Genetic Circuit Design for Extreme Environments Enabled by Models Extracted from Petabyte-Scale Perturbation Analyses
Abstract
Design and testing of genetic circuits is a laborious process requiring multiple design-test-build cycles whose processes, metadata, analyses, and naming conventions vary widely across groups performing synthetic biology. To alleviate the low-throughput and data-discrepancy challenges, we developed tools and techniques for automating high-throughput standardization, design, modeling, and sharing of genetic circuits and computational tools. SBOL and SynBioHub to facilitate the standardization, storing, and sharing of biological designs and relevant synthetic terms. Cello to standardize circuit design and modeling, and utilize SBOL for standardization. A full RNASeq pipeline from quality control, to mapping, to analysis, that leads to reproducible transcriptomics to help inform design and evaluation. A Landing Pad Selector, Genetic Circuit Analyzer, Genetic Circuit Simulator, and Whole Genome Simulator to analyze and simulate design of circuits. The resulting work for this group led to both novel computational tools and novel organisms that can be used in designs.
Document Details
- Document Type
- Technical Report
- Publication Date
- Sep 01, 2022
- Accession Number
- AD1179969
Entities
People
- Alexander J Triassi
- Alexander W. Cristofaro
- Amin E. Borujeni
- Benjamin A Garcia
- Benjamin Hatch
- Chris J Myers
- Christopher Voigt
- Daniel A Anderson
- Dany Fu
- David B. Gordon
- Douglas M. Densmore
- Elijah Jones
- Eric Yu
- Hamid Doosthosseini
- James Scholz
- Pedro Fontanarossa
- Rita Chen
- Samuel Oliveira
- Timothy S. Jones
- Una Saxena
- Yongjin Park
- Yuval Dorfan
- Zach Zundel
Organizations
- Massachusetts Institute of Technology