BIOS 615: Ecology

Dr. S. Malcolm

Biological Sciences

POPULUS 3.42

Overview:

http://www.cbs.umn.edu/software/populus.html/About/about.html

The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. Simulation models are chosen from menus, and students can move among the parameter boxes of an input window, changing initial defaults to values of their own choosing. Most modules offer several graphical outputs of model dynamics, and all provide help screens explaining the computational algorithms.

Versions:

http://www.cbs.umn.edu/software/populus.html/Download/Versions.html

Populus 3.42 for DOS running in Windows:

Populus 3.42 is a 1998 recompile of the most widely used DOS Populus, dating originally from 1994. It contains 50 different simulation modules spanning both elementary and advanced courses in ecology and evolution. This version has been patched to fix a Borland Pascal timing problem that caused crashes (runtime error 200) on computers clocked above 100 mhz. Version 3.42 will run without problems in the DOS window of Win95, Win98, WinNT and Win2K. The old DOS print drivers do not function on modern machinery, and this version will be dropped when all of its component models have been built into the Java version. Java conversion is about half complete at this posting in August, 2001, so there are still many reasons to run the old DOS Populus.

Populus 5.1 for Java Virtual Machines:

Populus 5.1 supercedes the 5.01 posting of November 2000, and contains about twice as many modules. The graphical interface links paired input and output windows so that toggled parameter changes show up instantly. Multiple input/output pairs can be placed onscreen simultaneously, allowing comparison of different models, or different instances of the same model. This version implements a new Interaction Engine, the visually appealing cellular automata, and the first three-dimensional plotting routines in Java; with 3-D output figures that can now be rotated and viewed from different perspectives.

Populus 5.1 for Macintosh OS X:

With the update to Mac OS X the Macintosh platform has finally caught up with the Java 1.2 API that we use to build Populus. Version 5.1 will run on Mac OS X just as it does on Intel/Windows; appropriate download and installation routines are provided on the download page.

Terms of Use:

http://www.cbs.umn.edu/software/populus.html/Download/termsOfUse.html

Populus is produced by Don Alstad at the University of Minnesota to foster instruction in population biology. IBM, the University of Minnesota, and the National Science Foundation have underwritten development, and the software is not a commercial venture. You may download Populus and distribute it gratis to students at your institution. You may incorporate links to this site, http://ecology.umn.edu/populus, in nonprofit material distributed within or beyond your institution. This is the only venue maintained to provide the current public version of Populus. By making a Populus download, you signify acceptance of these terms.

Download and Installation Guide:

http://www.cbs.umn.edu/software/populus.html/Download/download.html

How to download Populus 5.1 for

Windows 95 / 98 / 2000 / NT 4.0 / ME

Mac OS X

Linux / Unix

How to update Populus 5.01

How to download Populus 3.42 for Dos in Windows

1.Populus 5.1, August 2001

Here we summarize steps for installing a Java virtual machine and/or the Populus application on your computer. We also explain a simple procedure for updating Populus 5.0b or Populus 5.01 to the current Populus 5.1.

Populus Files:

Any Populus installation requires the following core files:

* Populus.jar

* jcchart401K.jar

* jhbasic.jar

* PopHelp.jar

* run.bat (unless you are an expert, and choose to run Populus from the java console)

and some extras:

* picon.ico

* Populus 5.1 (shortcut)

* PopulusUninstall.class

* readme.txt

For Windows 95 / 98 / 2000 / NT 4.0 / ME (Intel Platform):

There are two steps necessary to get Populus running on your computer.

a. Install a Java2 Runtime Environment (JRE). We did not bundle a JRE with Populus because it is likely that many users will already have one installed.

To determine whether you already have JRE 1.2.2, open a command (DOS) prompt and type: "java -version" followed by <Enter>.

If you don't have a JRE, or you have an earlier version than 1.2.2, you can download one without cost from Sun MicroSystems. Their download site is:

http://java.sun.com/j2se/1.3/jre/download-windows.html

The JRE download is approximately 5.4 MB, and is easy to install using the directions provided by Sun.

b. Install Populus 5.1 on your computer. We provide two methods. Most first-time users will prefer to use the installer file Populus 5.1. It will perform a complete installation from a single large download using an InstallShield Wizard, and add a shortcut to your start menu; this shortcut can be moved or copied to the desktop if desired.

Technically adept users may prefer to install Populus 5.1 more quickly by downloading the four "jar" files required to run the Populus program. Populus can then be run using a batch (".bat") file like the one placed in our distribution folder with the jar files. You may also write your own batch file; it must contain the following:

java -cp Populus.jar; jhbasic.jar; jcchart401K.jar; PopHelp.jar edu.umn.ecology.populus.core.PopRun

If you want easy access to this batch file (which must remain in the same folder as the jar files) you can create a shortcut; you can even assign it the Populus icon "picon.ico" for an aesthetic touch.

For Mac OS X:

To run Populus 5.1 on Mac OS X, you do not need to download a Java Runtime Environment from Sun MicroSystems; the Mac OS X comes bundled with one already in place.

On the Populus website we provide an application bundle specifically for Mac OS X, Populus 5.1. This is simply the set of 4 jar files with a wrapper to make it easier to run, and it is ready to use just like any other Mac OS X application.

Please note: the Java 2 tools (API) used in building Populus are not supported on Mac operating systems older than OS X. We presume that such machines will gradually be phased out or updated, and do not plan to support them.

For Linux, Unix:

Because this program was written in Java, Populus will run on Linux and Unix machines, but it has only been tested on Windows and Mac OS X. We assume that Linux and Unix users understand how to start a Java program. To run Populus, download the jar files and then use the console (or a script) to run the program. Note that the static main(String argv[]) method is in the class:

edu.umn.ecology.populus.core.PopRun

If you use Populus on either of these operating systems, we would appreciate feedback.

Updating from Older Versions:

In its current configuration, you can update Populus simply by overwriting both the Populus.jar and the PopHelp.jar files with newer versions. The two are available separately here. Simply find the folder with the old Populus.jar and replace it with the new one, which will have the same name. The same process is used to replace PopHelp.jar with an updated help file. If you want to update from Populus 5.01, then the process is similiar, but you will be replacing JPop12.jar with Populus.jar and you will have to modify the batch file, run.bat, to account for the change in the file name.

Mac OS X users will need to open the application bundle to replace the individual jar file. This is accomplished by:

1. ctrl-click on the application (or right-clicking if you have a 2-button mouse)

2. select "Show Package Contents"

3. open the folder Contents/Resources/Java

4. there you will find the Populus.jar file. Simply replace this with the Populus.jar file available on the website.

2.Populus 3.42 for DOS in Windows

Clicking Populus 3.42 will download the DOS version of Populus, placing the file Pop342p.exe on your computer. This file is a self-extracting executable; move it to the directory in which you would like it to run, and double click to unpack six Populus files. Then double click on the file Populus.exe to run the program. This version of Populus will run on Win95, Win98, WinNT and Win2K.

Comments, suggestions, or questions, about the installation process or Populus itself are welcome at: populus@ecology.umn.edu

Lab Manual:

http://www.cbs.umn.edu/software/populus.html/LabManual/labManual.html

A Populus lab manual offering computer simulation exercises for elementary ecology courses is now available from Prentice-Hall:

Alstad, Donald N. 2001. Basic Populus Models of Ecology. Prentice-Hall, Inc. Upper Saddle River, NJ 07458

ISBN 0-13-021289-X.

It is an inexpensive spiral-bound paperback of 144 pages, intended to supplement any of the major Ecology texts. It introduces the mathematical models taught in basic ecology courses, including

Density-Independent Growth

Lotka-Volterra Competition

Density-Dependent Growth

Continuous Predators & Prey

Demography & Age Structure

Infectious Microparasitic Diseases

The Populus manual expands on model derivations and explanations given in texts; it illustrates operation of the Java Populus software with exemplary input windows, output graphs, and the parameter values used to generate them; and it provides an extensive set of 10 to 15 detailed problems and simulation exercises that demonstrate the conceptually important aspects of each model. Instructors may request an examination copy of the Populus lab manual from at http://www.prenhall.com

Notes:

http://www.cbs.umn.edu/software/populus.html/Notes/notes.html

Java Populus 5.1 was posted in August 2001, replacing prior version 5.01 from November 2000. It contains about twice as many modules, including the discrete predator-prey models, cellular automata, and interaction engine, all enhanced beyond their counterparts in the old DOS Populus. It fixes a bug in the Age-Structured Growth Module which allowed computations to proceed without incorporating the final tabular data entry under some conditions. With this release, many complex programming issues have been settled in Java for the first time. These include the parser and numerical integration code for the interaction engine, the graphical representation of cellular automata, and the rotatable 3-D graphics. These advances are largely the work of Amos Anderson, building on the Java program structure initiated by Lars Roe.

With the release of OS X, the Macintosh platform has finally caught up with Java capabilities required for Populus. We have tested Populus 5.1 extensively and without problem on an iMac, and an iBook after giving it a cheap RAM boost and an OS X upgrade. Please note however, that we are using Java development tools that are not supported by Mac OS 9 and predecessors. The development of a simplified Populus interface based entirely on the older JDK 1.1.8, and therefore compatible with legacy Macs, would be a costly lateral move of short-lived value. We assume that these machines will be updated or fade away.

The late, unlamented, BLACK website previously at this url was cobbled together by DNA. The elegant replacement that you are now visiting is the work of Sharareh Noorbaloochi.

Contact:

http://www.cbs.umn.edu/software/populus.html/Contact/contact.html

The registration page posted with Populus 5.1 in August 2001 is not functioning properly, and a replacement is under construction. In the meantime, if you would like your email address added to the listing for automated Populus update notices, send an email to populus@ecology.umn.edu.