Search Results for "dna simulation"

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning. Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways, are often difficult to properly document as is evident from the poor state of documentation in the scientific literature. The pydna python package provide a human-readable formal description of cloning and genetic assembly strategies in Python which allow for simulation and verification. ...

The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.

You can watch the result of point mutation, insertion and deletion on a short strand of DNA, the complementary strand of RNA and the Amino Acids

In population genetics, the "site frequency spectrum" is an important summary statistic of the variation in aligned DNA sequences. This package contains implemented algorithms for the analytical calculation of the expected second and third moments of this spectrum (under the standard neutral Wright-Fisher model). Furthermore there are utilities to estimate these quantities from coalescent simulation (using output of the program 'ms', written by R.R.

This is a C++ code to simulate life processes and responses to external stimulii in multicellular organisms by replicating the data flow in an actual organism using a straightforward approach. It can simulate both stimulus response and life processes(like respiration,excretion etc.) at the same time using multi-threading techniques. Digital DNA simulation- translation and transcription of DNA template to RNA is now supported. Users can also simulate cells and tissues using inbuilt classes.

...There is growing evidence that transcriptional regulation is the complex behavior that emerges not solely from the individual components, but rather from their collective behavior, including competition and cooperation. Our framework describes individual regulatory components using generic action oriented descriptions of their biochemical interactions with a DNA sequence. All the possible actions are based on the current state of factors bound to the DNA. We developed a rule builder to automatically generate the complete set of biochemical interaction rules for any given DNA sequence. Off-the-shelf stochastic simulation engines can model the behavior of a system of rules and the resulting changes in the configuration of bound factors can be visualized.

The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations for isotropic and anisotropic plane-plane and cylinder-cylinder interactions with intervening interlayer materials, planar systems of up to 99 layers, and graded interfaces for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. The machine-readable optical property database is available...

Python program for the kinetic tile simulation of the growth of 2D tiled DNA structures. Requires UNAFold, Python 2.7, NumpPy, SciPy.

An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.

Redcode evolver. Uses a "soup" of warrior DNA to make super warriors. READ FORUMS for more information.

RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.

Simulation of a population of "Digibots" (imaginary creatures) in a 3-dimensional world. They have a DNA composed of 3 genes, controlling their moving mode, obesity, and a mortal disease. The world and some statistics are shown in realtime. Uses Xith3D

Simulation of arbitrary interactions of DNA with it's environment.

Given a reference sequence, simhtsd will create a large set of short nucleotide reads, simulating the output from today's high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

SimGen is Simulated Genetics. It simulates a simple DNA for moving within simple bacteria eating plankton. As good for Simulation it has Object-Oriented Design and is Coded in Java. It is a Applet and Dektop-Application and can be extended.

Distributions Networks Analyzer (DNA) is a tool for simulating (power flow) and analyzing electrical distribution networks. Users can easily implement and test their own power flow, optimal power flow and control algorithms.