Software for Programming Cells

Explore a comprehensive overview of programming living cells using advanced software tools in this 37-minute conference talk from Strange Loop 2013. Dive into the world of molecular circuits and genetic computation devices, learning how to characterize genetic parts and combine them into functional devices. Discover the potential of cell programming for breakthroughs in disease treatment, sustainable agriculture, and understanding life itself. Follow along as the speaker demonstrates a web-based software tool chain, presents a molecular program of an optimal consensus algorithm, and shows results of a working system compiled into DNA. Gain insights into DNA strand displacement, biophysical modeling, and the challenges of applying programming methods to biology. Understand the parallels between programming digital computers and living cells, and explore the future possibilities of biotechnology enabled by cell programming software.

Intro
Programming (biology) Molecules
Machine Code (DNA)
DNA codes the proteins
Strange loops
DNA strands
DNA Strand Affinity Short complementary segments bind reversibly
Bind, Migrate, Displace
Domain abstraction (assembler)
DNA strand displacement
A DNA Consensus Algorithm
Molecular components
Analysing function: Z3 SMT Solver
Programming cells Molecules
Cross-platform coding
Synthetic Biology Software
Cell programming
Transcription
Low-level DNA Language A simplified view of DNA instructions
Repressilator
Programming (macro)
Biophysical Modelling
Biophysical patterning
Biological Computation Group