Search Results for "evolution linux" - Page 7
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Showing 504 open source projects for "evolution linux"
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PTM-X
a solfware for predicting posttranslational modification cross-talk
The PTM-X (PTM cross-talk) project is a freely available bioinformatics software platform that allows to calculate the features of PTM pairs and the posterior probabilities of being cross-talk pairs. The prediction model is a naive Bayse classifier that integrats five features: protein sequence distance, tertiary structural distance, co-location in a disordered region, residue co-evolution, and modification co-evolution. An online tool is also available at http://bioinfo.bjmu.edu.cn/ptm-x/. -
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The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In...
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Git Time Machine
Atom package that allows you to travel back in commit history
git-time-machine is a user interface (often as an editor plugin or UI extension) that allows users to browse a file’s history visually, stepping back and forth through revisions in Git like a “time machine.” It shows changes to a file over time, lets users compare older states, and often provides diff and blame views to understand how the file evolved. Instead of just opening a commit log or diff, git-time-machine gives an interactive, incremental experience where you can slide through... -
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
This repository contains the most updated code version of MANTIS, the Multi-locus ANTIgenic Simulator R-package. MANTIS is developed and maintained by the Evolutionary Ecology of Infectious Disease (EEID) research group at the Department of Zoology, University of Oxford, UK. For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN... -
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D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of... -
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Archkur is the revised version of the EvoLution Linux project. Various errors have been fixed. Removal of multiple language support is only available in English and Turkish. https://github.com/EvoLutionLinux/archiso Archkur allows you to install various desktop environments with pure Arch Linux current packages. For example Minimal gnome, Gnome, Minimal Kde, Kde , Cinnamon, Lxde, Mate, Openbox + Evo (EvoBox) Enlightenment.
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popt4jlib
Parallel Optimization Library for Java
popt4jlib is an open-source parallel optimization library for the Java programming language supporting both shared memory and distributed message passing models. Implements a number of meta-heuristic algorithms for Non-Linear Programming, including Genetic Algorithms, Differential Evolution, Evolutionary Algorithms, Simulated Annealing, Particle Swarm Optimization, Firefly Algorithm, Monte-Carlo Search, Local Search algorithms, Gradient-Descent-based algorithms, as well as some well-known... -
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Graphcool Framework
Graphcool is an open-source backend development framework
Graphcool was an open-source framework for developing and deploying GraphQL-based backends. It acts as a “backend-as-a-service / framework” that lets you define your data model via GraphQL SDL (Schema Definition Language), and in turn generates a GraphQL CRUD API, supports nested mutations, filtering, pagination, and real-time subscriptions. Graphcool separates the business logic from stateful storage components, allowing the stateful parts (database, subscription engine) to scale... -
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blog_os
Writing an OS in Rust
“blog_os” contains the source code for Philipp Oppermann’s renowned "Writing an OS in Rust" blog series. Each tutorial is paired with a Git branch demonstrating the OS's incremental evolution, covering components like kernel setup, interrupts, paging, heap allocation, and async multitasking. The current version of the blog is already the second edition. The first edition is outdated and no longer maintained, but might still be useful. You can find the branch for each post by following the... -
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The goal of the Elle Project is to provide a general purpose modelling environment for the simulation of rock microstructure evolution. The code is based around a unified description of 2D microstructure.
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SW-DLP: Developing ontoLogy by Profiling
a tool for easing the ontologies editing and evolution (Semantic Web)
The DLP tool was ideated and developed by: Dr. Luca Mazzola, MsC. Patrick Kapahnke, and PD Dr. Matthias Klusch at the German Research Center for Artificial Intelligence DFKI GmbH (http://www.dfki.de ) in Saarbrücken, Germany. Copyright: DFKI, 2017, licence GLP see https://www.gnu.org/licenses/gpl-3.0.en.html For bug reports, technical problems and feature requests please contact: Luca Mazzola: luca.mazzola@dfki.de or mazzola.luca@gmail.com Patrick Kapahnke: patrick.kapahnke@dfki.de -
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MimicrEE (Mimicing Experimental Evolution) is a tool for forward simulations of entire genomes. It basically allowes to simulate adaptation from standing genetic variation, thus no 'de novo' mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs. Documentation: https://sourceforge.net/p/mimicree/wiki/Main/
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EQGRP
Decrypted content of eqgrp-auction-file.tar.xz
EQGRP is a public release of the so-called Equation Group hacking tools, originally leaked online in 2017. The repository serves as an archive and reference for security researchers, documenting the exploit frameworks, implants, and utilities that were allegedly used by a highly sophisticated threat actor. The tools include network exploitation scripts, backdoors, and frameworks targeting a range of platforms and services, many of which highlight previously unknown vulnerabilities. While the... -
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Mirrors
arbitrary physical system simulator using artificial evolution
"Mirrors" is a simulation of an arbitrary physical system, where the goal is achieved using artificial evolution. The simulation can be used to demonstrate how random mutations manage to create an overall progress towards perfection. Running this requires java 8 installed and on path. https://github.com/JoonasVali/mirrors -
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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
The "GeneticCode" C++ class is designed to generate versions of the genetic code subject to the requirements of the three major models of the genetic code origin and evolution (about these models see, e.g., Koonin & Novozhilov, 2009, IUBMB Life). This class was written specifically to perform statistical test for the paper Makukov & shCherbak (2017), but it might be used for a wider class of studies related to the genetic code. By default, the class "GeneticCode" generates... -
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Coastline Evolution Model
Modified version of the Coastline Evolution Model (CEM)
The Coastline Evolution Model (CEM), originally developed by Ashton et al. (2001), Ashton and Murray (2006) and Valvo et al. (2006), is a reduced complexity, one-line sediment transport model that simulates the evolution of coastlines via wave-driven alongshore sediment transport. The original CEM has no Graphical User Interface (GUI) and does not provide graphical visualisations during model runs. The modified version given here includes these features. This project forms part of a... -
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Evolutionary relationship of species provides a great deal of information about their biochemical machinery. So many researchers focus on the research of constructing the phylogenetic tree. A phylogenetic tree is a representation of evolution, tree normally describe the evolution of the species where the sequence are found.A method called the neighbor-joining method is proposed for constructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs...
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Lep-MAP2
Linkage map construction suite
Note: Lep-MAP3 is now available https://sourceforge.net/projects/lep-map3/. Expect 20x-1000x speedup over LM2 and more accurate maps. Lep-MAP2 is a novel linkage map construction software suite. Please refer to the wiki for its documentation. For further information, please contact Pasi Rastas, pasi.rastas@gmail.com. If you use Lep-MAP2, please cite Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example P. Rastas, F.C.F.... -
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PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution. Documentation: https://sourceforge.net/p/popoolation2/wiki/Main/
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component-watch
Describe and watch component structure of java programs
"Component-Watch" is a tool discovering, showing and assessing the structure of (big) java programs from their classes. It finds what are the components composing a program, analyse what are the relations between those components and compare those the the permitted relations between components. The tool helps to easily define and display UML-like diagrams showing components and their relationship. -
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus... -
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WOW-Auctions-API
Python classes to work with Blizzards API
Auction House API that consumes the official Blizzard's open API Help users to track and monitor AH prices from any World of Warcaft official Server Sends emails when the price of an object is below a treshold predefined by the user. Plot graphs of price evolution -
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TrajectorEE
Trajectories of Loci during Experimental Evolution
Visualizes trajectories of loci during experimental evolution using forward simulations -
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IQM-Plugin-FFI
FFI - fractal fragmentation index
This is an IQM plugin to compute the FFI index for binary digital images. This index represents a value for the compactness of an object. FFI is the difference between fractal dimensions of the area and its boundary. Fractal dimensions are computed with the popular Box counting method or the Pyramid method. Details can be found in: Andronache etal. Fractal analysis for studying the evolution of forests, Chaos, Solitons & Fractals, 2016, Vol 91, 310-318. Installation...
