Search Results for "k-stor"
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Showing 77 open source projects for "k-stor"
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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Armadillo
fast C++ library for linear algebra & scientific computing
* Fast C++ library for linear algebra (matrix maths) and scientific computing * Easy to use functions and syntax, deliberately similar to Matlab / Octave * Uses template meta-programming techniques to increase efficiency * Provides user-friendly wrappers for OpenBLAS, Intel MKL, LAPACK, ATLAS, ARPACK, SuperLU and FFTW libraries * Useful for machine learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. * Downloads:... -
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LINE Solver
Queueing Theory Algorithms
LINE is an open-source software package to analyze queueing models via analytical methods and simulation. The solver is available for Java/Kotlin, MATLAB, and Python. LINE features algorithms for the solution of open queueing systems (e.g., M/M/1, M/M/k, M/G/1, ...), open and closed queueing networks, and layered queueing networks. Additional details are available on the project website: http://line-solver.sf.net. -
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Conscious Artificial Intelligence
It's possible for machines to become self-aware.
...A number of prototypes will be developed as the project progresses. This project has 2 subprojects: Object Pascal based CAI NEURAL API - https://github.com/joaopauloschuler/neural-api Python based K-CAI NEURAL API - https://github.com/joaopauloschuler/k-neural-api A video from the first prototype has been made: http://www.youtube.com/watch?v=qH-IQgYy9zg Above video shows a popperian agent collecting mining ore from 3 mining sites and bringing to the base. At the time the agent is born, it doesn't know how to walk nor it knows that it feels pleasure by mining. ... -
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ransfoil
console to calculate airflow around an airfoil based on RANS approach
RANSFOIL is a console program to calculate airflow field around an isolated airfoil in low-speed, subsonic, transonic or supersonic regime by numerically solving the Reynolds averaged Navier-Stokes (RANS) equations using mature computational fluid dynamics (CFD) method. As postprocess results, the aerodynamic parameters of the airfoil, e.g., lift coefficient and drag coefficient, can be integrated from the airflow distribution near wall boundary. In addition, the coupling between airflow and... -
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illness index
illness_index A Computer Program of a Medical Textbook.
A computer scientist has attempted to program a textbook of British general practice (primary care) medicine, that is, Hodgkin K (1978) "Towards Earlier Diagnosis....", 4th Edition, Churchill Livingstone. If a patient types presenting findings (such as headache, cough), the program prompts the user for expansion/denial of appropriate findings, in order to construct a list of patient findings. The program also calculates a list of likely diseases, which the user can use the web to find out more about. ... -
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
...Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. In Silico Biology, 7(6). https://doi.org/10.3233/ISI-2007-00337 -
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Parallel and Distributed Process System
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20 pipelines of the QCAUS/PDPBioGen suites are undergoing consolidation for high-scale institutional research. Core 'Ford 2026' algorithms remain the proprietary IP of the Ford Peace and Justice Foundation. Academic users at partner institutions are currently performing validation; all other commercial inquiries must contact the author Computational Neuroscience: Large-scale neural population dynamics, brain-inspired... -
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JQM Java Quine McCluskey
JQM - Java Quine McCluskey for minimization of Boolean functions.
Java Quine McCluskey (JQM) implements the Quine-McCluskey algorithm with Petrick’s Method for minimizing Boolean functions. Designed for both education and industrial application, it handles up to 16 variables and functions. Uniquely, JQM bridges the gap between theory and practice: it visualizes the solution process with generated Karnaugh Maps for students, while supporting PLC engineers by exporting results to Structured Text (ST) and Ladder Diagram (LD). The software includes a GUI for... -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. ... -
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whiteboxgui
An interactive GUI for WhiteboxTools in a Jupyter-based environment
...Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. WhiteboxTools also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; etc. -
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MLPACK is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and flexibility for expert users. * More info + downloads: https://mlpack.org * Git repo: https://github.com/mlpack/mlpack
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XRD CUBIC
Simulate crystal cell length (a), Miller indices {h, k, l}, d-spacing
This is a basic computer program (coded in Python) to simulate possible unit crystal cell length (a), Miller indices - {h, k, l} and interplanar spacing (d) for cubic crystals from observed (experimental) X-ray diffraction (XRD) angle, 2-theta. It can simulate all these possible crystal lattice parameters for cubic crystal systems between the given 2–theta values within the range of specified cell length (a) limits. 1. Enter wavelength of X-ray (in Angstroms) 2. -
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XISMuS
X-Ray Imaging Software for Multiple Samples
...IMPORTANT FIXES in respect to base v2.0.0 version: v.2.5.0 introduces the Differential Attenuation and Cube Viewer utilities, and migrates user database to *.json files v2.4.3 fixes a with K element in the fit-approx method v2.4.3 fixes and issue where saving plots with fit-approx or a auto-wizard could freeze the software v2.4.2 introduces Image Viewer to Mosaic v2.4.1 fixes an issue in merging H5 or EDF datasets with Mosaic Full changelog at https://linssab.github.io/history X-Ray Fluorescence Imaging Software for Multiple Samples is an open source software to manipulate and study macro-X-Ray Fluorescence (MA-XRF) datasets. ... -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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An R package for metrology. metRology provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and (eventually) inter-laboratory metrology comparison studies.
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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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This application allow user to predict dissolution profile of solid dispersion systems based on algorithms like symbolic regression, deep neural networks, random forests or generalized boosted models. Those techniques can be combined to create expert system. Application was created as a part of project K/DSC/004290 subsidy for young researchers from Polish Ministry of Higher Education.
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ZeGrapher
Fast and easy to use plotting software.
ZeGrapher is a free and open source software for plotting mathematical objects (functions, sequences, parametric equations) and experimental data on the plane. This software is intended to be as easy to use as possible, suitable for high school students. -
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E-Plater
The firmware for the PIC18F2XK22 to do pulsed electroplating
"E-plater" is a device that was specially developed by Engenharia Caseira (engenhariacaseira.com.br) to make pulsed and reversed pulsed electroplating (PED). Research shows that molecules on the surface of electrically deposited material using direct current are sometimes disorganized which can result in uneven surface and color. It is possible to control the composition and thickness of the deposited layer in an atomic order by configuring the amplitude and width of a pulse. The... -
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...The program codes are written in the Fortran 90/95 language with MPI and OpenMP. Time dependent density functional theory (TD-DFT) calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
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PB-sQF_BacterialTyping
Bacterial Typing from either assembled or raw short reads file
Probability Binning - signature Quadratic Form, PB-sQF, types unknown sequence to one of the 628 bacterial library genomes which gives the smallest test statistics thus most similar library strain. The input file is the k-mer counts of the unknown assembled genome sequence or raw short reads file in decimal format generated by KAnalyze developed by P. Audano et al. (https://sourceforge.net/projects/kanalyze/). The download included the library index, the library name and sample unknowns. -
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Density-ratio based clustering
Discovering clusters with varying densities
...An existing density-based clustering algorithm, which is applied to the rescaled dataset, can find all clusters with varying densities that would otherwise impossible had the same algorithm been applied to the unscaled dataset. Reference: Zhu, Y., Ting, K. M., & Carman, M. J. (2016). Density-ratio based clustering for discovering clusters with varying densities. Pattern Recognition. http://www.sciencedirect.com/science/article/pii/S0031320316301571 -
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KAnalyze
DNA/RNA Sequence K-mer Toolkit
KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API. -
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Mass-based dissimilarity
A data dependent dissimilarity measure based on mass estimation.
This software calculates the mass-based dissimilarity matrix for data mining algorithms relying on a distance measure. References: Overcoming Key Weaknesses of Distance-based Neighbourhood Methods using a Data Dependent Dissimilarity Measure. KDD 2016 http://dx.doi.org/10.1145/2939672.2939779 The source code, presentation slide and poster are attached under "Files". The presentation video in KDD 2016 is published on https://youtu.be/eotD_-SuEoo . Since this software is licensed...
