Search Results for "logisim-evolution"
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Showing 103 open source projects for "logisim-evolution"
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Quantum++
Modern C++ quantum computing library
...The library's simulation capabilities are only restricted by the amount of available physical memory. On a typical machine (Intel i5 8Gb RAM) Quantum++ can successfully simulate the evolution of 25 qubits in a pure state or of 12 qubits in a mixed state reasonably fast. -
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caesar-lisflood
CAESAR-Lisflood landscape evolution model
Caesar Lisflood is a geomorphological / Landscape evolution model that combines the Lisflood-FP 2d hydrodynamic flow model (Bates et al, 2010) with the CAESAR geomorphic model to simulate erosion and deposition in river catchments and reaches over time scales from hours to 1000's of years. These sourceforge pages provide downloads of the .exe and the source code for CAESAR-lisflood and instructions and additional documentation can be found in the Wiki tab. -
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GenX
X-Ray and Neutron Reflectivity Modeling
GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program. -
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DEEP
Differential Evolution Entirely Parallel Method
The Differential Evolution, introduced in 1995 by Storn and Price, considers the population, that is divided into branches, one per computational node. The Differential Evolution Entirely Parallel method takes into account the individual age, that is defined as the number of iterations the individual survived without changes. The introduced improvements are: (I) allow several oldest individuals to be overwritten by the same number of best ones in the population, (II) new selection rule uses several objective functions in offspring evaluation. ... -
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ToxTrac
Free Animal Tracking Software
...If used, please cite: Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., Andersson, P. L. and Andersson, M. (2018). ToxTrac: a fast and robust software for tracking organisms. Methods in Ecology and Evolution. 9(3):460–464 Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., and Andersson, M. (2017). ToxId: an algorithm to track the identity of multiple animals. Scientific Reports. 7(1):14774. Contact and Support: Alvaro Rodriguez (Main Developer), a.tajes@udc.es Magnus Andersson, magnus.andersson@umu.se -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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Biogenesis Color Mod
Mod for evolution simulation and artificial life program Biogenesis
You can download the Color Mod at the Biogenesis main site too (included in the main download now). You also find the sourcecode there. If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. Original project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ Includes Tyler Colemans "Features Mod": https://sourceforge.net/projects/biogenesisfeatu/ Biogenesis discussion... -
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Dark Mode Leakage Radar
Quantum Radar for Dark Mode Leakage Detection Standard Radar Returns
...Features Live version Live try: https://stealthpdpradar.streamlit.app/ Beta Live https://qcaustfordmodel.streamlit.app/ PDP Quantum Filter: Implements photon-dark-photon kinetic mixing and von Neumann evolution Dark-Mode Leakage Detection: Reveals quantum entanglement signatures of stealth objects Blue-Halo Fusion Visualization: RGB composite highlighting stealth signatures Synthetic Test Generator: Creates realistic radar scenarios with configurable stealth targets Streamlit Web Interface: Interactive parameter tuning and real-time visualization Installation git clone https://github.com/tlcagford/StealthPDPRadar.git cd StealthPDPRadar pip install -r requirements.txt -
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QCI_AstroEntangle_Refiner
Quantum Cosmology & Astrophysics Unified Suite (QCAUS)
... 📸 Live Demo The application is deployed on Streamlit Cloud: Live App test now: https://qcuas-quantum-cosmology-astrophysics-unified-suite.streamlit.app/ QCI AstroEntangle Refiner – FDM soliton physics & image processing Magnetar QED Explorer – Magnetar fields, dark photons & vacuum QED Primordial Photon–DarkPhoton Entanglement – Von Neumann evolution in an expanding universe QCIS (Quantum Cosmology Integration Suite) – Quantum‑corrected cosmological perturbations 🔭 Overview These four projects form a complete computational framework for quantum‑inspired astrophysics. Together they enable: Image analysis of galaxy clusters (Abell, Bullet, etc.) using Fuzzy Dark Matter (FDM) soliton overlays. ... -
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Photon-Dark Photon-Entanglement
Photon Dark Photon Entanglement Theory
... 📸 Live Demo The application is deployed on Streamlit Cloud: Live App test now: https://quantum-cosmology-astrophysics-unified-suite.streamlit.app/ QCI AstroEntangle Refiner – FDM soliton physics & image processing Magnetar QED Explorer – Magnetar fields, dark photons & vacuum QED Primordial Photon–DarkPhoton Entanglement – Von Neumann evolution in an expanding universe QCIS (Quantum Cosmology Integration Suite) – Quantum‑corrected cosmological perturbations -
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Quantum-Cosmology-Integration
Quantum Cosmology & Astrophysics Unified Suite (QCAUS)
Quantum-Corrected Cosmological Perturbation Solver Live TRY https://qcuas-quantum-cosmology-astrophysics-unified-suite.streamlit.app/ or Beta https://qcaustfordmodel.streamlit.app/ License: Dual 🔬 Overview A complete computational framework for cosmological perturbation theory with first-principles quantum corrections. This package implements: Quantum-corrected Mukhanov-Sasaki equations with backreaction from quantum fields Full Boltzmann integration with quantum... -
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Magnetar Quantum Vacuum Engineering
Quantum Cosmology & Astrophysics Unified Suite (QCAUS)
... 📸 Live Demo Application is on Streamlit Cloud: Live App test now: https://qcuas-quantum-cosmology-astrophysics-unified-suite.streamlit.app/ Or try Beta https://qcaustfordmodel.streamlit.app/ QCI AstroEntangle Refiner – FDM soliton physics & image processing Magnetar QED Explorer – Magnetar fields, dark photons & vacuum QED Primordial Photon–DarkPhoton Entanglement – Von Neumann evolution in an expanding universe QCIS (Quantum Cosmology Integration Suite) – Quantum‑corrected cosmological perturbations 🔭 Overview These four projects form a complete computational framework for quantum‑inspired astrophysics. Together they enable: Image analysis of galaxy clusters (Abell, Bullet, etc.) using Fuzzy Dark Matter (FDM) soliton overlays. ... -
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AstroBioTools
Adaptive analysis of amino acid alphabets
A new, fast implementation of algorithms used for the adaptive analysis of amino acid alphabets as described in Philip, G. K., & Freeland, S. J. (2011). Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology, 11(3), 235-240. Ilardo, M., Meringer, M., Freeland, S., Rasulev, B., & Cleaves II, H. J. (2015). Extraordinarily adaptive properties of the genetically encoded amino acids. Scientific reports, 5, 9414. Ilardo, M., Bose, R., Meringer, M., Rasulev, B., Grefenstette, N., Stephenson, J., Freeland, S., Gillams, R. ... -
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Matrix Product State (MPS) Simulations
Numerical routines for variational matrix product state simulations.
Open Source MPS (OSMPS) is a collection of numerical routines for performing tensor network algorithms to simulate entangled, 1D many-body quantum systems. Our applications reach from ground state and excited states for statics to the dynamics of time-dependent Hamiltonians. We offer various time evolution methods with an emphasis on the support of long-range interactions through the matrix product state formalism. For more algorithms, see the list of features below. Please cite "M. L. Wall and L. D. Carr, New J. Phys. 14, 125015 (2012)" and "D. Jaschke, M. L. Wall, and L. D. Carr, Computer Physics Communications 225, 59–91 (2018)" if your publication involves OSMPS. -
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C++QED
A framework for simulating open quantum dynamics
...The basic idea is to allow users to build arbitrarily complex interacting quantum systems out of free subsystems and interactions (elements), and simulate their time evolution with a number of available time-evolution drivers. C++QEDv2 specifies a small grammar to describe composite quantum systems. Apart from providing a number of elements out of the box, there are tools which facilitate the implementation of new elements. These are being added continuously, as the need arises. The principal concept of the design of C++QEDv2 is that all information available at compile time should be processed as such, with the help of TMP. ... -
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CASUP
Cellular Automata library for SUPercomputers (CASUP)
CASUP is a Cellular Automata (CA) library for HPC and supercomputers. It can be used in materials science (microstructure evolution, grain coarsening, fracture etc.), physics (Ising magnetisation) and for many other CA. If you use the library, please reference it as: A. Shterenlikht, L. Margetts, Three-dimensional cellular automata modelling of cleavage propagation across crystal boundaries in polycrystalline microstructures, Proc. Roy. Soc. A 471:20150039, DOI: http://dx.doi.org/10.1098/rspa.2015.0039. ... -
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powerfactory-fmu
The FMI++ PowerFactory FMU Export Utility
...Additional files (e.g., time series files) and start values for exported variables can be specified. Currently, two types of simulations are supported: In quasi-static steady-state simulations a power system’s evolution with respect to time is captured by a series of load flow snapshots. RMS simulations allow to calculate the time-dependent dynamics of electromechanical models, including control devices (new in version v0.6). -
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...A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI: 10.1007/s13127-011-0056-0
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packeis
Check for selection of RNA secondary structure
PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons. -
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...Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. Other repositories: - https://github.com/jenetics/jenetics Maven: - https://mvnrepository.com/artifact/io.jenetics
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Coastline Evolution Model 2D
Numerical model simulating coastal morphodyamics and evolution
CEM2D is a reduced complexity coastal evolution model, capable of simulating fundamental cause-effect relationships in coastal systems and exploring the influence that sea level rise could have on sediment transport and the formation and evolution of morphological features and landforms over meso-scales. The model has been built from a 1D parents model - CEM - that was originally developed by Ashton et al. (2001), Ashton and Murray (2006) and Valvo et al. (2006). -
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
...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 ACCESS) At the moment, MANTIS is not available on CRAN. To build a source package of MANTIS, use the script buildPackage.R To install MANTIS use 'install.packages(file.tar.gz,type="src",repo=NULL)' To test use test_V3.3_code.R Contact the main author of the publication above for further details. ... -
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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 network flow and other graph algorithms. A fast parallel implementation of the network simplex method, and some full-fledged parallel/distributed MIP solvers will be added in the next version. ... -
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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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IQM-Plugin-PPI
PPI Index
...PPI is computed with the FFI index and the Lacunarity using the ToW algorithm: PPI = FFI^(Ltw) For FFI, please see: https://sourceforge.net/projects/iqm-plugin-ffi/ Andronache etal. Fractal analysis for studying the evolution of forests, Chaos, Solitons & Fractals, 2016, Vol 91, 310-318. For Tug of War Lacunarity, please see: Reiss, Lemmerer, Hanslmeier, Ahammer Tug-of-War Lacunarity-A Novel Approach for Estimating Lacunarity. Chaos, 201611. https://doi.org/10.1063/1.4966539. Installation instruction: Copy newest jar file to the "Plugins" directory which should be located in the directory of your local IQM main application. ...
