Open Source Mac Ecosystem Sciences Software - Page 2

Implementation of HYCOM physical ocean model with coupled biogeochemical component to study nitrogen fixation in the Amazon plume. This project is still in development, the code may not be functional at this time.

A simple python script for aquarists that figures tank volume, salinity, converts temp & volume, and calculates substrates based on their specific gravity.

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.

Program performs bird species recognition by their voices. In early stage of development but working well with some popular species and good samples quality.

birdweights is a a package of scripts to analyze data from an automated system for the measurement of mass and identification of birds at perches.

Project moved to GitHub: github.com/rejjir/CSESD-archiving

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

This project implements calculations for the Climate Equity Reference Project's Calculator (CERc).

The COMBO model projects climate change impacts to coral reefs based on estimated future changes in sea-surface temperature and ocean acidification. Outputs include estimated timing of bleaching events, changes in coral reef cover, and associated changes in economic values.

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.

DeepSee is an interactive workspace for deep ocean scientists to upload sediment core data and map images and see their sampling history displayed across multiple connected views at once! 🦑🦀🐚 🚀 For a live demo, visit: https://www.its.caltech.edu/~datavis/deepsee/ 🌱 To get started, visit our Wiki: https://sourceforge.net/p/deepsee/wiki/Home/ 🧑‍💻 To modify DeepSee for your own project, visit our GitHub repository: https://github.com/orphanlab/DeepSee/ --- Created by Adam Coscia, Haley M. Sapers, Noah Deutsch, Malika Khurana, John S. Magyar, Sergio A. Parra, Daniel R. Utter, Rebecca L. Wipfler, David W. Caress, Eric J. Martin, Jennifer B. Paduan, Maggie Hendrie, Santiago Lombeyda, Hillary Mushkin, Alex Endert, Scott Davidoff, and Victoria J. Orphan. Copyright (c) 2022-23 California Institute of Technology ("Caltech"). U.S. Government sponsorship acknowledged. All rights reserved. Open Source License Approved by Caltech/JPL APACHE LICENSE, VERSION 2.0 ---

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.

Electronics schematics, PCB images, firmware and documentation to create and deploy a network of ecology related sensors.

The Evolutionary Environment (EvENet) provides a P2P Network for guiding the evolution of Software Services and Service Compositions over time. This evolution is based on knowledge sharing and optimised using GA and Agent Systems. It is part of the DBE.

The Evolutionary Environment Simulator (EvESimulator) is an agent-based economy simulation framework which provides a broader view on evolutionary aspects within a Digital Business Ecosystem.

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

A library of R packages for use in fisheries modelling, including the evaluation of management strategies and stock assessment.

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.

Fuzzy Ecospace Modelling (FEM) is an R-based program for quantifying and comparing functional disparity, using a fuzzy set theory-based machine learning approach. FEM clusters n-dimensional matrices of functional traits (ecospace matrices – here called the Training Matrix) into functional groups and converts them into fuzzy functional groups using fuzzy discriminant analysis (Lin and Chen 2004 – see main text for more information). Following this, FEM classifies the functional entities from a second matrix (the Test Matrix) into the groups made using the Training Matrix, generating fuzzy membership values for each unit in the Test Matrix. These values are real numbers from 0 to 1, representing increasing degrees of “truth” regarding an organism’s membership in the fuzzy set (see main text). A value of 0 represents non-membership in the fuzzy set, and a value of 1 represents total membership in the fuzzy set. Values in between represent degrees of niche overlap.

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.

Identification of clines from allele frequency or genome-wide databases. Angular transformation. Sigmoid function. Parameterization of a cline: orientation, Pearson’s product-moment correlation coefficient, linear and sigmoid regression and coefficient of determination. Graphical representation of the cline. Confidence limits. Spatial autocorrelation. Moran's index. Isolation by distance. Exponential regression. Correlation Fst/Distance. Centroid method. Cline's expected vs. predicted heterozygosity. MDS. Sammon projection. Geographical distances. Fst distances. Export data to Arlequin, Phylip, Past and Poptree. User-friendly input data.

GIS data for Greece has been scarce. This project aims to provide methods, instructions and data for the construction of environmental maps of Greece with the help of open source GIS tools.

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