Synthetic Biology:ToolsWishlist

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This page is a place to park / discuss ideas about future synthetic biology CAD software tools.

Tools ought to be designed like an extensible integrated development environment (IDE) such as Eclipse. Usability should be a primary design goal. The tools should make work more productive for synthetic biologists from a variety of backgrounds. Tools should work together, sharing a common representation for biological parts, devices, systems, and strains. New functionality ought to be easy to add via a plug-in API, and should be able to take advantage of a common framework for displaying and manipulating DNA sequences, parts, devices, systems, and strains.

Use Scenario

The scenario assumes some capability that we don't yet have.

A user wishes to design and test a new gene regulatory device based on a circuit with a desired feedback topology. She knows the output of the device should be transcription of any gene of interest (PoPS) and the input should be a non-metabolized small molecule.

Using the design tool, she draws circuits that implement her desired topology. The nodes in the circuit are not yet bound to actual biological parts, but are purely defined by abstract parameters such as binding constants and kinetic rates.

Using the simulation tool, she might explore the parameter space of her circuit, collecting data on which combinations of parameters produce an acceptable input / output or dynamic behavior.

She then could use the design tool to search for actual biological components that embody the acceptable parameter sets. If a part doesn’t exist, she can enter a DNA or protein sequence and the create it.

With biological components bound to the circuit, she then uses the assembler to design how the implementing biological components will be introduced into an organism. First she might select an organism (or strain or chassis). A codon optimized DNA sequence for any protein coding components would be created. The cloning and transformation details would all be worked out here. Is she intending to synthesisze the DNA de-novo or clone from existing physical DNA? What cloning / DNA assembly system do the physical parts conform to? What DNA primers need to be ordered?

Specific tools

Common Frameworks

  • Nucleotide / Protein display and manipulation framework.
  • Circuit display and manipulation framework.
  • Formal language for specifying or connecting parts or devices?

Project management tool

Design tool

Assembly tool

Simulation tool