Search Results for "java" - Page 18
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Showing 691 open source projects for "java"
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Jazoo. The Zoo of virtual evolving creatures. Mostly focused on evolving communication between intelligent agents. It's in VERY early stage. Everyone's invited to join, participate, suggest, discuss etc.
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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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mzSquash is a compression tool for mzML files, an XML-based standard developed by HUPO PSI (http://www.psidev.info) for spectrometer output. All development has ceased. The tool may be useful educationally, but is not a recommended utility.
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TiMAT2 contains tools for low and high level genomic tiling microarray analysis using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments.
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Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.
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XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.
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Testing tools source code of the Integrating the Healthcare Enterprise (IHE) PIX and PDQ v3 Integration Profiles
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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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The Shrimp suite provides interactive visualizations of graph-based data. Creole (Eclipse plug-in) visualizes Java source code. Jambalaya (Protege plug-in) visualizes ontologies (including OWL), & Stand-Alone Shrimp visualizes RSF/GXL/PRJ/PPRJ files.
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BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.
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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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Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.
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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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http://ewi.utwente.nl/~biorange/rshell - The RShell project is a plugin for the Taverna workflow system. It enables one to execute R scripts within the Taverna workflow system. The RShell processor is built on the RServe project. For more info:
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User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files
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FreeLIMS | Free LIMS
Laboratory Information Management System
FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free. -
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A polynomial-time algorithm for constructing level-2 phylogenetic networks from dense sets of rooted triplets.
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Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
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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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A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. It contains functionalities of ESTs for EST submission, Batch BLAST and BLAST result parser, etc. easiEST contains JAVA GUI applications for analysing ESTs or other sequences
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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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SeEvolution is the first application that lets you see the effects of mutation events on 3D models of chromosomes. It takes you on a journey through time, showing you the changes that are necessary to go from the genome of an organism to another.
