The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
Open source steam property routines in C. Implements the IAPWS-IF97 steam tables from the International Association for the Properties of Water and Steam. Includes two-way property solvers and test suite. Can be used from C/C++, Fortran, Python, LabVIEW, Octave and ASCEND.
Object-oriented crystallographic library and program, for the analysis of Crystal structures from scattering experiments: optimized scattering computation, Graphical interface for structures and data, global optimization algorithms.
Periodic Table of Elements a quick reference tool
Periodic Table of Elements is a quick reference tool that allows you a quick glance to get general information about an element. The program is for educational purposes.
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with all...
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can be...
A library to easily analyse output of the Heidelberg MCTDH code
This project aims to provide a set of routines to easily read in and manipulate the output of the Heidelberg MCTDH code. The goal is to enable a new user to quickly get started with writing custom analysis programs. Also, it should enable more experienced users (== us) to write small, clean, and testable analysis programs, something that seems incompatible with the Fortran-77 code of the Heidelberg MCTDH package.
xylib is a portable library for reading x-y data from powder diffraction, spectroscopy and other experimental methods. Supported formats: VAMAS, pdCIF, Bruker, Philips, Rigaku DAT, Sietronics CPI, DBWS/DMPLOT, Koalariet XDD and others.
Animp is an OpenGL program to display movies of particles in motion where the movies are produced by adding calls to animp library routines to simulation code written in either C++ or Fortran. Animp can also display molecules read from PDB files.
OPEN GENERAL SCIENTIFIC INTERFACES homepage : http://www.opengsi.org
NanoHive is a modular simulator used for modelling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study and development of nanotech entities. The project will also focus on the simulation of complex biological applications such as Targeted Drug Delivery by simulating nanowires, magnetic nanoparticles and others. Updates will follow from January 2017.
FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
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.
Structlab is a machine learning C++ framework for structured domains, which provides a toolbox of learning methods and tools for preprocessing and visualization. It also provides a GUI to setup elaborate experiments in a visual and intuitive way.
Drchem is a set of various tools useful in my scientific work (I'm a chemist) e.g. GPC calculations, bibliography managment, some of perl scripts helpful in plots/graphs processing.
ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds. Together with Support Vector Machines, these kernel functions find natural applications for virtual screening of molecules.
ChemE aims to be a library for performing analytical operations specific to chemical engineering.
GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.
OBExtensions is a extension library for the chemoinformatics library Openbabel. It provides extensions to Openbabel, being mostly GUI widgets. OBExtensions has a 2D/3D viewer, 2D coordinates generator and some other extensions.
A multi-procedure, multi platform electron spectrum evaluation program, with special options for atomic physics and XPS/UPS spectroscopy.
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.
ARGonWin - Automatic retrosynthesis generator on (X)Windows: COMPUTERASSISTED ORGANIC SYNTHESIS / Chemoinformatics package to propose a chemical synthesis for an organic compound given its structural formula. (C++ XWindows/MSWindows). Based on OpenBabel.
A Qt-based implementation of matrix algorithms for solving linear equations. Includes common matrix operations such as addition, subtraction, multiplication, scaling, and more.
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.
NEMESIS - Molecular Modelling Package.