Large-scale example of Proto motif-based compilation: (a) a two-bit adder program, interpreted into a Proto computation and (b) transformed into an optimized genetic regulatory network (GRN) which is approximately half the size of the original network.

<p>The image is color coded to distinguish crossing edges; small-molecule binding reactions are elided. Note that although in this case the initial gene network has a one-to-one mapping between Proto operations and regulatory proteins, the final implementation logic is largely but not entirely inverted.</p

Optimization results for the four test systems.

<p>Optimization results for the four test systems.</p

Proto code for a two-bit adder, showing operators in color.

<p>Inputs are purple, logic operators are red, functions are blue-green, and outputs are in their corresponding color.</p

Simulation of automatically generated genetic regulatory networks executing for single-not, three-gate, and quad-not programs.

<p>The upper graphs for each network show small-molecule input concentrations and the bottom graphs show output GFP concentrations for the optimized (solid blue) and unoptimized (dashed black) networks.</p

Transfer function experiments and requirements.

<p>Model and parameters are based on sigmoidal behaviors documented in the experimental literature, as in the graph from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022490#pone.0022490-Subramanian1" target="_blank">[30]</a> shown in (a), showing sigmoidal responses of green and red fluorescence proteins upon Doxycycline (Dox) induction. In this network implemented in AINV15 cells, Dox binds rtTA and activates expression from the TRE promoter of an Enhanced Green Fluorescence Protein and mammalian-optimized LacI repressor. In turn, LacI represses production of DsRed2 from a Hef1a promoter engineered with lac operators. (b) Every sigmoidal curve has an input concentration window that results in large output variations. The curve shown is for transcriptional activation. Repression is represented by an analogous inverse sigmoidal curve.</p

Input/output logic table for quad-not system.

<p>Input/output logic table for quad-not system.</p

A Proto dataflow computation is compiled to an abstract genetic regulatory network in two stages.

<p>First, each operator is mapped to a motif and each dataflow edge is mapped to a regulatory protein (blue dotted lines). These elements are then linked together using the structure of the dataflow graph to form an abstract genetic regulatory network (red dotted lines).</p

Proto biocompiler architecture and example.

<p>(a) This paper extends the Proto spatial computing language with mechanisms for genetic regulatory network design (pink). (b) An example showing how a simple high level behavioral specification is converted first into a dataflow network, then into a genetic regulatory network, and finally optimized. In this example, green fluorescence is turned ON only when both small molecule inputs aTc and IPTG are not present (aTc, anhydrotetracycline. IPTG, Isopropyl -D-1-thiogalactopyranoside). A–F represent transcriptional repressors to be chosen later from a parts library.</p

Input/output logic table for single-not system.

<p>Entries on the left are inputs, and entries on the right are outputs.</p

Input/output logic table for three gate system.

<p>Input/output logic table for three gate system.</p