Projects tagged ‘genetics’

The GenoViz project provides tools for genomics data visualization. It consists of the following: 1) the GenoViz SDK, a library of re-usable components, 2) the Genometry data model to represent ... [More] relationships between biological sequences, and 3) the Integrated Genome Browser (IGB, "igbee"), an application built upon the GenoViz SDK and Genometry for visualization and exploration of genomes and corresponding annotations from multiple data sources. IGB supports the Distributed Annotation System (DAS) protocol, version 1 and 2, as well as other optimized binary data formats that are designed for efficient exploration of large, whole genome data sets. [Less]

Generic library for genetic programming in Haskell

The dANN project is a library to help facilitate artificial neural networks within other applications. It is currently written in Java, C++, and C#. However only the java version is currently in ... [More] active development. If you want to obtain a version other than the java version you will need to get it directly from SVN. Our intentions are two fold. First, to provide a powerful interface for programs to include conventional artificial neural network technology into their code. Second, To act as a testing ground for research and development of new AI concepts. We provide new AI technology we have developed, and the latest algorithms already on the market. In the spirit of modular programming the library also provides access to the primitive components giving you greater control. [Less]

Traveling Salesman Problem - Java Genetic Algorithm Solution Binary/Source/SVN/Documentation available. Application features Implementation and comparison of different genetic algorithms - ... [More] unisex random mutation - crossover algorithm - 2opt heuristics + unisex random mutation - 2opt heuristics + crossover algorithm Open source multi platform Java application with well commented source code Console and GUI application mode Parametrized configuration Multi threading computation engine Application thread priority settings Simple map file formats, exporting existing maps, using external maps - map of 192 real cities from CZ, coordinates in S-JTSK, distances in meters - fractal maps (circle, triangle, square, spiral, ... ) Descriptive XML and PDF reports, converting XML reports to PDF Web support General genetic algorithm problems Code the problem Define fitness function Select genetic algorithm engine (population and mutation handling, multithreading) Use good mutation algorithm to create offspring Implement random mutations Think about using heuristics Apply the right initial parameters (population size, mutation ratio, population growth) Initialize population Run the computation on proper hardware Links Definition and research of Traveling Salesman Problem http://www.tsp.gatech.edu/ Basic description of genetic algorithms http://en.wikipedia.org/wiki/Genetic_algorithm Suggested and probably best way for solving TSP using genetic algorithm and 2opt heuristic optimization described by Hiroaki Sengoku and Ikuo Yoshihara http://www.gcd.org/sengoku/docs/arob98.pdf [Less]

Yet Another Genetics Simulator Student(s) will design and implement a robust web application using Ruby on Rails to simulate basic genetics of inheritance. The resulting program will allow users to ... [More] conduct breeding experiments with virtual organisms (e.g., virtual fruit flies) that allow them to see patterns of inheritance and to determine the modes of inheritance that are in operation. In addition, the software will produce assessment/feedback reports that can be used by Biology faculty whom will serve as “clients” in this software engineering project. [Less]

This computes protein yield and reading frame displacement given a sequence of codons in addition to writing an infinite amount of tools to analyze or help generate those metrics. Throw in Perl for extra sexiness.

Project Hosting for CEPH and CNG OPERON Dev Mailing list : http://groups.google.com/group/operon-dev Wiki PagesArchitecture BerkeleyDBNotebook DatabasesUTermsDB XTermsDB

IntroductionEvaporative cooling (EC) feature selection is a command-line data mining software implementation in Java and Fortran for filtering genetic association data. EC integrates Random Forests ... [More] and Relief-F attribute importance measures in order to balance independent and interaction effects while removing attributes that are irrelevant to the phenotype. EC has been tested on single-nucleotide polymorphism (SNP) data. For those with access to a cluster, the parallel version of EC will be released soon. New Windows GUI version Quick Start for *nix command line FAQs RequirementsJava, Fortran 90 compiler (f95, ifort, or the like). EC has been tested on Linux systems. The code should work on Windows or Mac given a fortran compiler. ReferencesB.A. McKinney, D. M. Reif, B. C. White, J. E. Crowe Jr., J. H. Moore. "Evaporative cooling feature selection for genotypic data involving interactions." Bioinformatics 2007, 23: 2113-2120. pdf B.A. McKinney, J.E. Crowe, Jr., J. Guo, and D. Tian, "Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis," 2009, PLoS Genetics 2009, 5(3): e1000432. doi:10.1371/journal.pgen.1000432. open source AcknowledgmentsWe would like to acknowledge the developers of PARF (parallel Random Forests, written in Fortran 90) and WEKA (data mining software written in Java). Send inquiries to brett.mckinney@gmail.com. McKinneyLab [Less]

The Madeline 2.0 Pedigree Drawing Engine is a pedigree drawing program designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. Although the program takes ... [More] inspiration from Madeline v. 0.935, the Madeline 2.0 Pedigree Drawing Engine, or just Madeline 2.0 for short, is in fact a completely new program written from scratch. [Less]

My (mostly) java sources at the Center for studies of the Human Polymorphism (CEPH). Fondation. Jean Dausset