Search Results for "gnu" - Page 3
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Showing 80 open source projects for "gnu"
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A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.
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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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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.
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A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.
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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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CIP-FOSS will serve as a common entry page for Free and Open Source Software developed at the International Potato Center (CIP), Lima, Peru (http://www.cipotato.org).
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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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ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.
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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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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.
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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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Janocchio is an application or applet for viewing 3D molecular structures and calculating NMR couplings and NOEs
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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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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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IntiMap is a convenience tool to run the MS-DOS command-line tool MapPop for selective genotyping. It adds facilities to prepare genotyping data files, manage genotype sets and visualize mapping results (genetic marker maps).
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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, tracker, and source code repository can be found on https://jchempaint.github.io
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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
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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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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.
