The codebase for PuppeteerLite is intended as a proof of concept for users to replicate the results shown in the manuscript, using the example files supplied in the Supplemental Section.
A full web based version of Puppeteer is currently in development.
-
Python3
-
Pip
-
Dependencies
$ pip install biopython requests xlwt
-
Clone or download this repository
-
Detailed installation instructions are included in this repository for MacOS and Windows, see
Run_Puppeteer_MacOS_for_Biologists.docx or
Run_Puppeteer_Windows_for_Biologists.docx -
Enter the commands below to run Puppeteer Lite. The format is as follows: "./run_puppeteer_lite [input archive] [number of designs requested]" The example below uses the 'HeadtoHead2.zip' input archive and requests 42 combinatorial designs. The input archive must be in the same directory in which the user runs commands.
$ chmod u+x run_puppeteer_lite
$ ./run_puppeteer_lite HeadtoHead2.zip 42
- GenBank Files
- An example input archive, HeadtoHead2.zip, is in the repository Zip files must follow the same folder structure
-
PuppeteerLite currently uses the MoClo Assembly Protocol.
-
The PuppeteerLite scripts in this repository parses the input data and calls Constellation, a combinatorial design engine, to enumerate circuit designs with the specification "promoter then rbs then cds then terminator".
-
When the designs are returned, a backend engine is called to generate the build instructions, which is then parsed by PuppeteerLite to produce the output indicated below.
PuppeteerLite writes the following files to the local directory:
- Tecan_Directions.gwl
- Provides Tecan robot instructions.
- nGB_Sequences
- A directory with n GenBank files - one for each new design created.
- Experiment_Summary.xsl
- Provides a visual of source plate assignments, output plate, and lists parts used.