages, making synthetic biology specification less accessible.

Detailed presentation can see here

Installation

1. cd /violin

2. pip install -r requirment.txt

3. create your own requirement or add libraries, please use

   pip freeze > requirement.txt

4. Chrome Driver Installation

   1. check for chrome version: HELP->ABOUT
   2. download according to chrome version from Google
   3. If you are on windows, please add it to PATH

RUN(in CMD/cli)

1. pip install --editable .

2. violin(command example)

   1. violin --help

   2. violin startCello --input=pTac --input=pBAD --output=sigmaT7

   3. violin viewTruth

   4. violin viewVerilog

   5. violin createTruthTable

   6. violin compile

   7. violin emptyTruthTable
      how many input do you want? [1]: 2

Logic* Example*

• negation: 'not', '-', '~'
• logical disjunction: 'or'
• logical nor: 'nor'
• exclusive disjunction: 'xor', '!='
• logical conjunction: 'and'
• logical NAND: 'nand'
• material implication: '=>', 'implies'
• logical biconditional: '='

How we approached

3/20

• Study Python’s logic design syntax of specifying genetic construct (Li)Get familiar with Cello (Chen, Wang)*

4/3

• Learn how to compile python into Verilog (Wang)Learn how to run the compiled Verilog in Cello (Chen)*

4/17

• Find a way to get Cello output into Eugene and return the final design back to user (Chen, Wang)Write test code (Li)*

4/22 or 4/27

• (ALL)Complete the Video Prepare presentation*

Author

This project is for Boston University EC/BE 552

– Computational Synthetic Biology for Engineers -

Spring 2021

Instructor: Prof. Douglas Densmore (dougd@bu.edu)

1. Yaopu Wang
2. Yuxuan Chen
3. Yiming Li