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Welcome to the official website of Farming Simulator, the #1 farming simulation game by GIANTS Software. Mac OS X 10.5 Leopard. Get it for PowerPC or 32bit Intel. Mac OS X 10.4 Tiger. Mac OS X 10.4.7 or later is required. Get it for PowerPC or Intel. Mac OS X 10.3 Panther. QuickTime 6.5.2 or later is required. Get it for PowerPC. Mac OS X 10.2 Jaguar. Get it for PowerPC. Software Description: VSPlayer is a free media player designed for Mac OS. It provides an intuitive, easy to use interface to play digital media file, and supports a myriad of audio and video formats. In addition, it offers many advanced features, is extremely customizable, and is available in both Chinese and English. Apple Mac OS X, Xsan, and Productivity Applications Curriculum Mac OS X v10.5 courses Length Description Leads to Certification For Support Professionals and Technical Coordinators Leopard 100: Introduction to Mac OS X v10.5 1 day Provides an introduction to basic Mac OS X features and interface for those who are new. In Windows or on a Mac, you should be able to double-click the.jar file to launch the simulator. You can also launch the simulator from the command line of your operating system (such as Linux) by using the command java -jar (jarfile). You should see the simulator screen, much like the screenshot below.

A Gentle Guide to Using the LC-3 Simulator

0. Conventions

Throughout this document, commands that you have to type or buttonsyou have to click will appear like so.

1. Getting Java

The LC-3 Simulator is written in Java, which means Java must beinstalled on the computer you plan to use. Java should already beavailable on all public SEAS machines. If you plan to work on yourpersonal machine, you may need to install Java yourself. You can download Java here. TheLC-3 simulator requires Java 1.4 or newer (which is available forWindows, Linux, and Mac OS X).

2. Getting the Simulator

Next, you need to download the simulator. It is distributed in a .jarfile (short for Java ARchive) which you can download here. In Windows or on a Mac, youshould be able to double-click the .jar file to launch thesimulator. You can also launch the simulator from the command line ofyour operating system (such as Linux) by using the command java -jar (jarfile). You should see the simulatorscreen, much like the screenshot below.


If you have any problems starting the simulator, please post yourproblems to the CSE240 General Discussion Forum. This will ensure thefastest response.

We will not be distributing the source to the simulator, becausea later assignment will build parts of the simulator in C (which issimilar to Java in many ways).

3. Assembling and Loading Software

Now the simulator is running, but to get it to do anythinginteresting, we need to load some software. The first piece ofsoftware we should load is, naturally, an operating system. The LC-3operating system is very basic: it handles simple I/O operations andis responsible for starting other programs, such as the ones you'llwrite for this homework. Download the LC-3 OShere.

So that you can understand what the operating system does, wedistribute it as an assembly language file. But the LC-3 machinedoesn't understand assembly directly; we first have to 'assemble' theassembly code into machine language (a .obj file containing binarydata). The LC-3 simulator has a built-in assembler, accessible (as isthe case for most of its functionality) via the Command Line text box(see screenshot above). To assemble the operating system, type as lc3os.asm at the command line and hitenter. Make sure that the OS file is in the same directory as the .jarfile; the as command also understandsrelative and absolute paths if the OS is in a different directory. Used apple mouse. Output from the assembly process is displayed in the CommandLine Output Pane. Afterassembling the OS, you should notice that 2 new files, lc3os.obj andlc3os.sym, have been created. The .obj file is the machine languageencoding of the assembly language file, and the .sym file is a textfile that holds symbol information so the simulator can display yoursymbols. Recall that symbols are really just a convenience for sillyhumans; the machine language encoding knows only about offsets.

Now we can load the lc3os.obj file into the simulator, either via thecommand load lc3os.obj or by going to theFile menu and selecting Open .obj file. Notice that the contents of thememory change when the OS is loaded.

Now assemble and load the solution file forProblem 0 into the simulator. The memory has changed again, but youmay not notice since the relevant memory addresses (starting at x3000)aren't visible unless you've scrolled the screen. User-level programs(i.e., non-OS code) start, by convention, at x3000. If you type thecommand list x3000 the memory view willjump to x3000 and you can see the 1-instruction solution to thisproblem.

4. Running Code

To actually run code, you can use the 4 control buttons at the top ofthe simulator, or type commands into the command line interface (thecommand names are the same as the buttons). Note that the PC registeris set to x0200, which is the entry point to the operating system byconvention. Recall that the solution code for Problem0 increments the value in R2 and puts the result in R5. Set thevalue in R2 to something you fancy, either by double-clicking it inthe Registers section, or via the command set R2(value). Now, actually run the code by hitting the continue button. The value magically getsincremented and moved to R5. Neat-o! Also observe that the PC nowpoints to x0263, an apparently random value somewhere in the operatingsystem, and that the Status Display tells us the machine is halted.

4a. Running Code..slowly

Clearly, some things are going on here. But to determine what they areexactly, we need to slow the execution down. You can hit the stop button to pause the machine while it'sexecuting, but this doesn't give you very fine-grained control. Thecontinue command will start runninginstructions as fast as possible, but often we want to go just oneinstruction at a time. This is what the next and stepcommands allow us to do. They both go one instruction at a time, but thestep command will 'follow' function callsand traps, while next just goes from lineto line, 'over' function calls and traps and stopping only at the instructionimmediately after them. Both next and step will 'follow' branches. The LC-3 Manual has a more involved discussion,with an example, of the difference between next and step.

Let's try running the program again, but just one instruction at atime. Notice that from the halted state, the PC points to aninstruction that will branch us right back to the start of theoperating system. So we can hit next onceand start the cycle over again. Note that registers are as we leftthem. You can put a new value into R2 if you want, and the old valuein R5 will get overwritten. Sometimes, having old values lying aroundeverywhere can be problematic, and it's good to do a real 'reboot' viathe reset command. This clears allof memory and resets registers to default values, so you have toreload the OS and your program.

You can keep next-ing over the OS code;eventually you will hit the RTT instruction at location x0205 thatjumps to the start of our program at x3000. Now you can see the 2instructions that constitute our program. You can see the ADD beingperformed, and then the machine gets halted again.

Continue running the increment-R2-into-R5 code until, if ever, you getbored. Then move on to Problem 1.

4b. Running Code..for a little while

Going one instruction at a time is great, but somewhat tedious. Weneed a happy medium between not knowing what's going on at all, andhaving to go through every single instruction, whether we care aboutit or not. Breakpoints are this happy medium.

A breakpoint is set at a particular memory location, and tells thesimulator to stop execution upon reaching that point. Memory locationswith breakpoints set on them show up in the simulator with a redsquare in the 'BP' column. It is left as an exercise to the reader todetermine what 'BP' stands for. You can set a breakpoint at a memorylocation with the command break set (memorylocation), or by checking the checkbox in the 'BP' column. Youcan get rid of a previously-set breakpoint with the command break clear (memory location), or byun-checking a previously checked box. You can also set and clearbreakpoints at labels, instead of specifying a hex memory location.

When you tell the simulator to continue,it will only run until it hits a breakpoint (or the system halts orhas an error). When you are writing and testing your answer forProblem 1, you can use the command breakpointset START to set a breakpoint at the beginning of yourcode. Then, you can use continue to skipall the OS code and get to the instructions you care about. Then youcan next over your code to make sure it'sdoing what you want it to do.

5. Running Scripts

Now try running some of the test scripts that we've provided forProblem 1. You can do this with the command script (scriptfile). LC-3 script files are .lcsfiles, but are really just plain text, and the file extension doesn'treally matter. If you open the script file with a text editor, you cansee that the script commands are the same as those you type at thecommand line. For repetitive tasks, using a script file can save youtime, and perhaps the lifelong agony of RepetitiveStrain Injury.

Scripting is also a great way of testing your code. You can write afew test cases and check your code easily, especially for the problemsin this homework which are pretty easy to test. Use the check command to verify that a value is whatyou think it should be. We've distributed a few test scripts for theproblems in this homework, but they don't cover all the importantcases, so you should augment our scripts with some of your own.

6. General Help and Advice

This document doesn't cover all of the simulator's functionality; foran extended discussion of usage see the LC-3Simulator Manual. For quick help within the simulator itself,you can use the help command to see alist of all of the LC-3's commands. Use help(command) to get help on a specific command.

Many of the LC-3 commands have shortcuts - b is short for break, n fornext, and so forth. Use the help (or h)command to see what shortcuts exist.

The LC-3 Command Line has a history feature - use the up and downarrow keys to go backwards and forwards through the commands you'vepreviously entered.

If you resize the simulator window to make it bigger, the CommandlineOutput Pane will grow. If you have a small screen and the CommandlineOutput Pane still isn't big enough, you can open an external, resizableCommand Output Window by selecting the OpenCommand Output Window option from the File menu. This lets you see a lot more outputfrom the commands you run, and is particularly useful for viewing theerrors the assembler generates.

If you have trouble running the simulator, try checking the classforum in case someone else has had the same problem as you. Postingyour questions to the forum is a good idea in general, because thenother people can learn from your experience. The forum is checkedregularly by Professor Lewis and the TAs. Of course, you can alsoemail cse240@seas, or drop by office hours.

If you think you've found a bug in the simulator (which is,theoretically speaking, a possibility:), check the Simulator BugsPage to see if you've found a known bug with a workaround. Ifyou've found a new bug, post to the forums (if you want to embarrass us)or email cse240@seas (if you're feeling kinder). Be sure to include thefollowing:

  1. A description of the bug.
  2. What you were doing that caused the bug to occur.
  3. What version of the simulator you were using. Find this via the simulator'sAbout menu.
  4. What version of Java you were using. Find this by running java -version from the commandline of your OS.
  5. What operating system you were using - Windows, Linux, Mac.
Also look in the directory where you placed the simulator and checkfor a file called 'lc3sim_errorlog.txt', and email it tocse240@seas. This file is a stack trace generated on some errors,which may help us figure out how to fix the bug. It contains nosensitive system information - it's in plain text, so you can see whatit is that you're sending us.

version 4.03

November, 2016

This is a one-locus, two-allele genetic simulation program for use bystudents. It simulates multiple populations and allows you to see theeffect of natural selection, mutation, migration, and genetic drift. Itis freely downloadable. It is written in Java, and will run onWindows, Mac OS X, and Linux systems if they have Java installed on them.

At its web site evolution.gs.washington.edu/popgen/is a downloadable 'zip archive' which contains a Java archive file whichhas the Java executable as well as the Java source code. It also hasthis web page. There is also a folder imagesfor the screenshot images used in this web page. The compiled Java codein the Java archive file can be run on any system that hasa reasonably recent version of Java installed.

The Java source for popg is called PopGUserInterface.java and is in the folder src. It was developed in the Eclipse development environment but any environment you are comfortable with will do.Normally you will not need thesource code and you will not need to recompile the program. The source codeis there so you can see how things were done and use itas a base to make changes to the program and extensions of the program, should you wish to do so.

Getting PopG

You can fetch PopG using the links below.

We have posted a Zip archive of PopG, including Java archives and documentationfiles. This archive is file PopG.zip. To get it

  • Fetch it here.
  • Install it using the instructions below.
  • Make sure you have a version of Java on your computer.

Installing PopG

Here are instructions for saving, unpacking, and installing PopG from differentbrowsers, and on operating systems. We cover the Chrome, Firefox, Safari,and Internet Explorer browsers on the Windows, Mac OS X, and Linux operatingsystems.

Using Chrome on Windows, Mac OS X, or Linux

  1. Click on the link.
  2. A downwards-pointing animated arrow in the lower-left portion of thebrowser window will move, pointing to a tab there called PopG.zip.
  3. PopG.zip will now be found in your Downloads folder.
  4. Click (or if this does not work, double-click) on the PopG.zip file.The Zip archive will be extracted intothe Downloads folder. A folder PopG will be created in theDownloads folder.
  5. Move that folder to where you want it to be.

Using Firefox on Windows, Linux, or Mac OS X

  1. Click on the link.
  2. A dialog box opens and offers to let you Save File. Choose that.
  3. The Zip archive PopG.zip will be in your Downloads folder.
  4. Double-click on it. The archive will be extracted and a folderPopG created in the Downloads folder.
  5. Move that folder to where you want it to be.

Using Internet Explorer on Windows

  1. Click on the link.
  2. A dialog box opens and offers to let you Save File. Choose that.
  3. The Zip file PopG.zip will be downloaded into the downloads folder and will beautomatically extracted. A folder PopG will be created in theDownloads folder.
  4. Move it where you want it to be.

Using Safari on Mac OS X

  1. Click on the link.
  2. The Zip file will be downloaded into the downloads folder and will beautomatically extracted. A folder PopG will be created in theDownloads folder.
  3. Move it where you want it to be.

A MAC PROBLEM: On Mac OS X systems, when you attempt to extract the Zip archive, or when you attempt to run the Java executable, the system may complain that this is from an unknown developer. That is simply because I did not sign the file with my Apple Developer ID. You should be able to make the operation work by control-clicking on the icon and selecting the option to open the file, using the defaults suggested. Once it successfully gets past this, it will not bother you with this again.

The Java archive

The Java archive file PopG.jar will exist in the folder PopGonce you have downloaded and installed PopG.If you have Java installed on yoursystem, you should be able to run the Java program by finding the folderPopG and clicking ordouble-clicking on the icon of the file PopG.jar

The documentation page

The PopG folder also includes the present documentation web page which you are now reading. This can be read here or you can use the Save As menu item in the File menu of your browser to save a copy of it on your machine. The latest version of this page can be read on the Web using this link.

Older versions of PopG

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There are also older executable versions compiled for Windows, Mac OS X, andLinux systems, plus some even older operating systems.These can be fetched from folder old at our PopG site.Most users should not use these older executables, but if you do, you should start by reading theREADME file in that folder. One of the versions there is version 3.4,which has compiled executables for the three major operating systemsavailable as well as C source code. These may be useful if you do not haveJava and cannot install it on your system.

Where are the Android and iOS versions?`

We would like to make versions available for tablets and even phones.Unfortunately, a version of Java that can use the graphics functions doesnot seem to exist on the Android operating system and the iOS operatingsystem. We would have to rewrite the program separately for each of those. Ifyou know of a way to run our Java executables on either of those operatingsystems, and get it to work, please let us know how you did that.

Making sure you have Java on your computer

If you have Java installed you can run the PopG program. Generally,Java will be already installed on Mac OS X systems and on Linux systems. If you aren't sure if you have Java installed, you can type java -version in a command window and, it Java exists, it will tell you what the version is. If you get back a blank line, you need to either download Java or append where it is to your search path.On Windows systems and on Mac OS X or Linux systems that do not have Java,you can install a recent version of Java at no cost by using this link: java.com. Recent Linux and Mac OS X systemsusually have a recent-enough version of Java already installed. Mac OS Xsystems 10.4 (Leopard) and earlier may not have a recent-enough Java to beable to run PopG. Windows systems do not come with Java already installed,but it can be installed on them from the above web site.

Running the program

To run the PopG Java program you should simply click (or double-click) on theicon of the PopG.jar file (you can also run it from a command window by navigating to where PopG.jaris stored and typing java -jar PopG.jar). The start up screen looks like this:

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There are two menus, File and Run, that control PopG. They are in the upper left of the main PopG window.

The Run menu

The Run menu contains five items: Continue w/, Continue, New Run, Restart, and Display Whole Plot.

The first time it is picked, it looks like:

with all but New Run Might and magic x legacy cheats. grayed out. Once you have done your first run, all the selections will be active.

New Run
Initially only New Run is available. It brings up the following dialog:It contains all the parameters that control a PopG run. Note that usually you do not enter a Random Number seed unless you want to do two identical runs. When you are finished editing you can click the OK box to start the run. You can also click Cancel to not start the run and Defaults to reset all the data entry boxes to their default values.
Continue w/
This choice continues the run, for the same number of generations aspreviously entered in the New Run menu.
Continue
This continues the run, but presents the following dialog:which allows you to change the number of generations run in the next continuation of the run.
Restart
Don

There are two menus, File and Run, that control PopG. They are in the upper left of the main PopG window.

The Run menu

The Run menu contains five items: Continue w/, Continue, New Run, Restart, and Display Whole Plot.

The first time it is picked, it looks like:

with all but New Run Might and magic x legacy cheats. grayed out. Once you have done your first run, all the selections will be active.

New Run
Initially only New Run is available. It brings up the following dialog:It contains all the parameters that control a PopG run. Note that usually you do not enter a Random Number seed unless you want to do two identical runs. When you are finished editing you can click the OK box to start the run. You can also click Cancel to not start the run and Defaults to reset all the data entry boxes to their default values.
Continue w/
This choice continues the run, for the same number of generations aspreviously entered in the New Run menu.
Continue
This continues the run, but presents the following dialog:which allows you to change the number of generations run in the next continuation of the run.
Restart
This restarts the run with the same parameter values as before. If youwant to change some of the parameter values, use New Run instead.
Display Whole Plot
This plots all generations on the same plot. During a run the plots willnormally show only the last group of generations. This shows all generationsthat have been simulated so far. This is particularly handy when you have finisheda simulation and want to print the results of the whole run.

The random number generator

The program uses a random number generator which automatically initializesfrom your system clock. Thus it should give you a different sequence of random numbers and thus a different result every time yourun the program. In the menu for a new run, there is a setting forRandom number seed which is set by defaultto (Autogenerate), which will initialize from thesystem clock. You probably won't have any reason to change this,unless you are debugging PopG and want to do the same run, with thesame random outcomes, twice. If you do wish to do the same exactrun twice, enter a value in place of the (Autogenerate)string and PopG will use that to initialize the random number generator. Assuming you have not modified the calcPopG routine within the Java code,every time you start with that random number you will get exactly the same results.

The File menu

This contains four menu items. They are Save,Print, About and Quit.

The first time it is displayed, it looks like:

with Save and Print grayed out. Once you have done your first run, they will be active.

Save
This opens a standard save file dialog and allows you to save the graph as a JPG or PNG file. The default name is PopG with the appropriate extension to match to file format.
Print
This opens a standard print dialog and allows you to select a printer and print the graph.
About
Displays the program's copyright notice.
Quit
This is self-explanatory: the program quits.

Compiling it yourself

Most people will not need to compile the program themselves as the Java Jar package supplied should run on most versions of Java.So you should probably skip this section. But if you wish to modify the functionality of PopG or if you have some unusual Java environment that will not run the supplied Jar fileyou will need a Java compiler. We repeat: If you just need to run the program,you should run the Jar file that comes in our distribution. You do not need to compile anything (though you may need to install Java).

If you do need to compile the program, you will find a src directoryin the downloaded and unzipped folder PopG which you got from oursite. Import the file PopGUserInterface.java from srcinto your favorite Java editor (we used Eclipse). You can eitherexecute it directly from there or export a Java Jar from the editorand execute it. PopGUserInterface.java does not reference anyexternal libraries, everything it needs is in the JavaSE-1.6system library. If you are modifying our program, once you have finisheddoing that you should have no problems creating the Java Jar,

If you cannot do, tell us, since that would be a bug.

Simulating with PopG

This program simulates the evolution of random-mating populations with two alleles, arbitrary fitnesses of the three genotypes, an arbitrary mutation rate, an arbitrary rate of migration between the replicate populations, andfinite population size.

Shimo 4 1 3. The programs simulate simultaneously evolving populations with youspecifying the population size, the fitnessesof the three genotypes, the mutation rates in both directions (from A to aand from a to A), and the initial gene frequency. They alsoask for a migration rate among all the populations, which will make their genefrequencies more similar to each other. Much of the time (but not always!)you will want to set this migration rate to zero. In most respects theprogram is self-explanatory.

Initially there are ten populations. You can set the number ofsimultaneously-evolving populations to any number from 0 to 1000.The population size for each population can be any number from1 to 10000. Note that a larger population, a larger number of generations run, and a larger number of populations can lead to longer runs.

When you make a menu selection that causes the program to run,a graph of the gene frequencies of the A allele in each of thepopulations will be drawn in the window.Here is what the graph looks like when we run with an initial gene frequencyof 0.2 and fitnesses of AA, Aa, and aa set to 1.08, 1.04, and 1, with allother parameters in their default values. (Note that if you try this run,there will be different random numbers, so your result will be a bitdifferent).

Note that the window can beresized, and the graph should adjust to this. There is also a blue curve that shows what thegene frequencies would be in an infinite population (one with nogenetic drift). If the number of populations being simulated isset to zero, this curve is all you will see. The graph can be printed usingthe Printoption of the File menu, or saved to a Postscript file usingthe Save option in that menu.

Note that once the plot of the gene frequency curves reaches theright-hand side of the graph, the program prints there the number ofpopulations that fixed for the A allele (ended up with afrequency of 1.0) and the number that lost this allele.

Suggestions

The program can simulate a wide variety of cases, and you shouldexplore some of these. Here are some suggestions:

  • Try cases with no mutation, no migration, and all fitnesses 1.0 sothat there is no selection. Does genetic drift in a population ofsize 1000 accomplish roughly the same changes in 1000 generations asgenetic drift in a population of size 100 does in 100 generations?By running a largish number of populations, can you check whetherthe probability that an allele is fixed by genetic drift is equal toits initial frequency in the populations?
  • Try a case with no mutation or migration, with the Aallele favored by natural selection (with fitness of the AAgenotype set highest and fitness of the aa genotype setlowest). Start with a small frequency of A. Is it alwaysfixed? If one starts with a single copy of the allele, how doesthe probability that A is fixed compare with the selectioncoefficient favoring it in the heterozygote (the fraction bywhich the Aa genotype is higher compared to the fitnessof the aa genotype)? Is this fixation probability larger thanthe one you would get with the same initial frequency but with noselection?
  • Try overdominance (Aa having the highest fitness). Doesthe gene frequency converge towards an equilibrium? Why does itvary from this equilibrium frequency? How large do the selectioncoefficients have to be to cause the gene frequency to stay away fromfixation or loss for large amounts of time?
  • Try underdominance (Aa having the lowest fitness).Is there a starting gene frequency that will result in some populationsheading for fixation, and others heading for loss? If you add a smallamount of migration, what will happen in the long run? What will happen ifinstead you add a small amount of mutation in both directions?
  • With migration but no selection or mutation, how much migration isneeded to make the gene frequency curves be quite similar to each other?How much is needed to make them all end up at the same gene frequencyin the long run?How is that migration rate affected by the population size?
  • With mutation but no migration or selection, how much mutation isneeded to cause the gene frequencies to converge to a mutationalequilibrium gene frequency? How does this value relate to thepopulation size?
  • If an allele is selected against, can you set up mutation ratesthat will maintain it at low frequency in the population?
You should be able to use the program to get a good feel for the relative strengths of different evolutionary forces. It is worthwhiletrying many different kinds of cases and asking what values ofparameters are needed to make one evolutionary force be influential inthe presence of another.

Credits

Version 4.0 of PopG, the first Java version, was written by Ben Zawadzki.His enormously effective programming made good use of mentorship andadvice from our lab's Java wizard, Jim McGill.

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The original version of PopG was written in the 1970s in FORTRAN by Joe Felsenstein. The interactive version then was writtenin C with much work by Hisashi Horino, Sean Lamont, Bill Alford, Mark Wells, Mike Palczewski, Doug Buxton, Elizabeth Walkup, Ben Zawadzki and Jim McGill.Hisashi and Sean wrote the C version,and the screen graphics for IBM PC and the first part of the Postscript printing system. Bill greatly improved and expanded the Postscript printing and the X windows graphics. Mark Wells did the original Macintosh version. Mike Palczewski greatly improved the Windows, Macintosh and X Windows graphical user interface, and Doug Buxton modified the program to the 3.0 version and prepared the executables for different operating systems. Elizabeth Walkup improved the X windows interaction and prepared version 3.3. Small documentation changes after version 4.0 were madeby me.

Copyright notice

Copyright 1993-2016. University of Washington and Joseph Felsenstein. Allrights reserved. Permission is granted to reproduce, perform, and modifythis program. Permission is granted to distribute or provide access to thisprogram provided that this copyright notice is not removed, this program isnot integrated with or called by any product or service that generatesrevenue, and that your distribution of this program is free. Any modifiedversions of this program that are distributed or accessible shall indicatethat they are based on this program. Educational institutions aregranted permission to distribute this program to their students and stafffor a fee to recover distribution costs. Permission requests for any otherdistribution of this program should be directed to license (at) u.washington.edu.

Joe Felsenstein
Department of Genome Sciences
University of Washington
Box 355065
Seattle, WA 98195-5065, USA

email: joe (at) gs.washington.edu





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