Zombie Sim I - Revision history

Admin: /* The Parameters */

2017-04-26T15:50:06Z

The Parameters

← Older revision		Revision as of 17:50, 26 April 2017
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	Again, if the range of parameters looks a bit cluttered and complicated for the event you want to present, then perhaps [[Zombie Sim II]] is for you. Otherwise, read on. The tool comes with a few pre-defined epidemic scenarios. Selecting from the drop-down next to "Epidemic" will load in a set of parameters from a config file. There's a hacky way of editing that later.		Again, if the range of parameters looks a bit cluttered and complicated for the event you want to present, then perhaps [[Zombie Sim II]] is for you. Otherwise, read on. The tool comes with a few pre-defined epidemic scenarios. Selecting from the drop-down next to "Epidemic" will load in a set of parameters from a config file. There's a hacky way of editing that later.

	The parameters themselves are hopefully fairly obvious. The '''Natural History''' box lets you set the Latent period and Infectious period, measured in days, along with the probability of being symptomatic. The start of the infectious period, and the beginning of symptoms (if any) are assumed to happen at the same time. Next '''Reproductive Number and Seasonality''' lets you set R{{sub\|0}}, and allow that to vary over time. The graph shows you a preview of the resulting reproductive rate. The effect of amplitude is that R<sub>0</sub> is multiplied by (Y<sub>Centre</sub>+Y<sub>Amp</sub>) or (Y<sub>Centre></sub>-Y<sub>Amp</sub>) at the seasonal peaks and troughs respectively. The other variables set the timing offset, and the period of oscillation, which is sinusoidal.		The parameters themselves are hopefully fairly obvious. The '''Natural History''' box lets you set the Latent period and Infectious period, measured in days, along with the probability of being symptomatic. The start of the infectious period, and the beginning of symptoms (if any) are assumed to happen at the same time. Next '''Reproductive Number and Seasonality''' lets you set R<sub>0</sub>, and allow that to vary over time. The graph shows you a preview of the resulting reproductive rate. The effect of amplitude is that R<sub>0</sub> is multiplied by (Y<sub>Centre</sub>+Y<sub>Amp</sub>) or (Y<sub>Centre></sub>-Y<sub>Amp</sub>) at the seasonal peaks and troughs respectively. The other variables set the timing offset, and the period of oscillation, which is sinusoidal.

	The next panel lets you set '''Movement''' behaviour. The x-axis of the graph shows distance, and the y-axis shows probability. If you pick a random number between 0 and 1, find that point on the y-axis, then move to the right until you hit the line, then you have sampled the distance one person travels to make contact with another. The kernel function used is the simple 1/(1+(d/a)^b), where d is the distance, and a and b are the parameters you can set, with a maximum cut-off distance.		The next panel lets you set '''Movement''' behaviour. The x-axis of the graph shows distance, and the y-axis shows probability. If you pick a random number between 0 and 1, find that point on the y-axis, then move to the right until you hit the line, then you have sampled the distance one person travels to make contact with another. The kernel function used is the simple 1/(1+(d/a)^b), where d is the distance, and a and b are the parameters you can set, with a maximum cut-off distance.

Admin: /* Usage History */

2016-09-12T14:58:08Z

Usage History

← Older revision		Revision as of 16:58, 12 September 2016
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	Here are the events where we've used this tool - generally for quite scientifically interested crowds!		Here are the events where we've used this tool - generally for quite scientifically interested crowds!

	* [[March 2013 - Big Bang]]		* [[March 2013 - Big Bang Fair]]
	* [[October 2012 - Imperial Fringe]].		* [[October 2012 - Imperial Fringe]].

Admin: /* Usage History */

2016-09-12T14:57:52Z

Usage History

← Older revision		Revision as of 16:57, 12 September 2016
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	Here are the events where we've used this tool - generally for quite scientifically interested crowds!		Here are the events where we've used this tool - generally for quite scientifically interested crowds!

	* March 2013 - Big Bang		* [[March 2013 - Big Bang]]
	* [[October 2012 - Imperial Fringe]].		* [[October 2012 - Imperial Fringe]].

Admin: /* Credits and Thanks */

2016-09-12T14:46:02Z

Credits and Thanks

← Older revision		Revision as of 16:46, 12 September 2016
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	== Credits and Thanks ==		== Credits and Thanks ==

	The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson, [http://www.nature.com/nature/journal/v437/n7056/full/nature04017.html here] for instance. Special mention for Diane Pople in ~~drawing and~~ captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.		The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson, [http://www.nature.com/nature/journal/v437/n7056/full/nature04017.html here] for instance. Special mention for Diane Pople in captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.

Admin: /* Usage History */

2016-09-12T14:44:44Z

Usage History

← Older revision		Revision as of 16:44, 12 September 2016
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	== Usage History ==		== Usage History ==

	Here are the events where we've used ~~the~~ tool~~. Generally, the crowd~~		Here are the events where we've used this tool - generally for quite scientifically interested crowds!

	* March 2013 - Big Bang		* March 2013 - Big Bang

Admin at 14:44, 12 September 2016

2016-09-12T14:44:10Z

← Older revision		Revision as of 16:44, 12 September 2016
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	[[File:zs1_3.mp4\|500px\|right]]		[[File:zs1_3.mp4\|500px\|right]]
	[[File:zs1_4.mp4\|500px\|right]]		[[File:zs1_4.mp4\|500px\|right]]
	~~== Zombie Sim I ==~~

	=== Introduction ===		== Introduction ==
	This is the earlier, more complex older brother of [[Zombie Sim II]], which has more options than you might want, but a lot of flexibility if you want to describe spatial epidemic modelling to a fairly science-friendly crowd. It's a spatial individual-based simulation of a directly transmissible disease, such as influenza. It's a hands-on tool and models an epidemic with the popular tidal wave of infections and recoveries before your eyes. While absolute accuracy has been sacrificed for speed, it can be used to explore the effects of R0, latent and infectious period, temporal seasonality, characteristics of travel, vaccination, isolation or travel restriction for symptomatic cases, stochastic properties (random seeds!), and population density effects.		This is the earlier, more complex older brother of [[Zombie Sim II]], which has more options than you might want, but a lot of flexibility if you want to describe spatial epidemic modelling to a fairly science-friendly crowd. It's a spatial individual-based simulation of a directly transmissible disease, such as influenza. It's a hands-on tool and models an epidemic with the popular tidal wave of infections and recoveries before your eyes. While absolute accuracy has been sacrificed for speed, it can be used to explore the effects of R0, latent and infectious period, temporal seasonality, characteristics of travel, vaccination, isolation or travel restriction for symptomatic cases, stochastic properties (random seeds!), and population density effects.

	=== Installation and Download ===		== Installation and Download ==

	IT comes as a ZIP file containing source and binaries (that is, byte-code for Java). I compiled with Java 8u91, and it's a good idea to stay up-to-date anyway. So, install Java from [http://java.sun.com Oracle], and download Zombie Sim I pack [https://mrcdata.dide.ic.ac.uk/resources/zombie_i.zip here]. On Windows, unzip it to any folder you like. (Don't just run it from inside the ZIP - it won't work!). If you need an unzipper, try [http://7-zip.org 7-Zip]. Then click on '''runthis.bat''' in the root folder. If you like the command-line, or if you're on linux or mac, then simply java Z from the root folder will run it.		IT comes as a ZIP file containing source and binaries (that is, byte-code for Java). I compiled with Java 8u91, and it's a good idea to stay up-to-date anyway. So, install Java from [http://java.sun.com Oracle], and download Zombie Sim I pack [https://mrcdata.dide.ic.ac.uk/resources/zombie_i.zip here]. On Windows, unzip it to any folder you like. (Don't just run it from inside the ZIP - it won't work!). If you need an unzipper, try [http://7-zip.org 7-Zip]. Then click on '''runthis.bat''' in the root folder. If you like the command-line, or if you're on linux or mac, then simply java Z from the root folder will run it.

	=== Using the Tool ===		== Using the Tool ==

	==== Basic GUI ====		=== Basic GUI ===
	The top right chunk of the screen shows four graph panels. Top left is daily incidence in millions of people. Bottom left is the cumulative number of infections. Bottom right is a graph of the effective R - the actual number of infections generated per source case. And the top right shows a spatial map that animates as the epidemic progresses. Once the epidemic is done, you can drag the slider below the spatial map to show the frames of the movie, and to look very cool. Each of the three graphs can plot four graphs at once for you to compare - red, green, yellow and blue. Select the graph you want to plot with be clicking on the colour, or to remove a graph, click on the X button near that colour. The big button in the bottom right runs the spatial simulator, and the graph will start animating.		The top right chunk of the screen shows four graph panels. Top left is daily incidence in millions of people. Bottom left is the cumulative number of infections. Bottom right is a graph of the effective R - the actual number of infections generated per source case. And the top right shows a spatial map that animates as the epidemic progresses. Once the epidemic is done, you can drag the slider below the spatial map to show the frames of the movie, and to look very cool. Each of the three graphs can plot four graphs at once for you to compare - red, green, yellow and blue. Select the graph you want to plot with be clicking on the colour, or to remove a graph, click on the X button near that colour. The big button in the bottom right runs the spatial simulator, and the graph will start animating.

	==== The Parameters ====		=== The Parameters ===

	Again, if the range of parameters looks a bit cluttered and complicated for the event you want to present, then perhaps [[Zombie Sim II]] is for you. Otherwise, read on. The tool comes with a few pre-defined epidemic scenarios. Selecting from the drop-down next to "Epidemic" will load in a set of parameters from a config file. There's a hacky way of editing that later.		Again, if the range of parameters looks a bit cluttered and complicated for the event you want to present, then perhaps [[Zombie Sim II]] is for you. Otherwise, read on. The tool comes with a few pre-defined epidemic scenarios. Selecting from the drop-down next to "Epidemic" will load in a set of parameters from a config file. There's a hacky way of editing that later.
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	Lastly, the colours of the map. If there have never been any cases of the epidemic in a pixel, it remains grey scale, which indicates population density - brighter is more dense population. Once cases have been reported in a pixel, then the colour is a gradient from blue to red, where pure blue implies everyone who has been infected has now recovered, pure red would imply everyone who has been infected is still infectious. To put it another way, if blue is zero, and red is one, then then colour of the pixel would be I/(I+R), whenever (I+R)>0, where I is infectious and R is recovered people.		Lastly, the colours of the map. If there have never been any cases of the epidemic in a pixel, it remains grey scale, which indicates population density - brighter is more dense population. Once cases have been reported in a pixel, then the colour is a gradient from blue to red, where pure blue implies everyone who has been infected has now recovered, pure red would imply everyone who has been infected is still infectious. To put it another way, if blue is zero, and red is one, then then colour of the pixel would be I/(I+R), whenever (I+R)>0, where I is infectious and R is recovered people.

	==== Useful Command-line Options ====		=== Useful Command-line Options ===

	There are two. '''/MOVIE''' will cause screenshots of the whole app will be dumped - which I used for making the movies on this page. They'll have the name gui_1_123.png - where the first '1' is the number of the run being executed which increases each time you click the go button, and the 123 is the frame number of the simulation. To make a movie out of this: '''ffmpeg -r 15 -f image2 -s 1024x700 -i gui_1_%d.png -crf 25 -pix_fmt yuv420p output.mp4'''		There are two. '''/MOVIE''' will cause screenshots of the whole app will be dumped - which I used for making the movies on this page. They'll have the name gui_1_123.png - where the first '1' is the number of the run being executed which increases each time you click the go button, and the 123 is the frame number of the simulation. To make a movie out of this: '''ffmpeg -r 15 -f image2 -s 1024x700 -i gui_1_%d.png -crf 25 -pix_fmt yuv420p output.mp4'''
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	This is a snapshot of the current parameters. If you edit the file z_conf.xml in the root of the Zombie folder, you can paste this in the <creatures> tag, (change the name from "Base" to something more useful). Then when you re-run the Simulator, that configuration will be available in the Epidemic drop-down box.		This is a snapshot of the current parameters. If you edit the file z_conf.xml in the root of the Zombie folder, you can paste this in the <creatures> tag, (change the name from "Base" to something more useful). Then when you re-run the Simulator, that configuration will be available in the Epidemic drop-down box.

	=== Data and Algorithms ===		== Data and Algorithms ==

	The code and approach is taken from the [http://globalepidemics.sourceforge.net Global Epidemic Simulator] we've been working on for some years. The population data is a 10% sample of UK and Ireland households, taken from the synthetic population generated for the GES for the UK and Ireland. Hence, the individual-based simulation involves around 6 million people. The synthetic population itself is derived from Landscan 2008, transformed using population distributions and household size distributions. It's a long story.		The code and approach is taken from the [http://globalepidemics.sourceforge.net Global Epidemic Simulator] we've been working on for some years. The population data is a 10% sample of UK and Ireland households, taken from the synthetic population generated for the GES for the UK and Ireland. Hence, the individual-based simulation involves around 6 million people. The synthetic population itself is derived from Landscan 2008, transformed using population distributions and household size distributions. It's a long story.
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	We use OpenMP then to run the infection process in parallel, but because we are not critically worried about accuracy, the results are not totally deterministic. To explain: the main loop is running in parallel with the different cores of your processor working together. On occasion, two cores might run processes whereby two infected people might try to infect the same susceptible. In the GES, I handle these properly and chronologically, so the result is deterministic, and the earliest infection. In the Zombie Sim, that correction is not done, so you can on occasion get slightly different outcomes from the same run.		We use OpenMP then to run the infection process in parallel, but because we are not critically worried about accuracy, the results are not totally deterministic. To explain: the main loop is running in parallel with the different cores of your processor working together. On occasion, two cores might run processes whereby two infected people might try to infect the same susceptible. In the GES, I handle these properly and chronologically, so the result is deterministic, and the earliest infection. In the Zombie Sim, that correction is not done, so you can on occasion get slightly different outcomes from the same run.

	=== Technical Computing ===		== Technical Computing ==

	The interface is written in Java, and the pretty widgets are part of a library of tools (GKit) developed for the first Global Epidemic Simulator release. The simulation itself is written in C++ (mostly pure C actually), using OpenMP with as many threads as your machine reports. The source is platform-independent, with binaries for Windows, Linux and Mac provided; Java detects the platform and calls the right one automatically. The Windows executable was compiled with Microsoft VS 2014, and therefore vcomp140.dll is in the same folder. The compiler optimisation for the binaries is set conservatively to avoid any processor compatibility issues (which I found I could not avoid in the latest Intel compiler). If you want to eke out a little more speed, compile the C++ source code yourself - it doesn't need any special treatment - just put your executable in the job folder. (Test it first!)		The interface is written in Java, and the pretty widgets are part of a library of tools (GKit) developed for the first Global Epidemic Simulator release. The simulation itself is written in C++ (mostly pure C actually), using OpenMP with as many threads as your machine reports. The source is platform-independent, with binaries for Windows, Linux and Mac provided; Java detects the platform and calls the right one automatically. The Windows executable was compiled with Microsoft VS 2014, and therefore vcomp140.dll is in the same folder. The compiler optimisation for the binaries is set conservatively to avoid any processor compatibility issues (which I found I could not avoid in the latest Intel compiler). If you want to eke out a little more speed, compile the C++ source code yourself - it doesn't need any special treatment - just put your executable in the job folder. (Test it first!)
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	The source for the C++ executable is the same for this version, and for [[Zombie Sim II]].		The source for the C++ executable is the same for this version, and for [[Zombie Sim II]].

	=== Usage History ===		== Usage History ==

	Here are the events where we've used the tool. Generally, the crowd		Here are the events where we've used the tool. Generally, the crowd
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	* [[October 2012 - Imperial Fringe]].		* [[October 2012 - Imperial Fringe]].

	=== Credits and Thanks ===		== Credits and Thanks ==

	The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson, [http://www.nature.com/nature/journal/v437/n7056/full/nature04017.html here] for instance. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.		The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson, [http://www.nature.com/nature/journal/v437/n7056/full/nature04017.html here] for instance. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.

Admin at 15:08, 8 September 2016

2016-09-08T15:08:12Z

← Older revision		Revision as of 17:08, 8 September 2016
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	=== Credits and Thanks ===		=== Credits and Thanks ===

	The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.		The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson, [http://www.nature.com/nature/journal/v437/n7056/full/nature04017.html here] for instance. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.

Admin at 15:07, 8 September 2016

2016-09-08T15:07:08Z

← Older revision		Revision as of 17:07, 8 September 2016
Line 70:		Line 70:

	The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.		The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.
	~~=== Credits and Thanks ===~~

	The Zombie II Sim interface, simulation code and widget kit was written by Wes Hinsley, with particular design and presentation help on the simplification of [[Zombie Sim I]] from Harriet Mills and Rafal Nostowy. The Synthetic Population generation part of the GES was written by Pavlo Minayev. Many thanks to all others who have demonstrated the tool and given feedback.

Admin: /* Credits and Thanks */

2016-09-08T15:06:50Z

Credits and Thanks

← Older revision		Revision as of 17:06, 8 September 2016
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	=== Credits and Thanks ===		=== Credits and Thanks ===

	The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.		The Zombie I interface, simulation code and widget kit was written by Wes Hinsley, for the Imperial College Fringe Event in South Kensington, November 2013. The Synthetic Population generation part of the GES was written by Pavlo Minayev. And the underlying methods used for spatial simulation were established by Neil Ferguson. Special mention for Diane Pople in drawing and captivating a pretty big crowd demonstrating this at the Fringe Event, and to all the presenters who used it and gave feedback at the Big Bang festival.
			=== Credits and Thanks ===

			The Zombie II Sim interface, simulation code and widget kit was written by Wes Hinsley, with particular design and presentation help on the simplification of [[Zombie Sim I]] from Harriet Mills and Rafal Nostowy. The Synthetic Population generation part of the GES was written by Pavlo Minayev. Many thanks to all others who have demonstrated the tool and given feedback.

Admin at 12:05, 8 September 2016

2016-09-08T12:05:35Z

← Older revision		Revision as of 14:05, 8 September 2016
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	=== Installation and Download ===		=== Installation and Download ===

	IT comes as a ZIP file containing source and binaries (that is, byte-code for Java). I compiled with Java 8u91, and it's a good idea to stay up-to-date anyway. So, install Java from [http://java.sun.com Oracle], and download Zombie Sim II pack [https://mrcdata.dide.ic.ac.uk/resources/zombie_i.zip here]. On Windows, unzip it to any folder you like. (Don't just run it from inside the ZIP - it won't work!). If you need an unzipper, try [http://7-zip.org 7-Zip]. Then click on '''runthis.bat''' in the root folder. If you like the command-line, or if you're on linux or mac, then simply java Z from the root folder will run it.		IT comes as a ZIP file containing source and binaries (that is, byte-code for Java). I compiled with Java 8u91, and it's a good idea to stay up-to-date anyway. So, install Java from [http://java.sun.com Oracle], and download Zombie Sim I pack [https://mrcdata.dide.ic.ac.uk/resources/zombie_i.zip here]. On Windows, unzip it to any folder you like. (Don't just run it from inside the ZIP - it won't work!). If you need an unzipper, try [http://7-zip.org 7-Zip]. Then click on '''runthis.bat''' in the root folder. If you like the command-line, or if you're on linux or mac, then simply java Z from the root folder will run it.

	=== Using the Tool ===		=== Using the Tool ===