Tools, Software, and Data

BacterAI

• Read the BacterAI paper here.
• Check out our lab's automation hardware.
• Code is available on our GitHub page.
• Download growth data for all experiments in the paper.

Web Tools

	CutFree Design pools of DNA barcodes compatible with restriction enzymes. [website] [code]
	PrimerLiner Quickly check alignment of primers and oligonucleotides. [website] [code]
	Enzyme Kinetics Interactively fit enzyme kinetics data. [website]
	EduSeq Create hand-on lessons for learning DNA assembly. [website] [paper]

Data & Code

• OligoRL: A reinforcement learning framework for pooled oligonucleotide design. (David 2021)
  • Julia code (GitHub)


• gapsplit: Efficient random sampling for COBRA models. (Keaty 2019)
  • Matlab and Python code (GitHub)


• Cached Flux Coupling and FALCON (Pradhan 2019)
  • R package for cachedFCF, FALCON, and delete-and-couple
  • Python package for cachedFCF
  • R code and data for simulations and figures