Modelling and Simulation Links

Registers and Sources of Ecological Models

• WWW Server for ecological modelling
• EPA Center for exposure assessment & modelling
• EPA's Council for Regulatory Environmental Modeling - Models Knowledge Base
• ORNL Biogeochemical Model Archive
• CAMASE register of agro-ecosystems models
• SOMNET Soil organic matter models and data sets
• Canadian Environmental Modelling Centre
• EPA page on data and software
• CEE/ODU Civil/Environmental Computer Model Library (CEML)
• EPA, Watershed Tools Directory
• The Surface Water and Water Quality Models Information Clearinghouse (SMIC)
• International Ground Water Modeling Center (IGWMC), Software List
• Hydrology Modeling
• Systems & Simulation links

Documents

• Population ecology by A. Sharov

• V. Perminov and D. Sarancha:
  Application of direct simulation Monte Carlo method to ecological objects modeling.
  Modeling a tundra animals population.
  View/download full text: Postscript , PDF

• Forest Ecosystem Dynamics (FED) Project

(mathematical) concepts in modelling:

• Petri Nets
• Random Numbers and Monte Carlo Methods
  • The WWW vitual library: Random Number and MONTE CARLO methods
  • The Basics of Monte Carlo Simulations (1996) by Joy Woller
  • Monte Carlo Methods in Parallel Computing (1995) by Chuanyi Ding & Eric Haskin

• Software Design for 1-D Moving Mesh Method by Shengtai Li

• Object & Individual Oriented concepts
  • Object-Oriented Analysis and Design Methods a Comparative Review (1995)
    by Sjaak Brinkkemper, Shuguang Hong, Arjan Bulthuis, Geert van den Goor
  • Individual-Based Models (1999) by C. Reynolds

• bond graph
  • BondGraph.info by Dr. Arun K. Samantaray, HighTech Consultants
  • The Bond Graph Compendium by F. E. Cellier

• cellular automata
  • Methods for Designing Cellular Automata with "Interesting" Behavior by H.A. Gutowitz and C.G. Langton
  • Artifical life index
  • Cellular Automata by: Jiri KROC

• Sensitivity Analysis
  • Identification and Review of Sensitivity Methods. (2000) by Frey, H.C. & Sumeet R.P.

Simulation Modeling Methodolgy and Guides:

• Modeling & Simulation Resources, (by Hossein Arsham)
• A Collection of Modelling and Simulation Resources on the Internet by Andrea Emilio Rizzoli
• Design Guidelines for Shallow Lake Systems
• Lake Water Quality Models and Benchmark Criteria
• Integration and Coupling of Hydrological Models with Water Quality Models: Applications in Europe
  (Berit Arheimer and Jonas Olsson)
• Computer Simulation: The Art and Science of Digital World Construction by P. A. Fishwick
• Web-Based Simulation

dictionaries, thesauri:

• Web Dictionary of Cybernetics and Systems
• AGROVOC FAO thesaurus

online journals:

List of books/virtual libaries:

• List of ecological modelling books by M. Knorrenschild

Lectures:

• lecture notes disappeared from the web??

Databases

• ORNL Distributed Active Archive Center for biochemical dynamics
• CEDAR - Central European Environmental Data Facility
• USGS Internet resources

Simulation software

Documents about simulation and simulation software

• OR/MS - Survey of discrete-event simulation software
• Information about Selecting Simulation Software
• Software Benchmarks (ARGESIM)
• McLeod Institute of Simulation Sciences
• simulation software development frameworks
• INCOSE - Tools Database, International Council of Systems Engineering

Model/Data description languages

• VHDL
  • IEEE 1076.1 Analog and Mixed-Signal Extensions to VHDL
  • VHDL easy
• Modelica
• SME Spatial Modeling Environment
• ECOBAS_MDL
• NMM XML Numerical Model Metadata
• EML Ecological Metadata Language
• CERF data and information guidelines

List of products (general):

• 20-sim, Controllab Products Inc.
• ACSL
• ANDECS, Dsblock, DLR
• AnyLogic
• AutoMod
  • AutoMod (english)
  • AutoMod (german)
• Berkeley Madonna
• BuildSim, Tritera
• CSIM19, Mesquite Software Inc.
• C++SIM simulation package Simula-like simulation classes in C++
• Delsi, Softland
• Dymola, Dynasim
• DYNAST, TU Prag
• MSC.EASY5
• Ecolego Toolbox for Radioecological Risk Assessment
• extendsim (Imagine That, Inc.)
• GPSS, Wolverine Software
• javasim
• Maple 12 (page opens in a new tab)
• MapleSim high-performance multi-domain modeling and simulation tool (page opens in a new tab)
• MATLAB/SIMULINK, The MathWorks Inc.
• NI MATRIXx Model based design, simulation and embedded code generation
• MINOPT A Modeling Language and Algorithmic Framework for Linear, Mixed-Integer, Nonlinear, Dynamic, and Mixed-Integer Nonlinear Optimization
• ModelMaker, Family Genetics Ltd.
• MS1, Lorenz Simulation
• Octave
  Octave Manual
• PSM++
• POSES++
• Powersim, Powersim Corp.
• ProModel, PROMODEL Corporation
• Ptolemy II, heterogenous concurrent modeling and design
• QSIM
• RAMAS Library of Ecological Software
• SAAM II
• Scilab, INRIA
• SDX, Eclipse Software
• SEMoLa, Simple Easy Modelling Language
• SIGMA: The Scientists' Intelligent Graphical Modeling Assistant Project
• SimCAD
• SIMFLEX/3D
• SIMILE: simulation of complex dynamic systems in the earth, environmental and life sciences
• SIMPLORER, SIMEC
• SIMJAVA
• SIMSCRIPT, SIMPROCESS
• SIMsystem, Applied Dynamics
• SimOS, Stanford
• SIMUL8, Visual Thinking (page opens in a new tab)
• SME , Spatial Modelling Environment
• Stella/iThink
• SystemView, ELANIX, Inc.
• Flexsim
• Parallel software tool for ecological simulation (TEMPEST)
• THINK, Microfusion Eng. Lab. Inc.
• ULM - Universal Life Models by S. Legendre
• Vensim, Ventana Systems, Inc.
• VisSim, Visual Solutions Inc.

Cellular automata:

• JCASim: Cellular automata simulation system

Individual oriented modelling & simulation:

• EcoTools
• Swarm (a general purpose simulation software package)
• Repast 3 Recursive Porus Agent Simulation Toolkit
• CORMAS

Neural Networks:

• SNNS Stuttgart Neural Network Simulator

Parameter estimation, inverse modelling:

• PEST : Parameter Estimation for any Model (free download)
  (S.S. Papadopulus & Associates Inc. at: http://www.sspa.com/)
• PEST : Parameter Estimation for any Model
  (Scientific Software Group at: http://www.scisoftware.com/)
• UCODE: A COMPUTER CODE FOR UNIVERSAL INVERSE MODELING (free download)
  (International Ground Water Modeling Center at: http://typhoon.mines.edu/zipfiles/)
• Clausnitzer, V., and J.W. Hopmans. 1995. Non-linear parameter estimation: LM-OPT. General-purpose optimization code base on the Levenberg-Marquardt algorithm.
  Land, Air, and Water Resource Paper No. 100032, University of California, Davis, CA.

Curve Fitting and Function Optimization:

• GraphPad Software, Inc.:    A complete guide to nonlinear regression
• Wikipedia:    Curve fitting
• The Industrial Physicist:    Curve fitting made easy by Marko Ledvij
• The MathWorks:    Curve fitting guide
• The MathWorks:    Evaluating the Goodness of Fit

• NLREG - Nonlinear regression analysis, surface and curve fitting
• IDL Curve Fitting and Function Optimization
• MatLab: Curve Fitting Toolbox     ( Documentation)
• Systat Software Inc.:     Sigmaplot, Table Curve, PeakFit etc.
• FindGraph

Qualitative and semi-quantitative modelling:

• Qualitative Reasoning about the Physical World (Benjamin Kuipers; kuipers@cs.utexas.edu)
• Qualitative Simulation as a Task of Qualitative Reasoning

Finite Element Method

• ALGOR
• ANSYS
• COMSOL Multiphysics
• freeFEM
  • freeFEM++
  • freeFEM3D
  • FreeFem++-cs
• Fluent
• simulia
• Internet Finite Element Resources An excellent collection of links to information related to FEM.
• FEMur - The Finite Element Method Universal Resource

• CFD-ACE+ (CFD-ACE+, CFD-Fastran, PAM-Flow etc.)
• IDEA, Internet Differential Equations Activities

Libraries:

• Numerical Recipes (Home page)
  • Numerical Recipes (2. edition, free)
  • How to Install the FileOpen Plugin for Adobe Reader7/8
    (needed to read Numerical Recipes)
• Computational Fluid Dynamics by Abdusamad Salih
• CFD codes list - free software
• Free and Low-Cost CFD Software
• Serial Fortran Solvers for ODE Initial Value Problems by Alan C. Hindmarsh
• CMLIB NIST CORE MATH LIBRARY
• NAG
• IMSL
• PETSc Portable, Extensible Toolkit for Scientific Computation
• GSL - GNU Scientific Library
• Netlib Netlib is a collection of mathematical software, papers, and databases.
• GAMS Guide to available Mathematical Software
• MBSSIM - An Integrator Library for Simulation of Multibody Systems
• Netlab neural network software

Initiatives

• Simulation server by S. Lundberg
• WWW Virtual Library. Sustainable development
• Mission Earth of the SCS
• Australia strategy for sustainable development
• The EnviroComp Institute
• International Long-Term Ecological Research (ILTER) network
• The Long Term Ecological Research (LTER) Network

Societies

• ASIM German Simulation Society
• ISEM International Society for Ecological Modelling
• Society for Mathematical Biology
• ESA Ecological Society of America
  • ESA Data Sharing and Archiving » Resources and Tools
• SCS Society for Modeling and Simulation International
• ECMS European Council for modelling and Simulation
• UKSim UK Society for Modelling and Simulation
• EUROSIM (Federation of European Simulation Societies)
• INFORMS College on Simulation
• ACM Special Interest Group on Simulation

Departments, research centers

• Multiscale Experimental Ecosystem Research Center (MEERC) at the University of Maryland
• Geographic Systems Modeling Laboratory University of Illinois at Urbana-Champaign
• USDA-ARS: Remote Sensing & Modeling Lab (RS&ML) at Beltsville
• The Natural Resource Ecology Laboratory (NREL) at Colorado State University
• Ecosystems Modelling Laboratory at Institute of Physicochemical and Biological Problems of Soil Science RAS, Moscow
• ICRAF (INTERNATIONAL CENTRE FOR RESEARCH IN AGROFORESTRY)
  • ICRAF south east Asia

Journals

• Elsevier Science Table of Contents
• Springer
• Nature
• Science (page opens in a new tab)
• Simulation, SCS
• Transactions of SCS
• Simulation Practice and Theory, Elsevier Science B.V.
• Simulation News Europe, ARGESIM Wien
• CIT, Journal of Computing and Information Technology
• Integrated Assessment

FAQ Frequently Asked Questions

• Soft Earth - software by P. Ingram
• Virtual Earth - connections by P. Ingram
• Numerical analysis by P. Sullivan
• Nonlinear science by J. Meiss
• Meteorology - introduction by I. Stern
• Science data formats by I. Stern
• Satellite imagery - part1 by N. Kew
• Geographic Information Systems by L. W. Nyman
• About Cellular Automata edited by H. Gutowitz
• All other FAQs

Extensive Lists of Links

• Virtual Library. Environment
• The Environment Directory
• Sites for ecologists by A.R. Brach and J. Thioulouse
• Environmental resources sites by J.T. Oris and J.W. Gooch
• Design Methods: Analysis: Simulation
• Discrete Event Simulation
• Statistics on the Web by C. Helberg