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         Molecular Science
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162 projects in result set. Projects sorted by: Ranking (Top Ranked First)
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1. ABFF - Project for develop force fields with using ab-initio calculations

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2. Agent-Based Multiscale Tissue Model - Agent-based multiscale model of cancer proliferation dynamics

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3. aisconvert - Toolkit for processing genetic data in RAW (23andme) format. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED conversion; regions of homozygousity

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4. 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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5. 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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6. arrayplex - ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

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7. 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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8. Ascalaph Quantum - is a graphic interface and models builder for the quantum mechanics packages NWChem, CP2K and PC GAMESS/Firefly.

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9. Atomic-Clusters - This project is intended to perform Monte-Carlo-Simulations to calculate small clusters (2 to 13 atoms) of the rare gas "argon".

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10. 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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11. 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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12. BASILISK - BASILISK is a model of side chain conformational space in proteins. Unlike rotamer libraries, does BASILISK model the chi angles in continuous space. Furthermore features BASILISK an also continuous backbone dependence.

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13. Bio-SPICE - Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.

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

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15. Bioinformatics Template Library - The original Bioinformatics Template Library (BTL) uses templates to implement generic programming in same way as the Standard Template Library (STL). Biolib aims at continue developing this library.

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16. 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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17. Biomolecule Toolkit - The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.

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18. BioNLP UIMA Component Repository - The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

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19. BioSpring - BioSpring is a molecular simulation software based on spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics.

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20. Bowtie - Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

Click here to download.  
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21. 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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22. 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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23. CAIROTEP - ORTEP-III with CAIRO graphics backend

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24. Camaro - Camaro manages cDNA and RNAi screens and their resulting datasets, detects and visualizes common artifacts, and analyzes the data in the context of a single screen or in a control-treatment configuration of several screens.

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25. 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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26. CDKTools - The Octet-CDK interoperability package.

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27. Cellogica - Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.

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28. 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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29. 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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30. ChIPOTle 2.0 Peak Discrimination Tool - ChIPOTle 2.0 is a user friendly tool for performing peak detection in ChIP-chip signal. The tool also has functions for probe sorting, signal normalization, replication merging, and multiple correction testing in a windows interface or *nix command line.

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31. cnsFace - cnsFace is a GUI for the Crystallography and NMR System.

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32. CoCOOT - CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.

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33. Collaborative Genome Annotation - A platform for Web-Based Collaborative Genome Annotation.

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34. Colloids - A C++ library to process both experimental and simulation data of colloidal particles. Includes a tracker (Crocker&Girer) in 2D and 3D (+time), a Leica file reader, Steindhard bond orientational order calculation, etc.

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35. CoMPAS Pro - Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

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36. Cryo-EM Segmentation and Registration - Software for segmentation and registration of 3D density maps obtained using cryo-electron microscopy.

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37. 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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38. DIY Genomics - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

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39. DNA Ninja - A Smooth DNA Editor - DNA Ninja will be designed as a DNA editor allowing to modify DNA files, annotate features, make restriction maps and virtual gels, pick primers and find ORFs. The main goal is that the program is intuitive to use and runs fast.

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40. DNAStrider - Mac upgraded to OSX, Lepard which do not support os9 anymore. This project is build to help DNA Strider user to get their data out and perform some basic DNA analyze function.

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

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43. esra - Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.

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44. EYPID_PROJECT - A logical model to describe and encode protein-protein interaction data into a machine-readable format. The model (in UML) must contain information about the state of the interactiong proteins before and after the interaction for pathways building.

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45. 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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46. Force - FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

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47. 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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48. 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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49. FuncNet - Client tools for the FuncNet protein function analysis platform: http://funcnet.eu/

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50. 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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51. GamaComp - GamaComp - A graph comparative metabolic pathway tool to find shortest path using JUNG Library.

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

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

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54. GeneWave - This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

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55. genome - This project provides visual interactive interfaces to custom algorithms used in genomes research.

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56. gfit - gfit creates an interface between computational models and experimental data and provides tools for their analysis

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57. GlycanEditor - A visual editor for the definition of Carbohydrate structures, computation of masses and derivation of fragments.

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58. GSim - tool for NMR spectroscopy - GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.

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59. Hanalyzer - The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.

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60. 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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61. iMD - iMD: interactive/intuitive MD (Molecular Dynamics) simulation analysis.

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62. intron marker pipeline - IMP is an automated tool for intron-flanking primer design based off of Expressed Sequence Tags (ESTs). It's intended for use in species with limited to no genomic sequence data available.

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63. IsoFind - Project to create a set of algorithms which will identify and isolate mRNA isoforms through primer design for RT-PCR techniques.

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64. Janocchio - Janocchio is an application or applet for viewing 3D molecular structures and calculating NMR couplings and NOEs

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65. JChemPaint Applet and Swing Application - The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads and source code repository can be foun

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66. JMolDraw - 2-D chemical structure drawing program

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67. JPhysChem modeling tool - JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.

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68. kristy - the nice crystal viewer - Kristy will be a crystal visualization tool for scientific or educational use. We like to focus on crystal planes (e.g. the macroscopic surfaces) and surface charge calculations.

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69. LAMMPS - LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields and boundary conditions and can be easily modified and extended.

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70. LineageEvolver - LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.

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71. lr3 - A software package for superposition of binding sites, clustering for common amino acids in this binding sites and a search algorithm to screen novel proteins for the occurrence of such a binding site on the surface.

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72. lrrr - Extraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.

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73. mateo - Python scripts implementing new systematic approaches for the prediction of the properties of molecular materials. Version 1.0 starts with crystal densities: Acta Crystallographica, Section B, Vol. 63, pp.277-284 (2007).

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74. Mazridge - Mazridge is a free rigid body dynamics engine written in C/C++ for use as a library.

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75. MBPT (Molecular Biology Perl Tools) - MBPT (Molecular Biology Perl Tools) is a toolkit for Molecular Biologists that focuses mainly on sequence analysis/representation, as well as format conversions.

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76. MCDL - MCDL is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. Features include accurate structure diagram generation, and Kekule chemical structure creation from aromatic bond list.

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77. MDDriver - MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.

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78. Meredys - Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)

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79. Metabolic Pathway Designer and Analyzer - Crude Metabolic Pathway Analysis visualization software. For a software engineering class.

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80. MitoMAS_membrane - Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.

Click here to download.  
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81. Molevolve - Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.

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82. Molsketch - Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.

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83. MolWgt - Given the chemical formula, MolWgt calculates the molecular weight of a substance.

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84. Mychem - Mychem is a chemoinformatics extension for MySQL.

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85. mzmatch - mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

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86. 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)

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87. Ninja - an InChI toolkit for Java - Ninja is an object oriented toolkit for manipulating InChI identifiers.

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88. NMR Restraints Grid - The NMR Restraints Grid (NRG at http://www.bmrb.wisc.edu/WebModule/MRGridServlet) contains the original NMR restraint data (distance, dihedral angle and RDC) and the parsed, converted, and filtered for ~4,000 protein and nucleic acid structures with corr

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89. NMRShiftDB - NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.

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90. NOCH - NOC is a open source development toolkit and a powerful molecular explorer for protein structure visualizing,analysis,crystallographic mapping, modeling, and refinement, Gromacs/Amber MD trajectories displaying,movie making...

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91. NOSE - NOSE is a package for simulation of linear and non-linear optical and infrared spectra, including absorption, fluorescence, circular dichroism, pump-probe, photon echo and other.

Click here to download.  
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92. NullAllEst - NullAllEst is the implementation of a maximum likelihood algorithm to estimate the frequency of a null allele in microsatellite genetic data. A Markov Chain Monte Carlo simulation is used to solve the likelihood function.

Click here to download.  
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93. Octet - Octet is an object-oriented molecular representation framework written in Java.

Click here to download.  
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94. Olex2 - Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers.

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95. Open Babel - Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas.

Click here to download.  
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96. open enventory - Web-based Electronic Laboratory Notebook (ELN) with integrated Chemical Inventory by the group of Prof. Goossen (TU Kaiserslautern, Germany), based on PHP/MySQL. Allows (sub-)structure search, reaction planning, management of spectra and literature.

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97. Open ESR - A set of Fortran 77/95 libraries and drivers for the analysis of CW/Pulsed Electron Paramagnetic (Spin) Resonance spectra.

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98. Open3DQSAR - Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).

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99. openSputnik - openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database

Click here to download.  
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100. PAICE: Next-gen pathway visualization - PAICE is a rapid bioinformatics pathway-visualization tool for Illumina Solexa and Affymetrix datasets, taking into account duplicate gene copies and conditions. PAICE is designed to rapidly visualize such datasets on top of KEGG biochemical pathways.

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