Search Results for "reaction" - Page 2
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Showing 58 open source projects for "reaction"
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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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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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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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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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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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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
GNAT is an open source, platform-independent MATLAB based toolbox. It is written in MATLAB and Java. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms. The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]). The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional... -
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Oscill8 is a suite of tools for analyzing dynamical systems which concentrates on understanding how the dynamical behavior depends on the parameters using bifurcation theory and reaction network theory.
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Easily find and extract specific chemical reactions from the BioModels database.
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SPSens
Stochastic parameter sensitivity analysis for chemical networks
SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives. Additionally the package... -
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Building controls often have a PID Loop (Proportional Integral Derivative). Adjust PI&D terms in realtime and visually see what the reaction to the system will be. This is a real-time simulator with speed adjustment. Software requires the old MS Java Machine to run. Interested in an updated desktop version? Please drop me a note in the forum or my blog: http://right-handed-monkey.blogspot.com/
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ezBioNet is a biological modeling and simulation tool of molecular interaction that occurred in a cell. We aim that this software can be used for collecting biological data and making biological models to simulate it by biological researchers. ezBioNet can build a detailed biological model including signal transduction, enzyme kinetics, expression network, etc. It also support number of numerical analysis method to simulate the biological reaction networks.
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A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.
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Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.
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FLXLab is a program for running psychology experiments. Capabilities include presenting text and graphics, playing and recording sounds, and recording reaction times via the keyboard, joystick/button box, or a voice key. Windows/Mac/Linux.
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CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.
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The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
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Intended for measurement reaction human on simple event. Program ask some info about and make test. After show statistic.
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DRCS (Dimensionless Reaction Coordinate Software) calculates a dimensionless reaction coordinate for chemical reactions that can be used to classify transition states (and other geometries along a reaction path) as either early or late.
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A matlab/octave based reaction transport model describing microbially mediated isotope fractionation processes in porous media.
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Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.
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Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.