Engineering BioBrick vectors from BioBrick parts/Colony PCR protocol - source code

#include "BioCoder.h"

void main()
{
	start_protocol("Engineering BioBrick vectors from BioBrick parts - Colony PCR");

	Fluid pcr_mix = new_fluid ("PCR SuperMix High Fidelity");
	Fluid vf2 = new_fluid("VF2 primer", "5'-TGCCACCTGACGTCTAAGAA-3'");
	Fluid vr = new_fluid("VR primer", "5'-ATTACCGCCTTTGAGTGAGC-3'");
	Fluid colony = new_fluid("colony suspension", "1 colony diluted in 100 μl water");
	Fluid water = new_fluid("de-ionized water");

	Container tube1 = new_container(STERILE_PCR_TUBE);

	Symbol x = new_symbol("X", "concentration of primers (µmole/µl)");

	// PCR mix
	//
	//    * 9 μL PCR SuperMix High Fidelity
	//    * 6.25 pmoles VF2 primer
	//    * 6.25 pmoles VR primer
	//    * 1 μL colony suspension
	//          o dilute 1 colony in 100 μL water 
	//
	first_step("PCR mix");
	Fluid fluid_array[5] = {pcr_mix, vf2, vr, colony, water};
	Symbol y = divide(vol(0.125, UL), s_vol(x));
	Volume* volume[5] = {vol(9, UL), s_vol(y), s_vol(y), vol(1, UL), vol(XVAL, UL)};
	char* tubes[1] = {"Colony PCR"};
	mixing_table(2, 6, fluid_array, tubes, volume, vol(20, UL), tube1);

	//PCR conditions
	//
	//   1. 95°C for 15 minutes
	//   2. 94°C for 30 seconds
	//   3. 62°C for 30 seconds
	//   4. 68°C for 3.5 minutes
	//   5. Repeat 2-4 39 times.
	//   6. 68°C for 20 mins
	//   7. 4°C forever 
	next_step("PCR conditions");
	pcr_init_denat(tube1, 95, time(15, MINS));
	thermocycler(tube1, 39, 94, time(30, SECS), 62, time(30, SECS), 68, time(3.5, MINS), NORMAL);
	pcr_final_ext(tube1, 68, time(20, MINS), 4);

	end_protocol();
}