Open Source Java Ecosystem Sciences Software

An easy to use application to design your kitchen garden or your house farm. Helps you plan your plants ( vegetables, fruit trees, herbs, flowers ) so that it respects the rules of crop rotation and companion planting. Based on square foot gardening. Requires Java 8.

Software for sustainability assessment, highly modular; initially focused on Life Cycle Assessments.

The PAMGUARD project develops software to help detect, locate and classify marine mammals using Passive Acoustic Monitoring. This project is being migrated to github at https://github.com/PAMGuard. Please go there for the latest updates. thank you sourceforge for hosting us for all these years.

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.

A cross-platform Java program to turn a simple Geiger counter into the equivalent of a state-of-the art digital model, plus some – using your laptop computer.

VLE is a multi-modeling and simulation environment to study complex dynamic systems. VLE is based on the discrete event specification DEVS. and it implements the DSDE formalism (A merge of Dynamic Structure DEVS, DSDEVS, with Parallel DEVS, PDEVS). VLE provides a complete set of C++ libraries, called VFL (VLE Foundation Libraries), to develop DEVS models, to gets results of simulations, to launch simulation on cluster. The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. VLE have also three ports to use the VFL with Python, Java and R programming languages.

Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.

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 BioEnergy Allocation and Simulation Tool (BEAST) is a tool dedicated to assess political goals of woody bioenergy production in the context of available biomass potentials and corresponding economic and ecological criteria on a regional level. It is a useful tool in participative decision making processes by iterative simulation and visualization of complex issues. BEAST is a data- and model-driven Decision Support System (DSS) evaluating woody biomass potentials from forests, hedges and trees outside forests as well as short rotation coppice (SRC). The latter one is modelled spatially explicit. This opens the possibility to identify prefered areas for SRC production under different restrictions and goals. Forest wood and wood from outside forests are treated only aggregated.

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.

You can download the Color Mod at the Biogenesis main site too (included in the main download now). You also find the sourcecode there. If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. Original project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ Includes Tyler Colemans "Features Mod": https://sourceforge.net/projects/biogenesisfeatu/ Biogenesis discussion forum: https://sourceforge.net/p/biogenesis/discussion/ Biogenesis runs faster (at least for myself) if you open a Google Chrome window (don´t know why :D)

Customizable Observation Video imagE Record. COVER software has been designed and developed by Ifremer / LEP in complement of existing software for underwater vehicle videos/photos analysis.

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

An online database and cross-platform, game-like client where gardeners/farmers (small or large scale) can log their actions and measurements (such as weather, yield, current plant size). Any user can then play it back visually, or play with the data and see a simulation inferred from the knowledge database, or calculate an optimal design within given constraints, inferred from the knowledge available at that time. This is both a tool for playing, in order to entertain and inspire people, as well as a serious feedback and design tool. There will be a user feedback system to value the accuracy of the data. It is allowed to enter and share mock farming data, as long as it's tagged as being fantasy, to exclude it from the analyses. Things like dietary information, tiredness and bio-constructions will be included as well, to improve optimizations of a garden design with (partial) self-sufficiency in mind. The UI will resemble a garden, and can switch to simplified views.

DIET Agents is a lightweight, scalable and robust multi-agent platform in Java. It is especially suitable for rapidly developing P2P prototype applications and/or adaptive, distributed applications that use bottom-up, nature-inspired techniques.

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.

The EDAM ENCHILADA - The Exploratory Data Analysis and Management Project's Environmental Chemistry Data Processing and Mining Application.

FishLAB is an easy-to-use program for tracking aquarium water chemistry. With FishLab you can monitor pH, hardness, NH4, NO2, NO3, Fe, CO2 (the software converts units where needed). The graph function warns you of bad trends in water quality.

GridSweeper makes it easy to perform batch runs of scientific simulation programs on computational grids/distributed resource management systems.

JaWator is a Wa-Tor JavaApplet; a predator-prey simulation resembling a natural ecosystem, this Cellular Automaton delivers fluctuations similar to the Lotka-Volterra equation. Inspired by A.K. Dewdney, Wa-Tor ecosystem (Scientific American, 1984)

KalypsoBASE is a Desktop-GIS built on Eclipse. It's focus lies on modelling gis data using GML Application-Schemata. Features contain generic dialogs based on GML, maps based on OGC's SLD, and other tools like a charting framework or API for timeseries

MBAS -- Macro-Biological Analysis System -- provides a set of interoperable tools for aid in the analysis of biological data. The backing database is currently PostgreSQL and the primary language is C, though some data entry tools are written in Java.

The main objective of the ONE project is to enrich Digital Ecosystems with an decentralised negotiation environment and enabling tools that will allow organisations to create contract agreements for supplying integrated services as a virtual organisation

This will be next version of PHIbase.

Moved to: http://parkermills.github.io/phagetherapy/