GutSim/parameters.xml at master · marknormanread/GutSim · GitHub

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<?xml version="1.0"?>
<!-- THIS FILE SPECIFIES GUTSIM PARAMETERS -->
<params>
	<timestep>0.1</timestep>
	<diet_code>const</diet_code>
	<exp_dir>test</exp_dir>
	<end>26.0</end><!--experiment duration, hours-->
	<force>1</force><!--1 = overwrite existing files-->
	<verbose>1</verbose>
	<tag>CONTROL</tag><!-- added to end of output directories-->

	<output>
		<mouse_graphs>1</mouse_graphs><!--1=plot graphs, 0=don't-->
		<bacteria_graphs>1</bacteria_graphs><!--# of hours pre-termination to plot-->
	</output>

	<mouse></mouse><!--integer; 'all' runs all mice; blank defers to command line-->

	<diet_regimes>
		<inulin><!--amount of inulin added to the diet in grams-->
			<adlib>0.0</adlib>
			<timed><!--TRF inulin administration-->
				<dose>0.0</dose>
				<start>0.0</start>
				<duration>0.0</duration>
			</timed>
		</inulin>
		<time_restricted><!--periodic fasting within 24 hour window-->
			<!--time at which food is made available in 24h cycle. 0..24-->
			<start>0.0</start>
			<!--duration for which food available, hours, 0..24-->
			<duration>12.0</duration>
		</time_restricted>
		<five_two>
			<!--days numbered 1-7. Value of -1 means no diet-->
			<day1>4</day1>
			<day2>1</day2>
			<!--proportion of full day's intake consumed on diet days. 0..1-->
			<diet_quantity>0.2</diet_quantity>
		</five_two>
		<alternate_day>
			<!--proportion of full day's intake consumed on fasting days. 0..1-->
			<diet_quantity>1.0</diet_quantity>
		</alternate_day>
	</diet_regimes>

	<bacteria>
		<maxInternalisationRate>500.0</maxInternalisationRate>
		<CtoNRatio>5.2</CtoNRatio>
		<mean_internalised_carbon_lifetime>2.5</mean_internalised_carbon_lifetime>
		<mean_internalised_nitrogen_lifetime>10.0</mean_internalised_nitrogen_lifetime>
	</bacteria>

	<mouse>
		<scale_factor>30.0</scale_factor>
		<bacteria_peristalsis_rate>0.2</bacteria_peristalsis_rate><!--cm/peristalsis-->
		<nutrient_peristalsis_rate>0.2</nutrient_peristalsis_rate><!--cm/peristalsis-->
		<excretion_rate>0.05</excretion_rate><!--float, 0 to 1-->
		<gut_carrying_weight>0.3</gut_carrying_weight>

		<init_Grf>100</init_Grf><!--integers-->
		<init_Grm>100</init_Grm>
		<init_Gpf>100</init_Gpf>
		<init_Gpm>100</init_Gpm>
		<init_Gmm>100</init_Gmm>
		<init_Gmf>100</init_Gmf>
		<inoculation_rate>0.000003</inoculation_rate>
	</mouse>
</params>