Search Results for "differential equation python" - Page 3
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Showing 131 open source projects for "differential equation python"
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DataMelt
Computation and Visualization environment
DataMelt (or "DMelt") is an environment for numeric computation, data analysis, computational statistics, and data visualization. This Java multiplatform program is integrated with several scripting languages such as Jython (Python), Groovy, JRuby, BeanShell. DMelt can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Neural networks and various data-manipulation methods are integrated using powerful Java API. ... -
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XISMuS
X-Ray Imaging Software for Multiple Samples
ATTENTION: Cumulative update 2.5.0 has been released!! The update works for any previous 2.x.x version. If upgrading from version v1.x.x, please download and install v2.0.0 first. 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... -
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Python/FEniCS Examples
phase-field simulation and other examples with Python/FEniCS
The main goal of this project was developing phase-field simulations of lithium dendrite growth with FEniCS programmed in Python. The problem was based in the grand potential-based model of Zijian Hong and Venkatasubramanian Viswanathan (https://doi.org/10.1021/acsenergylett.8b01009) . Some simpler examples were developed before for a first approach with FEniCS: heat equation and combustion model. -
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C++QED
A framework for simulating open quantum dynamics
C++QED is an application-programming framework for simulating open quantum dynamics in general. It has demonstrated the ability to simulate full Master equation of up to several thousand, and quantum trajectories of up to several hundred thousand dimensions. 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... -
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Synchrorep
Synchronize directories
Synchrorep is a one click directory synchronization software. All modification will be reported to one to the other and vice versa. Usefull for nomads or speedup differencials backup. -
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CFD Python
Sequence of Jupyter notebooks featuring the 12 Steps to Navier-Stokes
CFD Python, a.k.a. the 12 steps to Navier-Stokes, is a practical module for learning the foundations of Computational Fluid Dynamics (CFD) by coding solutions to the basic partial differential equations that describe the physics of fluid flow. The module was part of a course taught by Prof. Lorena Barba between 2009 and 2013 in the Mechanical Engineering department at Boston University (Prof. -
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HBV interventions model
ODE HBV model and MCMC for fitting HBsAg, HBcAg and HBeAg data.
This code implements the MCMC and ordinary differential equation (ODE) model described in [1]. The core MCMC and ODE code is implemented in C/C++, and is wrapped with an R front end. This is not an R-package (although there are plans to extend the code and eventually make it into an R-package). Please read the PDF file supplied for further instructions on how to use this code. [1] HBV vaccination and PMTCT as elimination tools in the presence of HIV: insights from a clinical cohort and dynamic model https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-019-1269-x -
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Virtual Laboratory Environment
A multi-modeling and simulation environment to study complex systems
...VLE provides a complete set of C++ libraries, called VFL (VLE Foundation Libraries), to develop DEVS models, to gets results of simulations, to launch simulation on cluster. The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. VLE have also three ports to use the VFL with Python, Java and R programming languages. -
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...Although novelty is encouraged in regards to the algorithm, proposals could entertain approaches such as: a. Implementing the non-linear mixed effects theory, b. Maximum log-likelihood algorithms (stiff, non-stiff Ordinary Differential Equation solving methods with linearization)
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,... -
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Construct2D
COmputational fluid dyNamics STRUctured grid CreaTor for 2D airfoils
Construct2D is a grid generator designed to create 2D grids for CFD computations on airfoils. The grids are generated in Plot3D format. The only required input file is the set of coordinates defining the airfoil geometry, using the same format as XFoil, the popular vortex-panel code for airfoil analysis. Construct2D can create grids with O topology (recommended for airfoils with a blunt trailing edge) or C topology (recommended for airfoils with a sharp trailing edge). Now available in... -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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UAV Drone
Airborne avionics platform for drone system identification and control
UAV Drone is a suite of software and hardware which is hosted on Raspberry Pi for the purpose of drone system identification/mathematical modelling and control law development. This platform measures critical aerospace measurements of Pitch, yaw, Roll via AHRS, location through GPS, and air data through Pitot Static system. Control of the drone is provided through user developed Control law based on critical aircraft parameters to 16 configurable PWM outputs to servos or motors... -
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SODE
Program to solve differential equations using long Taylor series
Program to generate a program to numerically solve either a single ordinary differential equation or a system of them.It is a Ruby program, now called omnisode, which generates either Ruby, C, C++, Maple or Maxima code. Code can be generated for all languages under Linux. Ruby can be generated under Windows. All can be generated under cygwin, but would need work on execution of Maple. Omnisode itself is Ruby, which is needed in all cases to generate the program. -
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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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WordMat
Math in Word
WordMat is an add-on to Microsoft Word which creates a tab with math functionality. Part of the Math functionality is provided by other open-source applications like Maxima, GeoGebra, Graph and GnuPlot. -
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
RAtom solves nonlinear Kohn-Sham equation for the neutral atom. The adaptive algorithm based on finite element method (FEM) is implemented. Discretization of the differential eigenvalue problem is done by finite element method with Lobatto polynomials as a basis functions. High order Gauss quadratures are applied in order to obtain the total energy of atom with absolut accuracy of 1E-6 hartree. -
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EpiMINE
program for mining epigenomic data
EpiMINE is a program designed for mining epigenomic data. This application performs genome wide based quantitative and correlative analysis between different annotated or raw chip-seq like datasets in the regions of interest (RI). Apart from this the tool takes the advantage in linking results with expression data. It is available both in graphical user interface and in command line form. It can be executed in Mac and Linux platforms. Dependencies: python >= 2.7 version python... -
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SpliceSim is a collection of Python scripts designed for realistic simulation of RNA-seq reads for in silico differential AS studies. For software support and information on their distribution licenses, please proceed to: https://github.com/mingjiewong/SpliceSim
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WavePacket
Dynamics of quantum systems, controlled by external fields
WavePacket is a toolkit for numerical simulation of distinguishable particles. It can solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, as well as classical or quantum-classical Liouville equations. External electric fields can be added within the semiclassical dipole approximation, thus WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics or chemistry, including... -
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diffeqs
Solving differential equations in Octave and Matlab
A set of scripts which help in solving differential equations by Octave and Matlab. This project currently contains scripts for professional timing, plotting graphs, and generating and displaying animations based on the solutions of equations. In the future there will be also scripts for numerically solving several forms of differential equation while tracking precision and controlling chaos. -
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Programs for Numerical Methods
Didactic program to aid students in learning Numerical Methods.
The program contents and capabilities are the following: 1. Matrices. 1.1 Matrix definition and special types of matrices. 1.2 Determinant of a matrix. 1.3 Inverse of a matrix. 2. Linear equation system. 2.1 Direct methods (Inverse of a Matrix, Cramer's Rule, Gauss Jordan, Montante). 2.2 Iterative methods (Jacobi, Gauss-Seidel). 3. Nonlinear equation systems (Newton 1st order, Newton 2nd order). 4. Roots of equations. 4.1 Bracketing methods (Bisection, Inverse Linear Interpolation, Regula-Falsi). 4.2 Open Methods (Newton-Raphson, Bailey). 5. ... -
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Mathpad
A Python based command line math utility.
Mathpad is a command line utility. It will later have a GUI, but not at this time. -
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EpidermalERKMAPK
Scripts for Modelling Human Epidermal ERK-MAPK Activation
...Regulation of ERK-MAPK Signalling in Human Epidermis. BMC Systems Biology. doi: 10.1186/s12918-015-0187-6 The model was developed using a set the normalized-Hill differential equation framework, as specified by [Kraeutler, Soltis & Saucerman, (2002). BMC Systems Biology; doi: 10.1186/1752-0509-4-157]. This package includes: - MATLAB code containing the model definition, together with a script to perform non-linear least squares optimisation for a subset of parameters - python scripts which use libSBML to create an SBML representation of the model - SED-ML scripts which execute the SBML model under a range of conditions, produce output plots to recapitulate results shown in Cursons et al. (2015).
