Search Results for "using" - Page 15
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Showing 582 open source projects for "using"
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chipexo
model based analysis of ChIP-exo data
...MACExo has the following four steps: 1) sequencing data normalization and bias correction; 2) signal consolidation and noise reduction; 3) single nucleotide resolution border detection using Chebyshev Inequality; and 4) border matching using Gale-Shapley’s stable matching algorithm. When applied to yeast Reb1 and human CTCF ChIP-exo data, MACE is able to define TFBSs with higher sensitivity, specificity and spatial resolution, as evidenced by multiple criteria, such as motif enrichment, sequence conservation, nucleosome positioning, and open chromatin states. -
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SCaVis
Scientific Computation and Visualization Environment
...SCaVis can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Elements of symbolic computations using Octave/Matlab scripting are supported. The project was migrated to DataMelt. -
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gMol
gMol molecular graphics
We've moved to https://github.com/tjod/gMol/wiki gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces. -
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MICA-aligner
Next-generation sequencing short reads aligner based on Intel® MIC
Latest Code in GitHub: https://github.com/aquaskyline/MICA-aligner To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is ~4.85 times faster than the CPU-(multi-core)-based BWA-MEM and about the same speed as the GPU-based SOAP3-dp. Furthermore, MICA’s simplicity allows very efficient scale-up when multiple MIC boards are used in a node (3 cards gives a 14-fold speedup over 6-core BWA-MEM). -
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PDI Data Vault framework
Data Vault loading automation using Pentaho Data Integration.
A metadata driven 'tool' to automate loading a designed Data Vault. It consists of a set of Pentaho Data Integration and database objects. Thel Virtual Machine (VMware) is a 64 bit Ubuntu Server 14.04, with MySQL (Percona Server) and PostgreSQL 9.4 as the database flavours and PDI version 5.2 CE. NB: Directory version_2.4 contains the most recent Virtual Machine. The readme.txt contains info about that VM. -
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EplSite ETL
ETL Based on Perl With WEB Interface
EplSite ETL is a tool to do easy the data migrations, doing extraction, transformation, validation and load in a very fast way. It was built by people involved in data migrations so, it contains the necessary to do the migration(Extract Transformation, validation and load) and do it well. -
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ThermV
Comprehensive thermal analysis software package
ThermV thermal analysis software package aims to provide the most sophisticated automatic analysis of thermal analysis data (TG/DTG, DTA and DSC). It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. The project is... -
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KMeansAniX
Animation of kmeans clustering using X Window System
Open source animation of kmeans clustering in X Window System using the C++ libplotter library. Supports Linux, Mac, and BSD. Includes common initialization methods such as Forgy, Macqueen, random, and angular. Sample videos are available through the Files Tab above. The SVN repo is accessible thorugh the Code Tab above. Requires a C++ compiler, libplot-dev, and libncurses5-dev Mac alternative to libplot-dev: macports plotutils +x11 -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
...Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf files as an input file, our program identifies the majo -
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VertyCal
calendar based vertical table cell data management application
VertyCal, short for Vertical Calendar, is a PHP MySQLi application for creating calendar based vertical table cell data managed entries; with the output being viewable to the public and the input functions restricted to a log in access only. Removing entries may only be executed by log in status as well as adding notation to each entry as an update query. Now a WordPress plugin. see: https://wordpress.org/plugins/vertycal/ -
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Fractal Zoom Explorer
Fractal Zoom Explorer
Fractal Explorer supporting FTF and common .NET standard supported formats -
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CMIS Input plugin for Pentaho
Allows querying Content Management Systems that use the CMIS.
Imagine being able to extract from your Enterprise Content Management System, all the metadata of your documents using simple queries with a query language very close to the traditional SQL. Imagine using the information extracted for statistical purposes, for creating reports and, more generally, to analyse your document archives in a way unthinkable until now with the current tools available. All this is possible within the Pentaho Suite, the Open Source Business Intelligence platform, which is useful to the extraction and analysis of structured and semi-structured data. ... -
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LogisticBell
Here we test the Logistic Map using finite and infinite precision...
Here we test the Logistic Map using finite and infinite precision floats (Apfloats). More decimals produce longer sequence (longer chaotic signal for certain parameters). Shorter decimal precision makes the sequence converge to zero eventually. In the process, number of decimals rises and then drops for some reason, forming a bell-shaped curve with long tail. On second consideration, this does not look like a bell-shaped curve at all. -
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Debrief is an Open Source Java application used for viewing maritime vessel tracks in 2 and 3 dimensions. Tracks are read in using a number of flat-file ASCII formats, including AUTEC (RAO), PMRF and AFWTF.
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TeachingDemos
Bioinformatics related demos and tutorials using the R programming lan
Bioinformatics related demos and tutorials using the R programming language for large biological data. Licence: Creative Commons Attribution-NonCommercial 4.0 International License -
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code. -
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The Bio2RDF project aims to transforms silos of life science data into a globally distributed network of linked data for biological knowledge discovery. Bio2RDF creates and provides machine understandable descriptions of biological entities using the RDF/RDFS/OWL Semantic Web languages. Using both syntactic and semantic data integration techniques, Bio2RDF seamlessly integrates diverse biological data and enables powerful new SPARQL-based services across its globally distributed knowledge bases.
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The API library call CI5010RS422.DLL
This library designed for use with weighing terminal CI-5010A
This library, then DLL, designed for use with weighing terminal CI-5010A on the RS-422/485 or RS-232 via a physical or virtual COM port over USB in OS NT/2000/2003/XP/Vista/7/8 and reads and decodes the data of the operation, gross weight, net weight, unit number, value and sign weight, units and features indicators. Restoring communications using virtual serial port automatically. ORDER use and limitations: 1. You can optionally set the COM port in the procedure 'reinit()' with constantly raised the flag of activation in the library is being processed. 2. Parameter gl_count procedure 'getdata' indicates the number of received packets of COM-port. 3. Implemented AutoTrack pulling converter RS-485/USB (via SetupAPI) and reconnect to the specified port initialization. -
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The aoetools are programs for users of the ATA over Ethernet (AoE) network storage protocol, a simple protocol for using storage over an ethernet LAN. The vblade program (storage target) exports a block device using AoE.
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GEMPlot
GUI Program for GEMPAK
GUI Program for plotting Model & ReAnalysis Data using GEMPAK. Users can perform Model Analysis, Surface Analysis, Objective Analysis, Cross-Sectional Analysis, Isentropic Analysis, and ReAnalysis. Soundings can also be plotted for a selection of upper air stations within the CONUS. -
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giServer
giServer the easy to use and extensible batch and integration server
The giServer is an easy-to-use integration server for process automation and event-driven or scheduled execution of batch jobs. Instead of using complex XML configuration files an elaborate GUI for batch job management is included. Some possible usage scenarios are: - Automatic processing of incoming data files - Big Data applications - Process automation - Data Mining/Aggregation applications - Automatic Reporting - Processing and analysis of database records -
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XNBC: neurobiology simulation tool
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site. -
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flot
Attractive JavaScript charts for jQuery
...Works with Internet Explorer 6+, Chrome, Firefox 2+, Safari 3+ and Opera 9.5+. Additional examples are bundled with Flot. Also take a look at the Flot Usage Wiki for screenshots and stories from people and companies using Flot. Take a look at the the examples in examples/index.html; they should give a good impression of what flot can do, and the source code of the examples is probably the fastest way to learn how to use flot. Just include the JavaScript file after you've included jQuery. You need at least jQuery 1.2.6, but try at least 1.3.2 for interactive charts because of performance improvements in event handling. ... -
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QPNet
Synchronous Petri Nets' emulator
QPNet (Quick Petri Net) is a fast Petri Nets' emulator, created by students of Moscow State Technical University of Radio Engineering, Electronics and Automation. It brings benefits for the educational process, while being under further development and extension. QPNet это быстрый эмулятор сетей Петри, созданный студентами МИРЭА. Он применяется в учебном процессе, а так же продолжает разрабатываться и эволюционировать. -
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Tockit tries to build a framework for Conceptual Knowledge Processing (CKP) and Formal Concept Analysis (FCA) in Java, using a component-based approach, XML formats and a three-tier architecture.
