Search Results for "research"
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Showing 49 open source projects for "research"
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AquaTerm is a Mac OS X grahics renderer. It allows command line applications written in ObjC, C, FORTRAN, Lisp, Perl or Python to display vector graphics, text and images using a simple API. Adapters for gnuplot, PGPLOT, and PLplot exists as well.
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GPLIGC is a program for analysis and 3D visualization of GPS tracklogs (in igc format) as recorded by flight data recorders used by glider pilots.
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scriptLattes is an open-source system to create academic reports of groups based on curricula vitae of the Brazilian Lattes Database.
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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the...
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MOIRAI
Simple Scientific Workflow System for CAGE Analysis
Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data.... -
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ZENBU is a data integration, data processing, and visualization web system based around three main web interfaces : an expression data enhanced genome browser interface, a secured user system for data upload and secured data sharing, and a data explorer interface to find and manipulate data across the many supported experimental data types and to find shared user configurations ZENBU is built as a web2.0 client/server application with javascript web clients and c++ server infrastructure.
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular... -
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CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.
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bnns
Research tool for interactive training of artificial neural networks.
BNNS is a research tool for interactive training of artificial neural networks based on the Response Function Plots visualization method. It enables users to simulate, visualize and interact in the learning process of a Multi-Layer Perceptron on tasks which have a 2D character. Tasks like the famous two-spirals task or classification of satellite image data. -
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ActiveGEM contains a set of perl/Tk graphical interfaces for the GEMPAK meteorological diagnostics and plotting package. These research-oriented interfaces provide easy access to low-level GEMPAK functions and allow for the maximum possible flexibility.
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allink
Software for data analysis, image processing, simulations, solver.
Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the... -
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ValiTerms
Validation of terms in corpus
ValiTerms is a tool that helps the validation of terms in corpus. It finds their occurrences and allows terminologists to choose if a term is relevant or not. ValiTerms is developed at LIPN (http://www-lipn.univ-paris13.fr), RCLN team. Please consult the wiki for instructions about installation and usage. -
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Plotmeister is a data exploration tool. It parses your ASCII data and generates a simple (text-based) table format. You can modify this table and eventually create nice looking figures.
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Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.
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The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.
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CNV-WebStore is an integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Contact system admin at http://cnv-webstore.uantwerpen.be for installation scripts
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PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.
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breve is a free, open-source 3D multi-agent simulation package designed for simulating decentralized systems and artificial life.
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IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
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A set of command line tools to extract, manipulate, and present multidimensional data. These tools are targeted specifically at summarizing results of simulation experiments.
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Quaternions are numbers with 4 parts: one for time, three for space.This project creates command line functions that generate thousands of points of quaternions, for the animation software. Think: analytical animation! See VisualPhysics.org examples.
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Peakplot is a Perl implemented freely available software application which labels peptide tandem mass spectra retrospectively after a Mascot database search. Availability: http://fgcz-peakplot.uzh.ch/
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Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.
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