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         Chemistry
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280 projects in result set. Projects sorted by: Ranking (Top Ranked First)
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1. 3DMolvis - 3DMolvis is a tool designed to make easy learning of basic structure and function of biological molecules.

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2. ABFF - Project for develop force fields with using ab-initio calculations

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3. aCell - a framework to build data-driven models of biological cells

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4. Adaptive Biasing Force - This is an implementation of the adaptive biasing force method (ABF) in NAMD. The code for ABF was developed by Eric Darve, Stanford University. ABF is a method created by E. Darve and A. Pohorille to calculate the free energy of bio-molecules.

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5. Algorithms in Spectroscopy - The aim of the project is to provide open source collection of algorithms in the field of spectroscopy: data handling and processing, modeling and artificial intelligence tools.

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6. Ambit - chemical structures database - AMBIT consists of a MySQL database and functional modules providing storage of chemical compounds and allowing a variety of flexible structure, similarity and other queries. Written in Java, with the use of The Chemistry Development Kit.

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7. Amino Acid Finder - Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them

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8. AMORSS: redox enzymes simulation system - This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

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9. Analytical Data Interchange - This project provides open software for working with analytical instrumentation data using the ASTM "ANDI" standard.

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10. Analytical Information Markup Language - This project supports ASTM E13.15 "Analytical Data Magement" in it's work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry data.

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11. APBS - APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://apbs.sf.net/>.

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12. Ascalaph Graphics - Molecular Dynamics and Molecular Graphics program. Molecular model builder. Interface with the MDynaMix http://www.mmk.su.se/~sasha/mdynamix/

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13. AutoDock Software in Parallel with GPUs - 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/

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14. Avogadro - Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.

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15. 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 cells

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16. bc_scatterplot - bc_scatterplot is a scatterplot plugin for the bioclipse project

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17. Bika open source LIS/LIMS - Bika combines web content management and workflow processing for a one-stop web-based LIMS (Laboratory Information Management System) · Built in Plone · Professionally supported · Making waves · bi:ka (Zulu): tell it as it is

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18. BINViz - BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environment

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19. Bioclipse - An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

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20. Biological Network Analyzer - Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BN++ databases, but also as stand-alone tool.

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21. BlochLib-a fast NMR toolkit - 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.

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22. 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.

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23. 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 suite

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24. Burrow-owl - Burrow-owl is a software package for visualizing multidimensional nuclear magnetic resonance (NMR) spectra, with an emphasis on spectra used in macromolecular structure determination.

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25. calibration and maintenance for labs - QMS Application to track control, inspection, measurement and test equipment. It can be used for asset management and CRM. It is primarily for companies and labs adhering to ISO 9001 quality standards. There are plans to add a non-conformance management.

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26. Cantera - Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.

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27. CARMEL 'CARbon MEchanics Lab' - 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, NVE

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28. 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.

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29. cclib - cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, GAMESS, GAMESS-UK, Gaussian, Jaguar and PC GAMESS.

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30. ccwatcher - ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a Command Line Interface" to which it parses important output and plots SCF energies. Avogadro plugin capability is planned.

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31. 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.

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32. CDKTools - The Octet-CDK interoperability package.

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33. CellMC - CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.

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34. Chamber Interior Ballistics - chamber is a reactive hydrodynamic modeling tool specifically designed for small arms interior ballistics research. Multiple equations of state and burn models are supported. chamber is an adaptation of the BKW, SIN, 2DL and 2DE codes in one package.

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35. CheckCML - The CheckCML project is a collection of modules for the production and checking of chemical experimental data represented as CML. The core CheckCML library provides classes for the checking process; tools such as OscarData allow for the production of CML

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36. Chem Works - Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.

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37. ChemBot - Extensible 3-dimensional chemical reaction modeling tool that utilizes the known scientific rules and theorems to predict complex molecular reactions on an organismal level. Will serve as a starting point for developing a simulated organism.

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38. ChemBuddy - Cocoa/Objective-C chemical analysis and computation program; includes gas laws, solutions/solubility, stoichiometry, periodic tables, et alii.

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39. ChemClipse - Provide the chemical world with a frontend for entering and managing chemical data. This frontend will be made with the Eclipse Rich Client Platform. Additionally a Server component will be developed for storing and retrieving the data.

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40. Chemdraw in LaTeX - Conversion of CdXML files issued by ChemDraw into EPS files easily usable by LaTeX. This project has just been merged into Open Babel, and now consists in the design of an EPS export format for Open Babel. It might be delivered as a standalone as well.

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41. Chemical Calculator - Chemical Calculator that can calculate various aspects of compounds. The programs main features are: * Get information about an element * Calculate the amount of moles of an element * Calculate the Empirical and Molecular formulas of a compound

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42. Chemical Descriptors Library (CDL) - CDL provides a generic C++ framework to write algorithms for the calculation of molecular descriptors. CDL provides efficient substructure search, fingerprints and pharmacophore algorithms, and many more for the calculation molecular descriptors.

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43. Chemical Equilibrum - PyChemEq is an Open Source project which goal is to simulate chemical equilibrums. It provides classes (that are the project's "kernel" ) and a user interface using PyGtk and Glade. The whole project will be written in Python.

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44. Chemical Evaluation Framework - Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

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45. Chemical Markup Language - The development and curation of a range of XML-based tools for using Chemical Markup Language (CML), including XSD XML Schemas for validation, datatyping and constraining CML documents and XSLT Stylesheets for transforming, filtering and rendering.

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46. Chemical Structures - The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.

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47. chemicalInventory - chemicalInventory is a chemical intelligent tool for managing chemical inventories. Main features: Find chemicals via substructure or text searches. Manage container and shelf locations, check containers in and out or transfer containers between users.

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48. ChemiSQL - The ChemiSQL project intends to federate several open source chemical cartridge projects (Mychem, Orchem and Pgchem). The project provides documentation, examples and an unified graphical user interface for using these chemical cartridge.

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49. Chemistry structure file converters - Collection of scripts converting structure data files into different formats (e.g. CTRL to POSCAR).

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50. ChemMap - A Molecular Chemical Viewer using OpenGL and Platform independent provided for the study of Chemicals, including physical, chemical and visual properties.

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51. ChemNomParse - A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).

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52. ChemRuby - ChemRuby is a framework for developing cheminformatics applications in Ruby. It will let you retrieve chemical information from variety of data sources, fast substructure search, draw a chemical structure, and calculate chemical properties.

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53. chemsense - The ChemSense Studio software supports the creation and sharing of text, images, graphs, drawings, and storyboard animations of chemical processes. The ChemSense Animator can be run as a separate, stand-alone application. See http://chemsense.sri.com

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54. CICC Grid - Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

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55. Collaborative Computing Project for NMR - Collaborative Computing Project for NMR (CCPN)

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56. Computing with units - Java program for computations with values expressed in terms of physical or other units. Supports complicated mathematical expressions and user-defined functions. Invoked from scripts, line command, as GUI, or as applet. Extensive units data base.

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57. Crystalbuilder - An easy way for single crystal structure analysis. Graphical software for single crystal structure refinement. CRYSTALBUILDER uses SHELXL-97 software for the refinement and makes directly possible the molecular structure visualization.

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58. CT8K - CT8K is an experimental quantum chemistry program intended to bring state of the art methods to the desktop PC

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59. Data Collaboration - Framework for uncertainty propagation in predictive models targeted for collaborative science

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60. DAVE - DAVE is an integrated environment for the reduction, visualization and analysis of inelastic neutron scattering (scientific) data. It is built with IDL from Research Systems, Inc. DAVE is fully supported on Linux, Windows and MacOS X.

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61. DISCUS simulation package - DISCUS is a set of programs to simulate the atomic structure of disordered materials and calculate experimental properties such as diffuse scattering or the atomic pair distribution function.

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62. 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.

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63. DRCS - 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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64. EasyChem - EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.

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65. EChem++ - EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules.

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66. ED Software - ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.

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67. Effectopedia - Effectopedia is open knowledge aggregation and collaboration tool that provides a means of describing adverse outcome pathways in encyclopedic manner.

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68. EMERGY SIMULATOR - Diagram (JGraph) driven simulator. Bondgraphs > nonlinear differantial system > plot: implemented for economics and ecology. Network analysis: emergy propagation implemented. Would also fit for electronics, mechanics, cost, GWP, footprint analysis.

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69. EPeriodic - EPeriodic is the electronic periodic table. you can read the properties of each element in the table with a single click

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70. Eureka - Eureka is an open-source information management system alternative tailored to the academic community. It is designed to receive, process, and archive large amounts of data generated in the scientific laboratory setting.

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71. EvoGrid - The EvoGrid is an effort to develop a distributed simulation system to simulate potential pre-biotic chemical environments.

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72. Extended Bioaccumulation Framework - Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.

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73. FAUNUS: A Molecular Simulation Framework - FAUNUS is an object oriented class library for molecular simulation, written in C++/STL. It contains routines and utility programs for, Metropolis Monte Carlo sampling, Macromolecules, Proton Titration, Widom Analysis, POVRAY Visualization etc.

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74. FHSTOOLKIT - A combination of useful tools for High School classes, including math classes ranging from prealgebra to calculus, and science classes ranging from IPS to AP Physics.

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75. Fityk - Fityk is nonlinear curve-fitting and data analysis software. It is specialized in fitting peaks (bell-shaped functions like Gaussian, Loretzian, Pearson 7, Voigt) to experimental data.

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76. FlameBitmaps - Calculating 2D-Gray-scale bitmaps Calculation of a 3D-rotation-body form a detected area by using different image processing algorithms. Developed for the German Aerospace Center (DLR). Used Projects: Substance (GUI)

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77. Force Field X - FFX is a molecular biophysics tool written in pure Java. We have implemented the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field with special features for crystallography.

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78. ForceSolve - This is the first force-matching software published with the ability to do general coarse-graining for molecular systems.

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79. Frankenstein Project: Hack the Genome - Frankenstein Project: Hack the Genome A collection of valuable tools needed for genome analysis, such as: - molecule, protein 3d structure viewer - protein alignement machine - cloner - DNA manipulating tools - DNA-to-Protein translator and more

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80. FreeLIMS - FreeLIMS® is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights; more on: www.labmatica.com

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81. freesteam - 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 and ASCEND

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82. Frowns - Frowns is a chemoinformatics system written almost entirely in python.

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83. Gabedit - Gabedit is a Graphical User Interface for Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PC Gamess and Q-Chem computational chemistry packages.

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84. GAST-Viz - Atomistic Simulation Toolkit - 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.

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85. Gaussian Output Tools - Gaussian Output Tools is a package of simple scripts to extract data from Gaussian output files.

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86. GaussSum - GaussSum parses the output of ADF, GAMESS, GAMESS-UK, and Gaussian to extract useful information: progress of geometry optimisation, UV/IR/Raman spectra, MO contributions and more.

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87. gdis - This is a GTK/OpenGL based program for displaying isolated molecules, periodic systems, and crystalline habits. It also acts as a GUI to packages such as GAMESS, GULP, and POVRay to provide energy minimizations and publication quality rendering.

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88. GEMS - Grid-Enabled Molecular Simulation Repository (GEMS)

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89. Generating derivative structures - A Fortran 95 implementation of an algorithm for generating derivative structures of a parent lattice. The algorithm is discussed in detail in: Gus L. W. Hart and Rodney Forcade, "A new approach to generating derivative structures," Phys. Rev B. (2008).

Click here to download.  
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90. GenX - GenX is a scientific program to refine x-ray and neutron reflectivity data using the differential evolution algorithm. GenX is very modular and highly extensible making it very useful for sophisticated refinements and as a general fitting program.

Click here to download.  
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91. GlycanEditor - A visual editor for the definition of Carbohydrate structures, computation of masses and derivation of fragments.

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92. goldify - Goldify is a set of tools that allow automated addition of links into electronic documents. Its main purpose is to allow such addition of links into documents that wish to link to the IUPAC GoldBook (http://goldbook.iupac.org).

Click here to download.  
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93. gorbital - 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/).

Click here to download.  
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94. greylag - Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.

Click here to download.  
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95. Gridder - Gridder is a group of portlets that simplify the use and administration of grid services. Especially for job submission management. Gridder also extends and documents the functionality of the OGCE Bundle. It is plenty of useful documentation.

Click here to download.  
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96. GSim - tool for NMR spectroscopy - GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.

Click here to download.  
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97. GUI for macro/statistics/chemistry - JTabler is for the simple table manager to utilize other programs, including many internet utilities, statistics tools, especially adapted for chemistry data such as SDF and MOL

Click here to download.  
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98. HoloJ - A suite for Transmission Electron Microscopy holograms reconstruction and analysis

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99. hr - 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.

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100. I.S.A.A.C.S. - I.S.A.A.C.S. Interactive Structure Analysis of Amorphous and Crystalline Systems is a cross-platform software developed to analyze the structural characteristics of three-dimensional models built by computer simulations.

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