Polymerase Chain Reaction (PCR) protocol - source code

#include "BioCoder.h"

void main()
{
	start_protocol("PCR");

	Fluid buffer = new_fluid("Buffer");
	Fluid dntp = new_fluid("dNTPs");
	Fluid mgcl2 = new_fluid("MgCl <sub>2</sub>");
	Fluid dmso = new_fluid("DMSO");
	Fluid f_primer = new_fluid("Upstream primer");
	Fluid r_primer = new_fluid("Downstream primer");
	Fluid dna = new_fluid("Template DNA");
	Fluid water = new_fluid("dH<sub>2</sub>O");
	Fluid dnapol = new_fluid("DNA Polymerase");

	Container rxn_tube = new_container(RXN_TUBE);

	first_step("For Promega GoTaq:");
	{
		Fluid fluid_array[9] = {buffer, dntp, mgcl2, dmso, f_primer, r_primer, dna, water, dnapol};
		char* initial_conc [9] = {"5X", "1.25mM", "25mM", "50%", "50pmol", "50pmol", "??", "N/A", "5u/μL"};
		char* final_conc [9] = {"1X", "0.25mM", "2.5mM", "5%", "1pmol", "1pmol", "~0.5µg", "N/A", "1.25u"};
		Volume* volumes[9] = {vol(10, UL), vol(10, UL), vol(5, UL), vol(5, UL), vol(1, UL), vol(1, UL), vol(1, UL), vol(16.75, UL), vol(0.25, UL)};
		mixing_table_pcr(10, vol(50, UL), fluid_array, initial_conc, final_conc, volumes, rxn_tube);
	}

	next_step("For Roche High Fidelity:");
	{
		Fluid fluid_array[8] = {buffer, dntp, dmso, f_primer, r_primer, dna, water, dnapol};
		char* initial_conc [8] = {"10X", "1.25mM", "50%", "50pmol", "50pmol", "??", "N/A", "5u/μL"};
		char* final_conc [8] = {"1X", "0.25mM", "5%", "1pmol", "1pmol", "~0.5µg", "N/A", "2.5u"};
		Volume* volumes[8] = {vol(5, UL), vol(10, UL), vol(5, UL), vol(1, UL), vol(1, UL), vol(1, UL), vol(16.75, UL), vol(0.5, UL)};
		mixing_table_pcr(9, vol(50, UL), fluid_array, initial_conc, final_conc, volumes, rxn_tube);
	}

	next_step("An example program:");
	pcr_init_denat(rxn_tube, 96, time(5, MINS));
	comment("This denatures any double stranded DNA.");
	thermocycler(rxn_tube, 25, 96, time(1, MINS), 55, time(30, SECS), 72, time(1, MINS), NORMAL);
	pcr_final_ext(rxn_tube, 72, time(5, MINS), 4);
	comment("Final extension for incomplete strands and holding of sample at low temperature.");

	end_protocol();
}