Open Source Java Ecosystem Sciences Software for Linux

Niche Analyst (NicheA) was developed based on the BAM framework which allows users to create virtual spaces and virtual species, and to analyze ecological niches in both multivariate environmental and geographic spaces, linking views of the niche in the two spaces. The unique functionality in NicheA, not available in other software programs, is estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological niches. NicheA can display ecological niches; calculate their shape, density, location, and other attributes; and quantify similarity among multiple niches.

MetaMaster is a Java-based desktop application for defining, managing and manipulating metadata associated with a collection of data files or datasets (both locally and on the network) which are bundled together into "data packages". ANDS-funded

BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

CRAFTY is a large-scale ABM of land use change. It has been designed to allow efficient but powerful simulation of a wide range of land uses and the goods and services they produce. It is fully open-source and can be used without the need for any programming.

This software enable cannabis grower to manage and retrieve statistics about culture, tools included have the goal to help growing indoor cannabis.

DLESE (Digital Library for Earth System Education) is a community-supported digital library dedicated to the collection, enhancement, and distribution of materials that facilitate learning about the Earth. Sponsored by the US National Science Foundation.

KNeTS (Knowledge Elicitation Tools) is a survey tool to create multi-agent models based on local knowledge using pattern analysis to identify rules that are iteratively validated with the informant. The final output is a knowledge-based multi-agent model

The class libraries here provide infrastructure for creating simulations of low energy nuclear physics experiments, as well as some useful working programs that do simple simulations and analysis of experiments performed with magnetic spectrographs.

The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.

PhaenUhr is an easy to use graphical Java application to visualize the impact of climate change on seasonal biological phenomena as two nested phenological clocks. You can configure the clocks in many ways and export them to standard graphic formats.

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

Framework for storing and editing Forestry-related XML data, with a specialised graphical interface for each object type. Plug-in API for adding functionality. Coded in Java, uses WebStart for distribution, swing GUI, ~100k lines of code.

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.

mesoFON is an individual-based mangrove forest model. It is a Java implementation of the KiWi model done with RePast Simphony. It contains several new features: (1) You can add up to 10 species via the GUI. However, in principle, the number of species to be included programmatically is unlimited. (2) You can use a variety of growth functions via typing them in as a string on the GUI. (3) The model is transparent, sinc it comes with the Eclipse workbench of RePast.

powerPlant is a plant modelling tool based on parametric plant descriptions, producing highly detailed models that can be exported to 3ds. Deriving similar plants is a matter of 1 click! Complete scenes can be composited with the integrated scene editor.