More Info About AntsInFields

Felix Friedrich

[ short summary | implementation specific notes | some applications | version log ]

short summary

Oberon is the name of a modern integrated software environment. It is a single-user, multi-tasking system that runs on bare hardware or on top of a host operating system. Oberon is also the name of a programming language in the Pascal/Modula tradition. The Oberon project was launched in 1985 by Niklaus Wirth and Jürg Gutknecht. See also www.oberon.ethz.ch

Voyager is a project to explore the feasibility of a portable and extensible system for simulation and data analysis systems. It is mainly written in and for Oberon. The Voyager project is carried out by StatLab Heidelberg and was launched in 1993 by Günther Sawitzki, Martin Diller et al. See also www.statlab.uni-heidelberg.de/projects/voyager/

AntsInFields is a software package for simulation and statistical inference on Gibbs Fields. AntsInFields is written in Oberon and uses Voyager. It has been developed since 1997 by Felix Friedrich. It is intended for mainly two purposes: To support teaching by demonstrating well known sampling and estimation techniques and for assistance in research. By a clear concept the software meets today's typical demands like portability, flexibility, extensibility and modularity. Its object oriented design is very close to the mathematical structure, which - on the one hand - provides scientific re-usability and - on the other hand - allowes an implementation of interactive and consistent visualization, one of the principal items used for intuitively illustrating complex mathematical facts. AntsInFields contains handling and visualization of one, two and multi-dimensional data. It provides a general abstract framework for Markov Chain simulations and for Gibbs Fields. It includes concrete implementations of the Gibbs Sampler, Metropolis Hastings Algorithms, Simulated Annealing and Exact Sampling. Main focus is on techniques that use Markov Chains for two dimensional, finite, data like, for example used in the Bayesian image analysis approach. Various models like the Ising model, the Potts model, Graffigne's Phi-model, auto-models, and extensions have been implemented and are ready for experiments. Besides the MCMC based algorithms, parameter estimators for Gibbs Fields are provided for special cases. AntsInFields contains a ready-for-use graphical interface for beginners, students and for presentations, a command based interface for flexibility on an intermediate level and reusable modules for the scientist and the advanced programmer.

implementation specific notes

For Oberon-people, who are not interested in Markov Chains, Gibbs Fields and the like, some Modules might still be interesting, because of some its novel features, as for example: Panels are scalable - by modifying Organizers into antsOrganizers.Mod, their content (including Fonts) is scalable; closing a Windows-window stops the running thread if it is attached to the window; threads are controlled and activity is displayed; etc. Check it out, if you like, and excerpt parts that you find interesting.

The system distributed is designed for use with "ETH Plugin Oberon for Windows". Many many many thanks to E. Zeller for producing all the Windows views and dialogs etc. ! I tried to make it work with people who did not know anything about Oberon beforehand. And, I think it works.

The version on the web is not specifically designed for Windows but at the moment you need a Windows 95/98/NT/XP/ME/2000 operating system for an easy installation. If you use Oberon for Windows already, I recommend to perform a COMPACT installation (select "compact" while installation progresses), since then only the AntsInFields registry is written to disk without affecting your (Windows-) Oberon. AntsInFields is then installed separately from Oberon. (The installer does not provide an installation into an Oberon system)

some applications

At the Institute of Biomathematics and Biometry (IBB), Research Center for Environment and Health (GSF) near Munich - see http://www.gsf.de/ibb - simulations in various fields like Genetics, Developmental Biology, Brain Mapping, X-Ray Mammography, Image Analyis have been performed using AntsInFields/Voyager/Oberon. Among them are - more specifically -

image brain (Brain Mapping) One dimensional Potts-Model reconstructions of time series to identify activated regions of the human brain.
image mamography (X-Ray Mammography) A two dimensional modified Potts-Model approach as a prestep for more sophisticated detection of microcalcifications.
image PSM (Developmental Biology) Simulation of gene expression waves in the presomitic mesoderm of vertebrae.
image Biofilm (Biofilm) Ising like models for biofilm.
image Comet (Genetics) Simulation of COMETS assay - gel electrophoresis for quantification of rearrangement of destructed DNA

version log

2 Oct 2002 - First public version a1.01
current: a1.03

more info

Last edited: 2005-01-25 fof.