Demo models for repast

After struggling to remember how to get access to the repast demo models, which are EXTREMELY helpful when trying to figure out how repast works, they can be downloaded from http://repast.sourceforge.net/models.zip

After extracting the files, get the models into Eclipse easily by:

1. Select File -> Import Repast Examples from the Eclipse main menu

2. Check Select root directory: /home/rlr/Repast/Repast-Models/models (not: Select archive file)

3. Check the boxes for the example projects you would like to import select all copy projects into workspace

4. Click Finish

Now they all appear in the packages panel

On a Mac eveything should work fine, if working on Windows there may now be problems running some of the example models due to JOGL and Java3D errors.

Meghan Hutchins provides an excellent outline of how to fix these errors, please see the link on the left to her blog, or else click here for the specfici pages related to demo models and how to fix errors that may occur. (User guide to Eclipse/Repast)
http://meghanhutchins.com/pmwiki.php/Main/InstallJava3DLibraries

Eclipse plugins and configurations

Ok, so now I've moved on from netlogo, the decision of which interface and language to use is a pretty big one. After some considerable time looking into the pros and cons of different languages I settled on java, with its flexible use and wealth of support information available.

I trialled NetBeans for a while which I quite liked, but then settled on Eclipse after some recommendations from friends. The brilliant thing with Eclipse is also that i can use it for more or less EVERYTHING! Via plugins, I now use it as my base for java, python and LaTeX, linking it up to my university server repository via the subclipse plugin.

Some details on setting up plugins is as follows (all configured for the most recent Eclipse Indigo):

For LaTeX:
Texclipse - found at http://texlipse.sourceforge.net
In eclipse, go to Help > Install New Software > type the above URL in the  'work with' box and press 'Enter'

select the texlipse box and press next until the process is finished.

For Version Control
Subclipse - found at http://subclipse.tigris.org/update_1.6.x (this is the version for Eclipse Helios. There is currently no updated version for Indigo)

Again, go to Install New Software and enter the URL above.

After installing this there are several things to note. Using a windows machine, I had problems using the JavaHL interface, so I recommend using the SVNKit bundle instead (go to Windows > preferences > team > SVN > SVN interface - choose SVNKit.)

In order to checkout a project from an online repository:
go to the required perspective, right click > import > SVN > checkout from SVN > put the repository location in the URL, for me this was svn+ssh://username@svn.forge.ecs.soton.ac.uk/folder/repositoryProjectName

You dont seem to need the Tortoise SVN programme that is recommended for Windows machines if you use the subclipse plugin.

For Python
Pydev - found at http://pydev.org/updates

Install new Software > enter in URL > select Pydev (NOT PyDev Mylyn Integration)
> click next to finish.
A box should pop up asking you to trust the certificates, YOU NEED TO SELECT THE Antana PyDev; Pydev; Aptana CHOICE, OTHERWISE PYDEV WILL NOT INSTALL
You then need to restart Eclipse

Pydev then needs configuring - you need python already installed on your computer
Windows > preferences > pydev > interpreter Python > new > then browse to the current version of Python.exe > ok > select all of the options EXCEPT PySrc and python.zip > then ok as many times as needed to end the process

All of the information on the PyDev plugin and more can be found on:
www.rose-human.edu/class/csse/resources/Eclipse/eclipse-python-configuration.htm

For Repast Simphony
You need three separate installations for this plugin
1. Groovy-Eclipse
found at http://dist.springsource.org/release/GRECLIPSE/e3.7/ (3.7 refers to the version for Indigo, older version of eclipse will need the relevant version of groovy)
2. Web, XML & Java EE development
found at http://download.eclipse.org/releases/indigo (again you need the relevant site for the eclipse version you have)
under the Eclipse XML editors and Tools menu
3. Repast
found at http://mirror.anl.gov/pub/repastsimphony/2.0.0.beta

there are a LOT of example models available within the repast plugin that show a great range of things that repast can do.

I'm currently trying to work my way around repast, I hope to have more on this at a later date.

Student Conference on Complexity Science

If you are a PhD student researching a complexity science problem, then you are invited to submit an abstract for the first annual Student Conference on Complexity Science. This conference is an opportunity for postgraduate students to network and meet others in the complexity science community.

The SCCS will be held at the Stripe Theatre, Winchester University, from 5th to 6th of August 2011; attendance is free of charge. All prospective attendees to the conference must submit an abstract, and be prepared to either give a 20 minute talk, or to present a poster to share their research.

Due to the interdisciplinary nature of complex systems, research presented at this conference is expected to span a broad range of scientific disciplines. Work may be theoretical or applied and, for example, could cover social systems, networks, ecosystem dynamics, evolution, or non-linear systems.

Prizes will be awarded for the best presentation and for the best poster at the close of the conference.

If you are interested in presenting your work at this conference, please submit an abstract to sccs@soton.ac.uk by 8th July in the following format:

• Email subject: ABSTRACT - Poster/Presentation (please specify your preference)
• Project title
• Your name, University/department and supervisor(s)
• Contact information
• The abstract, which must have a maximum of 250 words and should outline your project, summarise your methodology and results, and include any conclusions you have drawn.

If you have any queries, please do not hesitate to contact the SCCS organisation team on sccs@soton.ac.uk.

PhD - first step

So first year over, now its on to some new research.


My first thought was, where do I go next?

My PhD is aimed at a real-life problems. My case study is a corridor area in Belize, in central america.

The issues remain the same as with the hedgehog work. How do mammals move through the landscape? How will increased habitat fragmentation affect the movement of mammals through the landscape? How do we measure landscape permeability? How can we best model the effects of landscape structure on the movement of mammals in a landscape?


These questions have huge implications on the persistence of populations in a landscape and on the amount of disturbance and development that a landscape can absorb before a population reaches a threshold tipping point. My research is really focused on questions surrounding ecosystem function and resilience.

"To halt the decline of an ecosystem, it is necessary to think like an ecosystem."

- Douglas P. Wheeler, EPA Journal,September-October 1990

The overall goal of my research is to attempt to understand how a species views and interacts with its environment. Exploring these issues and gaining some understanding of the relationship between animals and their environment can help us understand ecosystems function and how anthropogenic processes may affect ecosystem processes.