Projects tagged ‘ecology’ and ‘evolution’

Important: I am moving to Sourceforge. Check out the new website. I'll keep this old page up for a while, however. This is a simulation program written in C++ and meant for studying populations that ... [More] follow rules. It can be though of as a continuous analog to Conway's game of life, in a rough sense. Organisms are objects in the computer's memory and they can move around and interact, grow and die. There are many possibilities for studying ecology and evolution, as well as artificial intelligence. The user interface is extremely minimal and knowledge of C++ is required for meaningful work that differs from the programming that it so far contains. Please be aware that it is in prelease mode, and while the source code is available, there is no instruction at the moment on how to use it. I shall rectify this situation in due time. In the mean time if you need more information, please email me. Thus, it is not meant to be used by anyone at the current time. If you'd like to try you're more than welcome, of course. For now, check out the YouTube Video of it in action. Sorry for the low quality! NewsSunday, April 20, 2008: Added the option to turn graphics on or off in the configuration file: "graphics: 0" is off, "graphics: 1" is on. Also I want to move this page to Sourceforge so I can have more control over the website. I submitted my request today. Want To Help?Are you interested in modelling biology with computer simulation? I am inviting all such individuals to email me at: automorphism (at) gmail (dot) com If interested in being a volunteer developer for this project. The project is coded in C++ and is kept in a git repository. Git is not hard to learn if you're willing, though. You don't even have to know how to program, as I am also looking for beta testers, especially for other operating systems. Some of the immediate goals of this project are: Easy configuration of different environments Plugin type interface for defining new environment rules Good documentation Lots of testing on other systems Thanks to the kind people (particularly Petr Baudis) at repo.or.cz, anyone can now fetch a copy of the git master branch of this project (updated frequently) by using this command: git clone git://repo.or.cz/biocity.git Or through the slower http protocol: http://repo.or.cz/r/biocity.git See summary page. [Less]

DIM SUM: Demography and Individual Migration Simulated Using a Markov chainDIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation ... [More] of population demography and individual migration, while keeping track of genetic relationships. It does not rely on assumptions of the coalescent or of discrete population boundaries. It is extremely flexible, allowing the user to set the positions of borders, the reaction of an organism to a border, local and global carrying capacities, individual dispersal kernels, rates of reproduction, and strategies for sampling individuals. Spatial variables may be specified using image files (e.g., as exported from GIS software) and may vary through time. DIM SUM will be useful for testing of phylogeographic methods (e.g., nested clade phylogeographic analysis, coalescent-based tests, and continuous-landscape frameworks), landscape-genetic methods, and specific violations of coalescent assumptions, as well as visualizing hypotheses of biological invasions, and as a pedagogical tool. If you use DIM SUM, please cite: Brown, J.M., K. Savidge, and E. McTavish. 2009. DIM SUM: Demography and Individual Migration Simulated Using a Markov chain. Molecular Ecology Resources. Submitted. [Less]

Plantae is a web-based database of ecological and evolutionary data for plants. The success and utility of web projects, such as Entrez and Treebase demonstrate the power of collaboration on the ... [More] submission of and access to data. Our goal for Plantae is that it relieves evolutionary ecologists from the burden of collecting and maintaining private databases of relevant plant traits. Rather, as data is discovered it is submitted to the Plantae project and made available to all researchers. We all gain access to a growing collection of data that is easily searched, annotated, and updated. Plantae’s creation was guided by three principles to ensure the scientific utility of the project:    1. Open access: We do not restrict access to the website for people who want to search or view the plants and their associated traits. Anyone with access to a web browser can benefit from the data within Plantae.    2. Collaboration: Plantae’s usefulness increases with researchers’ contributions. Consequently, we encourage people to add data to Plantae. Although we do ask that they register before doing so to track collaborations and provide some control over the database. We also welcome suggestions for the addition of new traits to Plantae. We began with traits that were relevant to our particular research goals, but hope to cover all relevant plant traits with help from the community. Finally, we provide links to other web-based projects (e.g., iSpecies) whenever appropriate to link Plantae’s data with other efforts.    3. Scholarship: To ensure that Plantae contains accurate data, we require that each submission be accompanied by a peer-reviewed citation. These citations are managed by Nature Magazine’s Connotea project which further encourages collaboration among the users of Plantae. This decision ensures that any data contained within Plantae is as accurate as the primary literature and the linked citations can be queried for additional information on the study’s design and implementation. Plantae is written in the Ruby programming language and relies on the Ruby on Rails web framework and sqlite3 database. Consequently, Plantae is constructed with open-source software. Furthermore, the source code for Plantae itself is also governed by an open-source license and available from [Less]