Search Results for "dna computing simulator"
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Showing 51 open source projects for "dna computing simulator"
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Qulacs
Variational Quantum Circuit Simulator for Quantum Computation Research
Variational Quantum Circuit Simulator for Quantum Computation Research. Qulacs is a Python/C++ library for fast simulation of large, noisy, or parametric quantum circuits. Qulacs is developed at QunaSys, Osaka University, NTT, and Fujitsu. -
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Quantum++
Modern C++ quantum computing library
Quantum++ is a modern C++ general-purpose quantum computing library, composed solely of template header files. Quantum++ is written in standard C++17 and has very low external dependencies, using only the Eigen 3 linear algebra header-only template library and, if available, the OpenMP multiprocessing library. Quantum++ is not restricted to qubit systems or specific quantum information processing tasks, being capable of simulating arbitrary quantum processes. The main design factors taken in... -
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LAMMPS
Public development project of the LAMMPS MD software package
LAMMPS is a large-scale classical molecular dynamics simulator for modeling atoms, molecules, coarse-grained particles, and other particle-based systems. It is designed for high-performance computing and can run efficiently on desktops, clusters, and supercomputers. The software is widely used in materials science, chemistry, physics, nanotechnology, soft matter, and computational engineering. -
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AWS ParallelCluster Node
Python package installed on the Amazon EC2 instances
...You can build higher-level workflows, such as a Genomics portal that automates the entire DNA sequencing workflow, on top of AWS ParallelCluster. -
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AWS ParallelCluster Cookbook
The Chef cookbook used to build and bootstrap AWS ParallelCluster
...You can build higher-level workflows, such as a Genomics portal that automates the entire DNA sequencing workflow, on top of AWS ParallelCluster. Node.js is required by AWS CDK library used by ParallelCluster. -
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Amazon Braket PennyLane Plugin
A plugin for allowing Xanadu PennyLane to use Amazon Braket devices
The Amazon Braket PennyLane plugin offers two Amazon Braket quantum devices to work with PennyLane. The Amazon Braket Python SDK is an open-source library that provides a framework to interact with quantum computing hardware devices and simulators through Amazon Braket. PennyLane is a machine learning library for optimization and automatic differentiation of hybrid quantum-classical computations. Once the Pennylane-Braket plugin is installed, the provided Braket devices can be accessed... -
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newRPL
The classic RPL programming language reimplemented and reimagined.
This project reimplements from scratch the RPL language made popular by HP programmable calculators, in portable C/C++. The main goal is to release a complete computing environment for various targets. There's currently 4 active targets: the HP 50g, HP39gs and HP40gs calculators and a PC simulator (see the downloads section!). Other ports are planned for the future. -
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ARES
Antibiotic Resistance Evolution Simulator
ARES (Antibiotic Resistance Evolution Simulator) is a membrane computing-based model, able to simulate complex biological landscapes. It uses a nested membrane-surroundings entitites scheme formatted in a XML file. The created scenarios emulate entities as: i) Resistance genes, able to detoxify antibiotics. These genes can be located in the plasmid, in conjugative elements or in the chromosome; ii) plasmids and conjugative elements transferring genes between bacterial cells; iii) bacterial cells; iv) individual microbiotas where bacterial species coexist; v) hosts containing the microbiotic ensembles; vi) environment(s) where the hosts are contained. ... -
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ProjectQ
An open source software framework for quantum computing
ProjectQ is an open-source effort for quantum computing. It features a compilation framework capable of targeting various types of hardware, a high-performance quantum computer simulator with emulation capabilities, and various compiler plug-ins. -
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time-aware-computing
Model time-dependent behavior of technical and neural computing
...The theory is introduced in practice through producing computing objects in SystemC simulator, where those times are modeled by using delays, while working on a virtual time scale. The basic object set is extended towards imitating technical computing solutions and biological computing as well. Specialized test programs, demonstration programs and docs are included. References to the science background provided. -
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PeMSyn
Matlab/Scilab-FEMM based GUI to Assist the Design of Permanent Magnet
Release: PeMSyn 2.4 - 03.Sep.21 Requirements: - Matlab 2018a or later (with Parallel Computing Toolbox ) - Scilab 6.1.0 or later - FEMM 4.2 (21Apr2019 or later) Matlab/Scilab-FEMM based GUI to Assist the Design of Permanent Magnet Machines: - Surface Mounted PMSM: Inner Rotor / Outer Rotor - Inset Mounted PMSM: Inner Rotor / Outer Rotor - Spoke-Type PMSM: Inner Rotor - Coreless Machine - Different Slot types available - Permeance Coefficient Assistant --- No-Load and On-Load estimation for PC during the design process - Winding Wizard Assistant - Performance Simulator (FEMM Based) --- No-Load and On-Load parameters assessment considering armature reaction and saturation effects --- Torque Curve Capability assessment --- Parallel Processing (Matlab only) TUTORIAL included! ... -
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. ... -
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ScaffCC
Compilation and optimization framework for the Scaffold language
ScaffCC is a compiler and scheduler for the Scaffold programing language. It is written using the LLVM open-source infrastructure. It is for the purpose of writing and analyzing code for quantum computing applications. ScaffCC enables researchers to compile quantum applications written in Scaffold to a low-level quantum assembly format (QASM), apply error correction, and generate time and area metrics. It is written to be scalable up to problem sizes in which quantum algorithms outperform... -
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MarDRe
MapReduce-based tool to remove duplicate DNA reads
...Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. Written in pure Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for Big Data processing. -
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ECEbuntu
ECEbuntu - a customized operating system designed for ECE
ECEbuntu is a customized operating system designed for electrical and computer engineering (ECE) students. ECEbuntu is targeted to universities and students as it represents an environment that contains more than 30 pre-installed software and packages all catering to undergraduate course-work in ECE. ECEbuntu supports a range of tools including programming tools, tools for circuit analysis and pcb design, mathematical and numerical analysis tools, network analysis and tools for microwave and... -
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JSensor
high performance computing, Wireless Sensors Networks Simulators
How can we analyze the water quality of a river? How can we monitor streets, cities, provinces of a country? How can we predict and prevent problems coming from earthquakes, snowstorms, fire spreads and all kinds of natural disasters? How can we test some new drugs without using animals? These and many other problems are initially solved by using simulators. It is extremely expensive, and sometimes dangerous, to test initial ideas in a real environment. We must use simulators to achieve... -
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Emulator of EPOS-73
The behavioral model of the old Soviet calculator EPOS-73
This project introduces a console application designed for functional and behavioral emulation of the old Soviet calculator EPOS-73 (ЭПОС-73) also known as Elektronika B3-11 (Электроника Б3-11). The project is conceived as an auxiliary for verification of the switch-level simulator based on Verilog HDL of the said apparatus. Calculator model EPOS-73 is interesting in that it was one of the first models of Soviet computing performed at LSI, that were fully designed by Soviet engineers. It was used a set of four LSIs series K1ZHG451...4 (К1ЖГ451...4) or later designation K145HK1...4 (К145ХК1...4). The choice of this calculator as an object of modeling is due to the presence of (miraculously survived to this day) a sufficient set of design documentation for the technology applied in its LSIs, including a technical description of the device, revealing its calculating algorithms. ... -
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Dynamic Quantum Round Robin Simulator
Dynamic Quantum Round Robin Simulator with GUI
Simulates Traditional Round Robin Scheduling algorithm in addition to 2 Dynamic Quantum Round Robin Algorithms using a GUI. Algorithms can be found in: [1] Mohd Abdul Ahad, “Modifying round robin algorithm for process scheduling using dynamic quantum precision”, International Journal of Computer applications(0975-8887) on Issues and Challenges in Networking, Intelligence and Computing Technologies ICNICT 2012. [2] Debashree Nayak , Sanjeev Kumar Malla and Debashree Debadarshini,... -
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COMRAD-MPI
Compression of Large Genomic Datasets using Parallel Computing
COMRAD-MPI is a parallel computing algorithm for reducing the computational time for compressing the large genomic data sets based on COMRAD algorithm. It captures the long range repeat redundancies in large genomes there by providing a way to compress the large DNA data set. Three stages- Substitution, Clean up and Huffman encoding have been parallelized using message passing library. -
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FlexCloud
FlexCloud is a resource scheduling simulator for Cloud Data Centers
Cloud Data centers aim to provide reliable, sustainable and scalable services for different requests. Resource scheduling is a key part for Cloud services. To simplify the scheduling process, we propose FlexCloud, a new flexible and scalable simulator that enables simulating the process of initializing cloud data centers, allocating virtual machine requests, and providing performance evaluation for various scheduling algorithms. -
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Soft-DeCO
Software-Defined Cloud Orchestration
Software-Defined Cloud Orchestration: An Integrated Architecture and Deployment Process This is an expansion of the project xSDN, an Expressive Simulator for Dynamic Network Flows. Please cite the below papers, if you used this project or referred to this in your work. Kathiravelu, Pradeeban; Veiga, Luis, "An Expressive Simulator for Dynamic Network Flows," Cloud Engineering (IC2E), 2015 IEEE International Conference on , vol., no., pp.311,316, 9-13 March 2015 doi: 10.1109/IC2E.2015.43 -
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Cloud2Sim
Adaptive and Distributed Architecture for Cloud/MapReduce Simulations
An Adaptive and Distributed Architecture for Cloud and MapReduce Algorithms and Simulations. Please cite the below papers, if you used this project or referred to this in your work. Kathiravelu, P. & L. Veiga (2014). An Adaptive Distributed Simulator for Cloud and MapReduce Algorithms and Architectures. In IEEE/ACM 7th International Conference on Utility and Cloud Computing (UCC 2014), London, UK. pp. 79 – 88. IEEE Computer Society. Kathiravelu, P. & L. Veiga (2014). Concurrent and Distributed CloudSim Simulations. In IEEE 22nd International Symposium on Modeling, Analysis and Simulation of Computer and Telecommunication Systems (MASCOTS'14), Paris, France. pp. 490–493. ... -
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Octree Method For Particles
simulation of particles using an oct-tree
...the further away, the more zoomed out. thus, i/o traffic is greatly reduced. combine this with the fact that it's an O(N) algorithm, and what you get is an accurate particle-based physics simulator whose simulation speed scales with the number of particles per compute unit even for VERY large particle counts and VERY large computing arrays. In a phrase, simulation on a massive scale! -
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An easy-to-use simulator for decentralized distributed scheduling in Clusters, Grids, and Cloud ecosystem MaGate 2.0 is now available from github! https://github.com/huangye177/magate
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iTAM tile simulator
iTAM tile growth simulation
Python program for the kinetic tile simulation of the growth of 2D tiled DNA structures. Requires UNAFold, Python 2.7, NumpPy, SciPy.
