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MSQuant is a tool for quantitative proteomics/mass spectrometry and processes
spectra and LC runs to find
quantitative information about proteins and peptides. Though
automated it also allows manual inspection and change.
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.
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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.
Trelis is a graphical Monte Carlo simulation tool for modeling the time evolution of chemical reaction systems involving small numbers of reactant molecules, such as occur in subcellular biological processes like genetic regulatory networks.
Attn: the latest version of PeptideProphet must be obtained as part of the Trans-Proteomic Pipeline package at http://sourceforge.net/projects/sashimi/.
wacrgEIS is software developed for the West Australian Corrosion
Research Group (wacrg) for analysis of Electrochemical Impedance
Spectroscopy (EIS) data.
In many parallel scientific applications the process of grid generation, decomposition, message passing, and performance measurements are of similar stucture. The projects intention is to develop a generic function library that will contain all these.
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).
this is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs.
The goal is to provide several cuda and c based functions which can be easily accessed using java, groovy and python.
The project aims at building effective parameter estimation method using loopy belief propagation algorithm. The main application is in the field of molecular pathway study, such as Akt survival pathway.
QGAMESS is a queuing program for the popular molecule mechnanics program GAMESS, the General Atomic and Molecular Electronic Structure System. QGAMESS is a cross-platform replacement for GTK-Gamess.
dmcut2 is a scientific program designed to simulate chemical reactions at surfaces using Metropolis and Monte-Carlo methods. Short ranged interactions between adsorbates may be taken into account. Emphasis was put on code readability and usability.