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Hardware, Software, and Wetware Codesign Environment for Synthetic Biology.

Samuel M D Oliveira1,2, Douglas Densmore1,2

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Synthetic biology advances through biodesign automation, integrating software, robotics, and microfluidics. This "hardware, software, wetware" approach enables automated design of genetic circuits for diverse applications.

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Area of Science:

  • Synthetic biology and bioengineering.
  • Computational biology and bioinformatics.
  • Automation and robotics in life sciences.

Background:

  • Synthetic biology enables engineering of living systems for applications in materials, agriculture, medicine, and energy.
  • Traditional biological design is often slow and iterative.
  • Borrowing principles from embedded electronics design can accelerate biological engineering.

Purpose of the Study:

  • To present a "hardware, software, wetware" codesign framework for synthetic biology.
  • To introduce "biodesign automation" by integrating software, robotics, and microfluidics.
  • To enable parallel generation of hardware, software, and wetware from a single specification.

Main Methods:

  • Developing "genetic compilers" to translate high-level specifications into genetic circuits (wetware).
  • Designing automation equipment, workflows, and microfluidic devices (hardware) for circuit execution and testing.
  • Implementing scheduling and control algorithms (software) for system management and data analysis.

Main Results:

  • A unified "hardware, software, wetware" codesign approach derived from a single specification.
  • Enabling parallel generation of biological systems tailored to specific cost, performance, and structural needs.
  • Potential for massively parallel experimental platforms or distributed biosensing/bioremediation devices.

Conclusions:

  • Biodesign automation offers a powerful paradigm for accelerating the engineering of biological systems.
  • The integrated codesign approach streamlines the creation of complex synthetic biology applications.
  • This framework facilitates the development of future biological systems with predictable and customizable functionalities.