Open Source Ecosystem Sciences Software

We have moved, the project is now at http://distancesampling.org

The Dynamic Multispecies Metabolic Modeling (DyMMM [dĭm]) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework was formerly known as the DMMM framework. Please use the following citation for bibliographical purposes: Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2011). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. The ISME journal. Zhuang, K., Ma, E., Lovley, D. R., & Mahadevan, R. (2012). The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnology and Bioengineering.

soporte grafico/analitico para evaluaciones de impacto ambiental en actividades de la construccion

PredatorPreySimulation is a graphical Java application for simulating a predator prey ecosystem using the Volterra-Lotka equations.

A collection of modules and enduser tools designed to help design, test and use system models. While my research (hence, the examples) is focused on hydro-ecological systems, the program can be used on any system characterized by ODEs (and soon PDEs?)

Software made available by the Residual Analysis blog, primarily having to do with anthropogenic global warming, e.g. GHCN Processor.

That project aims at providing a clean API, and the corresponding C++ implementation, able to generate demand for travel solutions (e.g., from JFK to PEK on 25-05-2009) according to characteristics (e.g., Willingness-To-Pay, preferred airline, etc).

bioCity is a continuous space, discrete time simulation written in C++. It is meant to be of use to population biologists. Rules of behaviour are given to individuals that move, live, die, and procreate.

hSDM is an R package for hierarchical species distribution models. Such models allows interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.

We produced a software for scientists and managers working with marinas, and small harbor. Our software is able to predict the distribution of portuality and vulnerability risk.

Project moved to Google Code since SourceForce is a broken, buggy, non-responsive service. I had to re-log in over 100 times just to change this description. Please visit the project at http://code.google.com/p/starflighttlc/ for the latest version of th

phcfM is an R package for modelling anthropogenic deforestation. It was named after the REDD+ pilot-project 'programme holistique de conservation des forêts à Madagascar'. phcfM includes two main functions: (i) demography(), to model the population growth with time in a hierarchical Bayesian framework using population census data and Gaussian linear mixed models and (ii) deforestation(), to model the deforestation process in a hierarchical Bayesian framework using land-cover change data and Binomial logistic regression models with variable time-intervals between land-cover observations. The two functions use embedded Gibbs samplers written in C++ with the Scythe statistical library to reduce computational time.