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The ISOTOPIC PATTERN CALCULATOR is a small linux tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence.
GIPS is a GUI Version of the Isotopic Pattern Calculator.
We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.
runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.
qsims simulates quantum dynamics with an (almost) arbitrary time-dependent Hamiltonian. qsims uses a Chebychev polynomial expansion of the Schrodinger propagator, and the pseudospectral method developed by R. Kosloff.
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The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.
CHIMP aims to provide a complete suite of tools for the investigation and modeling of chemical systems. It currently is able to parse chemical reaction mechanisms and run kinetic Monte Carlo simulations on the reacting system.
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GAST-Viz is a toolkit allowing for the creation of OpenGL atomistic simulation applications using discrete element modeling methods. A number of sample applications are included.
This project provides an "embedded expert system", i.e. a limited ability inference engine, with a demo rule set, taken from the field of X-ray Photoelectron Spectroscopy.
COMSPARI (COMparison of SPectral And Retention Information) is being developed to 1) visualize mass spectrometric data and, more importantly, to 2) visualize 2 sets of mass spectral data simultaneously in a format that easily allows for comparison.
Console program solves for masses of ingredient chemicals given a chemical formula, solves for ingredient masses given the mass of one ingredient and the chemical formula, solves for the chemical formula given the masses of all ingredients.
gorbital is a atomic orbital viewer written using gtkmm (gtk--). gorbital displays a 3d interactive view of a electron orbitals. It is meant to be an open source viewer much like Orbital Viewer by David Manthey (http://www.orbitals.com/orb/).
OCW is a scripting language and interpreter for controlling complex operations of valves and pumps in microfluidic devices. The interpreter program uses parallel ports to interface with any automation project. The program runs on Linux and Windows.
BlochLib is an expression template library of generic data structures and algorithms to perform large scale nuclear magnetic resonance classical and quantum mechanical spin simulations, with many I/O capabilities,and integrated numerical routines.
wacrgEIS is software developed for the West Australian Corrosion
Research Group (wacrg) for analysis of Electrochemical Impedance
Spectroscopy (EIS) data.
Two Dimensional NOesy simulation (TDN) implementents an algorithm that creates a time-domain 2D NOesy spectrum. TDN does not calculated the nOe peak intensities, Therefore, you will need the CORMA (Complete nuclear Overhauser Relaxation Matrices).