Open Source Linux Ecosystem Sciences Software

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.

Biosphere3D targets interactive landscape rendering based on a virtual globe. It supports DEM, satellite and aerial images, 3D models (Collada), 3D plant models, and Shapefiles. Biosphere3D was initially developed by the landscape visualization group of the Zuse Institute Berlin by Malte Clasen and is now developed further by Lenné3D GmbH. For more information about the used concepts have a look at the thesis of Malte Clasen: Towards Interactive Landscape Visualization Doctoral Thesis published 2011 via Technische Universität Berlin https://doi.org/10.14279/depositonce-3005

TRiDaS is a universal data exchange standard for the dendrochronology community. This project contains the data standard itself as well as libraries and tools useful for reading, writing and converting dendro data files.

SeaBreeze is a device driver library that provides an interface to select Ocean Optics spectrometers. It is written in C/C++ and builds and runs on Windows (XP/7/8), MacOSX, and Linux (x86/x64/ARM).

MCC-LIDAR is a C++ application for processing LiDAR data in forested environments. It classifies data points as ground or non-ground using the Multiscale Curvature Classification algorithm.

ConGENER package is a set of combinatorial-computational tools to study families of halogen substituted molecules, so called congeners.

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.

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

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

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.

HydroSed2D is a two-dimensional numerical model for hydrodynamics and sediment transport on unstructured mesh.

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

Run-time libraries to support the Kitchen Sink, an all-purpose chemical process control board, based on the Atmel AVR ATmega1280 chip, using the Arduino core libraries.

Please use the MOHID code official site http://mohid.codeplex.com/, Thank you, The MOHID team

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.

Obs-dm aims to provide a robust and reliable way to collect, analyze, and share observational data. It is being designed for extendability into other areas such as fisheries and habitat science.

OpenAMIS (Open AgroMeteorological Information System) is customable free and open software for websites providing agrometeorological information to farmers and agroindustry.

PIHM is a multiprocess, multi-scale hydrologic model where the major hydrological processes are fully coupled using the semi-discrete finite volume method.

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.

Physical modelling of water transport in plants

PyPak is a Python library for communication with Campbell Scientific dataloggers through the PakBus interface over TCP/IP or serial lines.

Rachis, A Cross-platform Hierarchical Identification System. Rachis is an application for the cataloguing and identification of entities (taxa). It is being implemented from scratch, but is based heavily on the lessons learned from Taxabase.

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

*.xml files are uploaded to SAGA GIS toolchains 'Files' from where they can be downloaded: https://sourceforge.net/projects/saga-gis-rhotoolchains/files/ SAGA-GIS-toolchain_Burned_area.xml ___is presented in GitHub: https://github.com/RhoSpatial/Saga-gis-toolchain-for-burned-area-mapping- VIIRS_snow_tool_FINAL7.xml ___is a toolchain for snow cover retrival from VIIRS instrument imagery (NASA), input is study area cloud free VNP09GA product and DEM in GQ(nom 250m) resolution, it was developed to make high accurate snow cover analytics on Atlas mountains(Morocco). It was tested in 2017/18 snow season(output grids are available: mih.zemva@gmail.com). It is fairly complicated but not as much as toolchain for MODIS(not uploaded) with MOD09.. products input . * in line 139 polygon *.shp must be linked from drive; it's an additional retrieval of index values to monitor waterbodies and does not relate to snow cover analytics

Sandia National Laboratories’ (SNL) environmental assessment modeling tool helps optimize the design of MHK-turbine array layouts within ocean, tidal, and river systems to balance energy generation efficiency with environmental considerations. The new tool, SNL-EFDC, is an augmented version of US EPA’s Environmental Fluid Dynamics Code (EFDC) and includes; (1) a new module that simulates energy conversion (momentum withdrawal) by MHK turbine-like devices including commensurate changes in the turbulent kinetic energy and turbulent kinetic energy dissipation rate, (2) new, advanced sediment dynamics routines, and (3) augmented water quality modules. SNL-EFDC has been verified and validated against flume measurements of flow around sub-scale turbines and actuator disks.