Open Source Python Ecosystem Sciences Software

The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

Black Spot is a free stand alone software and method to estimate leaf area from images of leaves captured using standard flatbed scanners. This easy to use software allows the user to batch process a large number of samples from multiple species with minimal user input.

iTag has been designed for researchers that rely on photographic census techniques of animals that are hard to detect via image recognition algorithms and was originally developed for counting Grey Seals in the German wadden sea during March 2013. It has since then been further expanded and has now reached beta status. iTag allows Users to define up to 9 different categories and name them accordingly. In addition, 4 modifiers are available to further increase the options during a tagging session. Users are able to load a series of Images into a session and add tags on objects on these images within previously defined categories and modifiers. Upon ending the session, result files are produced including (if provided by the EXIF data) the gps information for each Picture, the number of objects in each category and a detailed result file that describes each individual object. In addition, all images that were tagged are saved.

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

BETR-Research (BETRS) is a modelling framework to create spatially resolved multimedia models for the environmental fate- and transport of chemical contaminants. It is intended to serve the research community and can be used as a teaching tool.

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.

CDPOPgui is a GUI Frontend for CDPOP What is CDPOP? CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics. The program implements individual-based population modeling with Mendelian inheritance on a resistant landscape. Simulation begins with an initial homogeneous population and followed by divergence through time as functions of individual based movement, breeding and dispersal on a continuous cost surface. Acknowledgements Allen Warren developed the GUI.The citation for this program is: Landguth EL, Cushman SA (2010) CDPOP: A spatially-explicit cost distance population genetics program. Mol. Ecol. Res. 10, 156-161. Updates to the software, including natural selection, can be referenced with Landguth EL, Cushman SA, Johnson NA (2012) Simulating natural selection in landscape genetics. Molecular Ecology Resources, 12, 363-368.

ECMWF parser is a software made in python (it has a version standalone and another python dependant) to work on the data provided by ECMWF. It uses WGRIB to convert binary data to ascii and operates over the last with several functions available.

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

This project has been moved to https://bitbucket.org/pbazant/evoversum/src/master/ . Evoversum is a fast Darwinian evolution simulator. The program simulates a 2D world populated with "animals" which struggle for food, reproduce and may also eat each other. The subject of evolution is their behavior, which may become quite complex. There is an updated video tutorial at http://www.youtube.com/watch?v=nPkZvyVDWJU !

The Hydroponic Automation Platform Initiative (HAPI) develops and provides hardware and software components for automating food production using hydroponic, aquaponics, and precision agriculture techniques. High-yield production in urban settings is one of the primary goals. Artifacts include hardware design (mainly Arduino-based), firmware, management software and reporting modules.

Nelder plot (Nelder 1962) is an experimental design for testing a multiple tree spacings in a single plot. The shape of plot is circular with some number of concentric wheels or arcs radiating outward and the spokes connecting the center. The intersections of spokes and arcs are the tree positions. The tree position on different wheels represent a different the tree spacing distance or tree density. This design eliminates the need for separate experimental plots for each tree density. The difficulties with Nelder plot design is their uncommon layout and complex parameterization (Parrott et al. 2012). This computer-aided tool for designing the Nelder plot can be very useful for the practical implementation of this experimental design.\r\n\r\nReferences\r\nNelder JA (1962) New kinds of systematic designs for spacing experiments. Biometrics 283–307\r\nParrott DL, Brinks JS, Lhotka JM (2012) Designing Nelder wheel plots for tree density experiments. New Forests 43:245–254.

Piko solar inverter interface. Get online real time data and status. Get also history data. Database management of data. Exports, graphs, ... Manage data and stats using a SQLite or MySQL database. Third party intergration. See the Wiki home page for more informations.

Physical modelling of water transport in plants

Plantlore is a botanical occurence database being written in Java. It also has a BIOCASE Provider software based web interface.

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

This project includes several Python and bash scripts designed to connect Geiger Muller counters to report their results to RadMon.org. Soon the script will also feature local logging, graphing and alerting. Just because the Cold War is "over" does not mean that there is no more threat of a radiological attack. In fact, the U.S. Homeland Security Council lists the "Detonation of a 10 Megaton Improvised Nuclear Device" as "Scenario #1" among the top 15 threats to American security. Or, if you do not believe that a nuclear bomb is likely, what about all the Chernobyl-style Soviet-era nuclear power stations still in service? The point is: let us work together as free people to jointly report and track radiation levels around the globe. Information is power--and more importantly, information can save lives. This project is known to work on Raspberry Pi and various Linux distributions. Both PyRadMon and RadMon.org are completely free, though donations are always appreciated.

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?)

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.

This is an simple ecological model for lakes and reservoirs that contains a very detailed description of the most relevant nitrogen processes. The model is not very complete, but the main intention is to develop a library to be coupled with other models and use the full-mixed model as a testing version. A lot of things can be improved. I will read all the suggestions but I cannot promise that I will include all of them. Every new part of the code will contain the name of the author. If someone contributes improving the capabilities of this model in a substantial way, I will include that person as co-author of the model in the next version release. I hope this will promote people to contribute. Of course, fixing bugs or minor changes will also be mentioned with the corresponding author. Thanks a lot. I hope this can be the seed of a Open Source Community of Ecological Modellers.

GeoSciPy is a set of C and Python functions that provide an API for all aspects of Geoscience and Remote Sensing Applications. Functions include reading/writing of many data formats, images, vectors, ..., and processing of images, vectors, ... including map projections, ... The library is written C, using HDF5 as the file format for storage of all remotely-sensed data and ancillary data, as well as processed data. The C functions assume a particular format for the HDF5 file contents, and provide functions for reading and writing data to such files. There is also a Python API that provides a procedural as well as an object-oriented interface to these functions. A Python GUI for interacting with such datasets is also part of the project. While there are other open-source GIS, and image-processing packages available, this one is designed to be comprehensive, work on 3 major platforms, user-extensible, fast, and able to handle huge datasets. Click the Blog tab for more info.

A toolbox of open source geospatial essentials

This is a collection of Python functions, with which data can be exported from the Python environment to a file which can be viewed in GoogleEarth.

A collection of python classes for computational ecology and evolutionary biology.