Search Results for "reaction" - Page 3
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Showing 143 open source projects for "reaction"
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FERN: Fast Explicit Reaction Networks
Quickly and explicitly solving sets of differential equations.
FERN is a CUDA program that implements new methods for solving large sets of stiff differential equations using explicit integration methods. For the theory behind the program (due to Mike Guidry), see http://arxiv.org/abs/1112.4778 . -
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LSDMap
Locally-Scaled Diffusion Maps from molecular dynamics trajectories
LSDMap is a set of Fortran90 codes parallelised with MPI for the calculation of Locally Scaled Diffusion Maps. The eigenvectors of the diffusion matrix can be used to form a small set of reaction coordinates describing the behaviour of a high-dimensional data set such as an equilibrium MD trajectory. -
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Reaction Blaze
How blazing are your reaction speeds?
A simple reaction game in which the player must use the keypad to press the number displayed on a tile. The objective is to correctly press as many keys as possibly in as short a time as possible. Press the wrong key once and it's "game over". -
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RMapViewer
A viewer for reaction maps among isomers
Coming soon... A viewer for reaction maps among isomers to find possible reaction paths from one ore more reactant to products within a specified energy band. An animation of a specified reaction path can be viewed on Jmol. Please click on the wiki tab for details. -
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VB .NET PHYSX (PHYSICS) DX9 - Engine
.NET - VISUAL BASIC NVIDIA +ATI PHYSX SLIMDX DIRECTX 9 -ENGINE/WRAPPER
Visual Basic .Net , Nvidia Physx (PHYSICS - ATI INTEL ETC. COMPATIBLE) , DirectX 9 (using SlimDX) 3D ENGINE/HELPER/WRAPPER This project incorporates these technology into a simple Open Source Engine, allowing simple access to Nvidia PhysX library using DirectX 9 (VIA - SLIMDX) to render "Simulations/Games" ALL IN VB.NET -with- C# and other .NET language compatibility. Visuals now include .X model loading with Animations and Skeletons (shaders) Level loading and AUTOMATIC object (mesh)... -
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Glycosylation Microviewer
An application create, simulate and adjust N-linked glycosylation.
... is used to adjust the kinetic parameters of Michaelis-Menten equations in glycosylation reaction network. A dynamic plot is supplied to show the value of mole amout and mole fraction of various glycoform. Thanks to Alexey Balakin and Alessandro Presta. Alexey Balakin supply mathgl(https://sourceforge.net/projects/mathgl) that make the implementation of dynamic plot in this application easily. Alessandro Presta supply fga(https://sourceforge.net/projects/fga) that provide a powerful use of GA. -
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SPTEmu
A synchrophasotron emulator
A simulator for people who are interested in physics. Have you ever tried to calculate, e.g., nuclear reactions? I was totally confused by all these quants, neutrinos, alpha and beta decays, so I decided to create this synchrophasotron simulator. You just enter the reacting isotopes and/or particles and it simulates the reaction for you! P.S. It's called 'Synchrophasotron simulator' because I wanted the program to simulate particle colliding, but it doesn't do it yet. It just calculates alpha... -
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MLSTEZ is designed for next generation sequencing technology (PacBio CCS or Roche 454 platform) based MSLT methods. MLSTEZ, can automatically identify the barcodes and primers used in the PCR reaction, corrects sequencing errors, generates the MLST profile for each isolate, predicts the potential heterozygous locus, and outputs different alleles. Now ver2.0 supports asymmetric barcode design, please check manual for more details.
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fep1d
a script for the analysis of reaction coordinates
Fep1d is a script for the analysis of one-dimensional reaction coordinates. The script allows one to construct conventional and cut-based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (re-scale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, etc. -
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Chain Reaction game in c graphics
Chain Reaction is a simple two player game.
Chain Reaction is a simple two player game. It is popular android game. The objective of Chain Reaction is to take control of the board by eliminating your opponents' orbs. Players take it in turns to place their orbs in a cell. Once a cell has reached critical mass the orbs explode into the surrounding cells adding an extra orb and claiming the cell for the player. A player may only place their orbs in a blank cell or a cell that contains orbs of their own colour. As soon as a player loses all... -
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OARS Android IMU & GPS Data Logger
OARS - Orientational Awareness Reaction Systems
The OARS app is a data logger developed to run on Android OS and devices containing an internal GPS ,along with micro-electro-mechanical systems (MEMS) chipset. Specifically the Invensence MPU-6000 or newer. This chip is a highly accurate inertial measurement unit, or (IMU). Contained within this small IMU is a 3-axis Accelerometer, 3-axis Gyro, and 3-axis Magnetometer. Along with a built in processor, it can calculate movements along 9-axis. Depending on platform and app setting, OARS can... -
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discremental
forever incremental hard disk based backups
This set of scripts is yet another rsync based backup solution. It uses the --link-dest option to create hard links to files that have not changed. Using this technique, each run results in a *full backup* even though the backup process used is incremental (only the files that changed since the last backup). This paradigm is sometimes called forever incremental backups. This utility exists because I wrote it a long time ago in reaction to the slow, cumbersome pace of the dirvish... -
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Cognitive Stability and Flexibility FIT
GPU Accelerated Fitting of Behavioral Data by a Physiological Model
... in the simulated paradigm and the activity of the rule 1 versus rule 2 representing population biases a decision module. The decision module implements a three dimensional nonlinear drift-diffusion process derived from a physiological winner-take-all network with four selective populations, representing the possible behavioral decisions. The decision module integrates top-down input from the rule module with bottom-up input from the decision module to produce decisions and reaction time distributions. -
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ThermV
Comprehensive thermal analysis software package
ThermV thermal analysis software package aims to provide the most sophisticated automatic analysis of thermal analysis data (TG/DTG, DTA and DSC). It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. The project... -
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RelKinema
Relativistic two-body kinematics calculator for nuclear reaction
Relativistic 2-body kinematics calculator for nuclear reaction, including mass data manager, result table browser and plotter. -
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simulate_pcr
PCR target prediction software
Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. This script predicts potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch tolerance and amplicon length range to be set by the user. The PCR amplicon simulation code also annotates... -
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ForStoch
Fortran Stochastic Simulator for Chemical Kinetics
ForStoch is a FORTRAN software suite for Stochastic Simulation of Checimal Kinetics. The stochastic simulation algorithm (SSA), proposed by Gillespie, is a cardinal simulation method for the chemical kinetics. Because the SSA simulates every reaction event, the amount of the computational time is huge when models have many reaction channels and species.This drawback motivates many attempts to improve the efficiency with the accuracy.The ForStoch includes orignial Gillespie SSA and other... -
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RSSA
Rejection-based stochastic simulation algorithm (RSSA)
Rejection-based stochastic simulation algorithm (RSSA) is an efficient exact algorithm for doing stochastic simulation of biochemical reaction systems. RSSA improves over state of the art of stochastic simulations by avoiding and collapsing as much the number of propensity updates. -
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Chemical Reaction
Balance chemical reaction and compute material balance
This Python program is used to balance a chemical reaction and to compute the material balance. Furthermore, it's able to check molecules and to write the condensed strutural formula from the name of an organic molecule. (Those both functionalities are still limited.) -
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modDFS
Find whether a KEGG module is complete in a proteome
Given module definitions and reaction information based on a KEGG database, modDFS does a depth first search to find whether a set of KOs are sufficient for completion of a module. For cases where only 1 absent KO would've been enough for module completion, that module is reported to be complete(only lenient). For cyclic modules, completion is defined as having all the module reaction steps present. Again, lenient completion cases are reported. Also, all absent reactions are reported so... -
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Rejection-based Reaction-Diffusion
Stochastic simulation of Reaction-Diffusion System
Rejection-based Stochastic simulation of Reaction-Diffusion System -
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DS-Frame2D
2D Frame Analysis, Linear Static Analysis, Mode Shapes
This is a free program for solving linear 2D framed structures under static loading and calculating the mode shapes. It is coupled with an easy-to-use GUI that provides the possibility to design the structure very fast. It calculates reaction forces, diagrams of axial and shear forces, as well as, diagrams of bending moments. Moreover, it calculates the mode shapes of the structure using various methods and it will be cabable of performing dynamic analysis soon. The program is written... -
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VirusSim
Java VSV Simulator
Reaction-centric model of vesicular stomatitis virus replication and production -
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Acuchem: A Computer Program for Modeling Complex Chemical Reaction Systems by Walter Braun and John T. Herron This project creates a Java user interface to create and convert input/output files from the Acuchem program.