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	Legal
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This code was created by Liam Brown at the University of Oxford. You may use it for whatever you feel like. If you would like to publish work that used this code, please cite the paper.
However, you accept that your use of this code is your own responsibility. I accept no blame if you (somehow) horribly break your system or lose data as a result of using this code.

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	Foreword on operating systems
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This code was created on Linux. It has been tested and it works on Windows under Cygwin, too. If you don't have Cygwin and don't want to install it, I don't think that there's any way to run it without editing the code to remove all graphical output. Sorry.

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	Installation requirements
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You will need boost as a minimum.
If you wish to use the pretty graphical output, you'll need GLSC3D ( http://www-mmc.es.hokudai.ac.jp/~masakazu/ ), OpenGL and SDL2. 
GLSC's manual is in Japanese, so I've provided the required header files in the directory and edited the Makefile to use the local directory. Hopefully that should suffice.
If you can't be bothered with the faff, Gnuplot is available as a backup graphical output... it's just not pretty.

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	Installation
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Simply use the makefile with no arguments, i.e.:
	cd ${directory}/c++
	make
This should run without issue. I hope that any errors you get are obvious.

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	Usage
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There are three executable files: StatLN, LinearLN and RandLN. The first runs the model with static dendritic cells. The second makes them migrate in a linear line from the lymph node's outer edge to their random position. The last gives them random movement akin to T cells.

Running 
	./StatLN --help 
, for example, will give you a list of commands:
	R:      radius                  default: 500
	b:      contactRadius           default: 20
	T:      numTCells               default: 5.23546
	t:      tCellDensity            default: 1e-05
	D:      numDendriticCells       default: 720
	N:      numAntigenInContactArea default: 500
	n:      tCellActivationThreshold        default: 20
	@:      cogAgInDermis   default: 0.2
	A:      cogAgOnArrival  default: 0.2*exp(-antigenDecayRate*firstDCArrival) = 0.0447036
	P:      firstDCArrival  default: 1080
	p:      DCArrivalDuration       default: 360
	k:      antigenDecayRate        default 0.00138728
	V:      tVelocityMean   default: 10.0635
	F:      freePathMean    default: 25
	f:      freePathStDev   default: 3
	s:      seed                    default: 6
	M:      numTimeSteps            default: day ; possible values: hour, day or 2day. If there are secondary vaccinations, this will be automatically increased to be e.g. a day after the last vaccination.
	m:      timeStep                default: 0.05
	w:      waveTimes               default: 0. This argument is given as a comma separated list.
	r:      numRepeats              default: 1
	c:      numChunks               default: 1
	y       plotting=ON             default: OFF
	z:      timePerGraphicUpdate    default: 10

So you can, for example, run
	./StatLN -D 100 -y

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	Help
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You can email me at brown@maths.ox.ac.uk if you have any basic questions. I might not be able to help you with particulars of your system, especially if it's Windows.