Software

Coral
DNA Design Software.

Coral is a Python library for encoding the process of designing synthetic DNA constructs. Coral mirrors the traditional design steps used in GUI-based sequence design (ApE, j5, Benchling, etc.) as operations on data structures, enables iterative design through analysis modules, and connects seamlessly to outside libraries. Through the use of Coral, you can translate your DNA design processes into concise, executable, and reusable scripts.

Aquarium
Your protocols will be assimilated.

Aquarium is a framework for semi-formally representing wetlab protocols and methods as executable computer code. You write protocols our new language, called Plankton, and keep them under version control in github. The protocols are interpreted by Aquarium by displaying each step to a lab technician working at the bench. Every step, every piece of data, every sample used, is tracked and detailed logs of the execution of the protocol are saved. Cameras, RFID readers, and other sensors track even more details. The result is 99% reproducible methods!

gro
The cell programming language.

gro is a language for programming the behavior of cells in growing microcolonies of microorganisms. An associated simulator models cell growth, cell division, intrinsic and extrinsic noise, diffusing molecular signals, and more. gro is used to prototype multicell behaviors and check that local interaction rules produce the desired global result. The language allows behaviors to be specified at whatever level of abstraction makes sense: from high level code, to low level biomolecular interations.