http://baoilleach.blogspot.com/2008/05/rss-feeds-for-chemistry-projects-on.htmlbaoilleach's RSS feed of Chemistry projects on SourceForgeFri, 03 Jul 2009 00:06:07 GMTPyRSS2Gen-1.0.0http://blogs.law.harvard.edu/tech/rsshttp://sf.net/projects/scaffoldhunter/Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.http://sf.net/projects/scaffoldhunter/Mon, 04 May 2009 00:00:00 GMThttp://sf.net/projects/dmolecularmodel/The Developement of 3D Molecular Simulation Enginehttp://sf.net/projects/dmolecularmodel/Fri, 01 May 2009 00:00:00 GMThttp://sf.net/projects/sawes/The SAWES (Self-Adapting Wavelet Electronic Structure) code performs density functional theory calculations using wavelet basis sets evolved concurrently with the self-consistent field iterations to optimally represent each wavefunction.http://sf.net/projects/sawes/Wed, 29 Apr 2009 00:00:00 GMThttp://sf.net/projects/confgen/ConfGEN - An Automatic Conformation GENeratorhttp://sf.net/projects/confgen/Tue, 28 Apr 2009 00:00:00 GMThttp://sf.net/projects/limsnet/A web-based LIMS developed by .NET techhttp://sf.net/projects/limsnet/Sun, 26 Apr 2009 00:00:00 GMThttp://sf.net/projects/spectrouvvis/Software to send command to and receive results from a UV-Visible spectrometer. Only the Secomam Prim Advanced is supported as this time.http://sf.net/projects/spectrouvvis/Fri, 24 Apr 2009 00:00:00 GMThttp://sf.net/projects/gpuautodock/Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/http://sf.net/projects/gpuautodock/Thu, 23 Apr 2009 00:00:00 GMThttp://sf.net/projects/moga/MoGa (Moleculator Gnome application) is an application for Gnome that calculates the molar mass of chemicals. MoGa is meant to be useful for both students and professional researchers.http://sf.net/projects/moga/Wed, 22 Apr 2009 00:00:00 GMThttp://sf.net/projects/shapega/Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.http://sf.net/projects/shapega/Wed, 15 Apr 2009 00:00:00 GMThttp://sf.net/projects/spectratools/An open-source library to retrieve data from infrared (IR) spectroscopy data files. Having the data in a plain-text format make it simple to use in other applications; for example, making a plot ready to be submitted as part of a journal article.http://sf.net/projects/spectratools/Sun, 12 Apr 2009 00:00:00 GMThttp://sf.net/projects/librysq/librysq is C/C++ implementation of the Rys quadrature for computing arbitrary electron repulsion integrals on CPU and CUDA GPUs. A FORTRAN interface is provided for compatibility with the existing chemistry packages.http://sf.net/projects/librysq/Sun, 29 Mar 2009 00:00:00 GMThttp://sf.net/projects/expertomica-eda/EDA is Graphical User Interface and Matlab compiled application for filtration of LC-MS or GC-MS, based on probalistic methods. Including peaks and compounds segmentation with various visualizations. This software can be used for metabolomics, proteomicshttp://sf.net/projects/expertomica-eda/Fri, 27 Mar 2009 00:00:00 GMThttp://sf.net/projects/ffx/FFX is a molecular biophysics engine for interpreting and predicting structural, thermodynamic and kinetic experiments. It provides high level Java force field and crystallographic APIs.http://sf.net/projects/ffx/Fri, 27 Mar 2009 00:00:00 GMThttp://sf.net/projects/brewj/An open source suite of utilities for brewers implemented in JavaFXhttp://sf.net/projects/brewj/Tue, 24 Mar 2009 00:00:00 GMThttp://sf.net/projects/almost/almost - all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.http://sf.net/projects/almost/Mon, 23 Mar 2009 00:00:00 GMThttp://sf.net/projects/openpes/Computer Aid Process Engineering software, based on cobra technology, which can provided simulating all industry processes. It will contain Physical Properties, Unit Operations, Simulator Executive, Reaction, Numerical Solvers, GUI/CLI.http://sf.net/projects/openpes/Fri, 20 Mar 2009 00:00:00 GMThttp://sf.net/projects/datagam/Datagam is a tool for extracting data from output or punch file produced by GAMESS(US) or PC GAMESS/FireFly.http://sf.net/projects/datagam/Thu, 12 Mar 2009 00:00:00 GMThttp://sf.net/projects/vbfret/This is a Matlab software package for single molecule FRET data analysis.http://sf.net/projects/vbfret/Wed, 11 Mar 2009 00:00:00 GMThttp://sf.net/projects/bruread/bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suitehttp://sf.net/projects/bruread/Sat, 07 Mar 2009 00:00:00 GMThttp://sf.net/projects/elims/eLIMS is Open Source web Based Laboratory Information Management System using MySQL / Oracle.http://sf.net/projects/elims/Sat, 07 Mar 2009 00:00:00 GMThttp://sf.net/projects/cdfread/cdfread is a program for people wirking with mass spectrometry datasets. cdfread implements the routines to read mass spectra and mass chromatograms from data files in netCDF ("Andi-MS") format. Centroid and profile data are supported.http://sf.net/projects/cdfread/Fri, 06 Mar 2009 00:00:00 GMThttp://sf.net/projects/isopat/'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.http://sf.net/projects/isopat/Fri, 06 Mar 2009 00:00:00 GMThttp://sf.net/projects/hires/hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.http://sf.net/projects/hires/Fri, 06 Mar 2009 00:00:00 GMThttp://sf.net/projects/hyperglossary/The HyperGlossary Project enables real-time annotations of web sites for the purpose of explaining jargon-heavy pages with pop-up definitions and other resources, such as powerpoints and videos.http://sf.net/projects/hyperglossary/Thu, 05 Mar 2009 00:00:00 GMThttp://sf.net/projects/labdb/The Analyses Database is a collection of software to archive and to track rawdata files from analytical instruments. The system is set up using freely accessible tools - MySQL, apache, PHP, Linux. Several utilities for MS Windows are provided.http://sf.net/projects/labdb/Mon, 02 Mar 2009 00:00:00 GMThttp://sf.net/projects/chemicaldb/The Chemicals Database is a simple yet effective approach to track a stock of products. It is accessible from any workplace over Intra/Internet (http). It was designed in particular to track chemicals in a laboratory, but is suitable for other items.http://sf.net/projects/chemicaldb/Mon, 02 Mar 2009 00:00:00 GMThttp://sf.net/projects/msgraph/MSGraph is a program designed for the interactive, fast, qualitative analysis of mass spectrometric (MS) data. It is a tool to provide fast and simple access to all the information contained in an LC/MS analysis run.http://sf.net/projects/msgraph/Sun, 01 Mar 2009 00:00:00 GMThttp://sf.net/projects/webbabel/WebBabel is a python web application using OpenBabel to convert files from one format to another. It runs under Windows, Mac or Linux on your desktop, workstation or laptop. It uses the Jmol (or Marvin) viewer to show the structures being converted.http://sf.net/projects/webbabel/Sun, 01 Mar 2009 00:00:00 GMThttp://sf.net/projects/chemfem/chemfem is a high order finite element method that can solve general partial differential equations and the reacting Navier Stokes equations in particular.http://sf.net/projects/chemfem/Mon, 23 Feb 2009 00:00:00 GMThttp://sf.net/projects/chembal/This project is intended to be used as a tool for chemistry students to automatically balance chemical equations by computing the correct reactant and product coefficients.http://sf.net/projects/chembal/Tue, 17 Feb 2009 00:00:00 GMThttp://sf.net/projects/sciencelabinv/Science Laboratory Inventory Control Database Systemhttp://sf.net/projects/sciencelabinv/Sun, 15 Feb 2009 00:00:00 GMThttp://sf.net/projects/remap/A matlab/octave based reaction transport model describing microbially mediated isotope fractionation processes in porous media.http://sf.net/projects/remap/Thu, 12 Feb 2009 00:00:00 GMThttp://sf.net/projects/basiclife/Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cellshttp://sf.net/projects/basiclife/Wed, 11 Feb 2009 00:00:00 GMThttp://sf.net/projects/oscilib/Oscilib (Open Science Library) aims to be a comprehensive suite of programs that provide a simple useful way to solve common scientific and mathematical problems.http://sf.net/projects/oscilib/Tue, 10 Feb 2009 00:00:00 GMThttp://sf.net/projects/cca-forum/Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.http://sf.net/projects/cca-forum/Fri, 06 Feb 2009 00:00:00 GMThttp://sf.net/projects/binarydistilati/MATLAB script(m-file) created to calculate binary distillation system(Benzene-Toluene). Plots the tray steps, temperature profile and concentration profile. Identify error situations.http://sf.net/projects/binarydistilati/Mon, 02 Feb 2009 00:00:00 GMThttp://sf.net/projects/carmel/CARMEL is a suit of parallel codes designed to perform classical molecular dynamics simulations of atomic and ionic systems Potentials : Lennard Jones, Yukawa, Tersoff Bond order Integrators : NPT, NVT, NVEhttp://sf.net/projects/carmel/Fri, 30 Jan 2009 00:00:00 GMThttp://sf.net/projects/pychemqt/Chemical Engineering process simulations programhttp://sf.net/projects/pychemqt/Fri, 30 Jan 2009 00:00:00 GMThttp://sf.net/projects/sqlmol/Implement molecule functions in SQL. It is hosted on Google code: http://code.google.com/p/sqlmol/http://sf.net/projects/sqlmol/Thu, 29 Jan 2009 00:00:00 GMThttp://sf.net/projects/spectroj/easy to use sepctrography software. allow to display spectrography curves, and to overlay severals curves. you can create firste or second derivatives from the curves, or place marks to identify peaks. finals drawings can be saved as png or pdf files.http://sf.net/projects/spectroj/Wed, 28 Jan 2009 00:00:00 GMThttp://sf.net/projects/specmark/SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.http://sf.net/projects/specmark/Tue, 27 Jan 2009 00:00:00 GMThttp://sf.net/projects/maltcms/Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.http://sf.net/projects/maltcms/Thu, 22 Jan 2009 00:00:00 GMThttp://sf.net/projects/metmask/Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.http://sf.net/projects/metmask/Thu, 15 Jan 2009 00:00:00 GMThttp://sf.net/projects/chemm/ChemM is a free chemical manager for storing and searching information about reagents in laboratory. Allows substructure/exac matching as well as searching by name/cas numbers/reagent codes.http://sf.net/projects/chemm/Tue, 13 Jan 2009 00:00:00 GMThttp://sf.net/projects/littool/A small collection of tools for organizing references in scientific work - cooperates with BibTeX.http://sf.net/projects/littool/Sat, 27 Dec 2008 00:00:00 GMThttp://sf.net/projects/armsrc/Automated Reaction Mapping. A suite of algorithms that can map atomic reactions efficiently. These algorithms are detailed in the book: Atomic Reaction Mapping: Algorithms for Evaluating Detailed Chemical Kinetic Mechanisms.http://sf.net/projects/armsrc/Wed, 17 Dec 2008 00:00:00 GMThttp://sf.net/projects/mdlab/MDLab is a molecular dynamics simulation prototyping environment, built with the scripting language Python.http://sf.net/projects/mdlab/Tue, 16 Dec 2008 00:00:00 GMThttp://sf.net/projects/quantumlog/Quantum Chemistry packets calculation analiser. Gaussian, Molpro, Molcas, etc. Sample of creating MDI programs with Visual Studio.http://sf.net/projects/quantumlog/Tue, 16 Dec 2008 00:00:00 GMThttp://sf.net/projects/xstar/A Collection of STAR/CIF processing libraries and related tools, including sub-projects: AStar, TEStar and others...http://sf.net/projects/xstar/Mon, 08 Dec 2008 00:00:00 GMThttp://sf.net/projects/forcesolve/This is the first force-matching software published with the ability to do general coarse-graining for molecular systems.http://sf.net/projects/forcesolve/Sat, 06 Dec 2008 00:00:00 GMThttp://sf.net/projects/theochempy/TheoChemPy is a python library providing common functionalities for Theoretical and Computational chemists.http://sf.net/projects/theochempy/Fri, 05 Dec 2008 00:00:00 GMThttp://sf.net/projects/sdf2svg/A tool to convert mol or sdf files to SVG - scalable vector graphics. Sdf and mol files are files containing information about chemicals. The tool is written in PHP.http://sf.net/projects/sdf2svg/Thu, 04 Dec 2008 00:00:00 GMThttp://sf.net/projects/openelis/OpenELIS is a robust Enterprise Laboratory Information System built around an extensible and scalable framework.http://sf.net/projects/openelis/Tue, 02 Dec 2008 00:00:00 GMThttp://sf.net/projects/cellmc/CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.http://sf.net/projects/cellmc/Wed, 26 Nov 2008 00:00:00 GMThttp://sf.net/projects/rings-code/RINGS "Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations. Its main feature is the analysis of the connectivity using ring statistics.http://sf.net/projects/rings-code/Wed, 19 Nov 2008 00:00:00 GMThttp://sf.net/projects/chemsearch/Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. The package generates SQL given SMILES or MDL files and submits it to a RDBMS.http://sf.net/projects/chemsearch/Tue, 18 Nov 2008 00:00:00 GMThttp://sf.net/projects/openproteome/An open source toolkit for the proteomics research community, OpenProteome provides a variety of tools to aid in the analysis and identification of proteins.http://sf.net/projects/openproteome/Sun, 16 Nov 2008 00:00:00 GMThttp://sf.net/projects/sudsy/Sudsy is a saponification calculator coded in Python using PyGTK and Glade. Sudsy allows you to enter the amount of each oil or fat you select for your soap recipe. Sudsy then displays all the information you need to make your own soap!http://sf.net/projects/sudsy/Fri, 14 Nov 2008 00:00:00 GMThttp://sf.net/projects/masas/Free Libre Open Source Software to manage the acquisition of Mass Spectra through a GPIB interface.http://sf.net/projects/masas/Fri, 14 Nov 2008 00:00:00 GMThttp://sf.net/projects/dmcut2/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.http://sf.net/projects/dmcut2/Wed, 12 Nov 2008 00:00:00 GMThttp://sf.net/projects/makebp/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.http://sf.net/projects/makebp/Mon, 10 Nov 2008 00:00:00 GMThttp://sf.net/projects/fsteam/fsteam is an implementation of steam tables from the International Association for the Properties of Water and Steam (IAPWS), published under IAPWS-IF97. It is able to calculate the entropy, enthalpy and oth parameters with error less than 0.1%.http://sf.net/projects/fsteam/Wed, 05 Nov 2008 00:00:00 GMThttp://sf.net/projects/jthergas/A java package (based on CDK) for calculating thermodynamic properties of chemical compounds given the bonding (2D) structure. The main application is for combustion. The package will try to use standards such as CML and CDK.http://sf.net/projects/jthergas/Tue, 04 Nov 2008 00:00:00 GMThttp://sf.net/projects/cain/Cain performs stochastic and deterministic simulations of chemical reactions. Cain offers optimized versions of the Gillespie's direct method, Gibson and Bruck's next reaction method, tau-leaping, ODE integration, and direct/tau-leaping hybrid methods.http://sf.net/projects/cain/Tue, 04 Nov 2008 00:00:00 GMThttp://sf.net/projects/flamebitmaps/Calculating 2D-Gray-scale bitmaps Calculation of a 3D-rotation-body form a detected area by using different edge-detection-algorithms. Used Porjects: Substance (GUI)http://sf.net/projects/flamebitmaps/Tue, 04 Nov 2008 00:00:00 GMThttp://sf.net/projects/periodicaatomic/This is a module to the software future Periodica, a virtual periodic table of the chemistry elements. Consists in an aplication to show the atomic structure.http://sf.net/projects/periodicaatomic/Wed, 29 Oct 2008 00:00:00 GMThttp://sf.net/projects/jdpp/Java Data Processing Project is a software to display, manipulate and treat scientific data such as time intensities set of data or spectrum.http://sf.net/projects/jdpp/Wed, 29 Oct 2008 00:00:00 GMThttp://sf.net/projects/platestats/The platestats software aims to provide a convenient solution for analyzing the results of biological assays performed in 96- and 384-well plates.http://sf.net/projects/platestats/Tue, 28 Oct 2008 00:00:00 GMThttp://sf.net/projects/refl2exafs/Refl2EXAFS is an utility for the analysis of extended x-ray absorption fine structure (EXAFS) data collected in total reflection mode (reflEXAFS).http://sf.net/projects/refl2exafs/Sat, 25 Oct 2008 00:00:00 GMThttp://sf.net/projects/gparticles/GParticles is a tool to simulate the growth behaviour of two- and three-dimensional nano particles based on a simple grid model, with adjustable (time-dependent) concentrations of the particle's different components.http://sf.net/projects/gparticles/Thu, 23 Oct 2008 00:00:00 GMThttp://sf.net/projects/nanoengineer-1/NanoEngineer-1 is an open source, cross-platform interactive 3D CAD software/ molecular modeling and simulation program for structural DNA nanotechnology (SDN). (keywords: nanorex, nanoengineer, nanoengineer1, ne1, nano)http://sf.net/projects/nanoengineer-1/Thu, 16 Oct 2008 00:00:00 GMThttp://sf.net/projects/pimpwhisky/Mjukvaran för Whiskyföreningens bidrag till eCraft Cup. Hantering av whiskyskåpets inventarie och spiklista mm.http://sf.net/projects/pimpwhisky/Tue, 14 Oct 2008 00:00:00 GMThttp://sf.net/projects/pendantdrop/Measurement of the interfacial tension between two immiscible fluids by using the pendant drop method.http://sf.net/projects/pendantdrop/Wed, 01 Oct 2008 00:00:00 GMThttp://sf.net/projects/chemistrycalc/Solve equations, view charts and graphs, make conversions, balance equations and more. Chemistry Calculator.http://sf.net/projects/chemistrycalc/Wed, 01 Oct 2008 00:00:00 GMThttp://sf.net/projects/jkinetics/JKinetics models chemical reaction kinetics. Chemical equations using familiar notation (A+B->C+D) can be integrated to predict concentration vs time or, with experimental data, used to compute rate constants for a set of reactions.http://sf.net/projects/jkinetics/Thu, 25 Sep 2008 00:00:00 GMThttp://sf.net/projects/micepfl/µic is a modelling engine for simulations of microstructural development. It takes localied behaviours as input from the user and integrates the global behaviour, with the calculation of all interactions as required by the application.http://sf.net/projects/micepfl/Fri, 19 Sep 2008 00:00:00 GMThttp://sf.net/projects/alc/ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.http://sf.net/projects/alc/Thu, 11 Sep 2008 00:00:00 GMThttp://sf.net/projects/imsplot/plotting spectra programhttp://sf.net/projects/imsplot/Wed, 10 Sep 2008 00:00:00 GMThttp://sf.net/projects/rnao/The goal of RNAO is to create a common, dynamic, controlled vocabulary (the RO), pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.http://sf.net/projects/rnao/Tue, 09 Sep 2008 00:00:00 GMThttp://sf.net/projects/wavepacket/WavePacket is a MatLab program package for simulating quantum-mechanical wavepacket dynamics, optionally interacting with electric fields, and with animated graphics. Being highly versatile, it can be used mainly in (photoinduced) physics and chemistry.http://sf.net/projects/wavepacket/Wed, 03 Sep 2008 00:00:00 GMThttp://sf.net/projects/loos/LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods.http://sf.net/projects/loos/Tue, 02 Sep 2008 00:00:00 GMThttp://sf.net/projects/iterate/Iterate is an implementation of the Bravais-lattice-finding algorithm from: Andrews and Bernstein, Acta Cryst. (1988). A44, 1009-1018 Lattices and Reduced Cells as Points in 6-Space and Selection of Bravais Lattice Type by Projections.http://sf.net/projects/iterate/Mon, 18 Aug 2008 00:00:00 GMThttp://sf.net/projects/beamish/Beamish is a simple program to beam correct bruker sfrm frame files which have been taken on Station 9.8 or 16.2 SMX between the years 2003 and 2008.http://sf.net/projects/beamish/Fri, 08 Aug 2008 00:00:00 GMThttp://sf.net/projects/multiplierz/Python based, interactive and scriptable environment for direct analysis of mass-spectrometry data using manufacturer DLLs, through the mzAPI set of procedure calls.http://sf.net/projects/multiplierz/Sat, 02 Aug 2008 00:00:00 GMThttp://sf.net/projects/edsoftware/ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.http://sf.net/projects/edsoftware/Fri, 01 Aug 2008 00:00:00 GMThttp://sf.net/projects/bni-tools/The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.http://sf.net/projects/bni-tools/Wed, 30 Jul 2008 00:00:00 GMThttp://sf.net/projects/htcontrol/controls high-temperature (HT) single-crystal XRD experiments on the STOE IPDSII and 2T diffractometers using the STOE Heatstream HT attachment. Cheap additional hardware (power unit Manson SDP2210, A/D Interface: ICP DAS I7019) is needed.http://sf.net/projects/htcontrol/Tue, 29 Jul 2008 00:00:00 GMT