Search Results for "research" - Page 55
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Showing 2809 open source projects for "research"
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MicrobeGPS
The Explorative Taxonomic Profiling Tool for Metagenomic Data
MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner. One main focus is reliability: the tool calculates quality metrics for the estimated candidates and allows the user to identify false candidates easily. -
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fitGCP
Fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for.... -
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*WARNING* gtburst moved to github (https://github.com/giacomov/gtburst). ########################################## gtBurst is a tool to download data, analyze and simulate Gamma-ray Bursts and Solar Flares as observed by the NASA Fermi satellite.
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Pymedia is a C/C++/Python multimedia module to allow encode/decode/play multimedia information in mp3,ogg,avi etc. formats. Based on ffmpeg with added features and simple Python interface. To be used in multimedia apps written in Python.
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Community Linux
USB Drive Writable Linux Distribution
Community Linux is a USB drive based fully functional writable Linux Distribution. It boots and runs with a comparable speed as a hard drive installation. Community Linux allows one to create a low cost solid state development and production platform. For new ComLin drive creation, one needs to download the full install (comlin-016.tar.gz) ... (not just the scripts) Update: Community Linux will now run on most every machine. Update: Added Sound drivers, Intelligent... -
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This project provides a Fortran90 library and a python module for singular spectrum analyses such as PCA/EOF or MSSA. It is intended for people interested, for example, in analysing climate or financial variability.
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MetaNet
Free portable library for meta neural network research
MetaNet provides free library for meta neural network research. MetaNet library contain feed-forward neural net realisation and several integrated dataset (MNIST). -
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SCaVis
Scientific Computation and Visualization Environment
SCaVis is an environment for scientific computation, data analysis and data visualization for scientists, engineers and students. The program is fully multiplatform (100% Java) and integrated with Java and a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. 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... -
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KEMP
A FDTD solver for electromagnetic wave simulations on a GPU cluster
KEMP is a fast FDTD solver on a GPU-based cluster. The FDTD (Finite-Difference Time-Domain) method is a popular numerical method for electromagnetic field simulations. KEMP enables hardware accelerations suitable for multi-GPU, multi-core CPU and GPU cluster. KEMP also provide easy configuration by using Python scripting language. -
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ccwatcher
A computational chemistry monitoring, parsing and plotting application
ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies. -
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xmipp
Image processing suite for Electron Microscopy
XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es -
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Valence
Fast, Dynamic, and Extendable/Mergeable Workflow Management System
Agile protocol development and workflow management of pipelines. Simple enough for a low barrier of entry, but powerful enough to manage large procedures. Includes APIs in Python, Ruby, Java, and Perl to assist in the creation of Drivers that can create new workflows on the fly. Greatly facilitates merging and extending pipelines between groups/developers. -
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Research Master
wxpython research organization tool with LaTeX flashcards
ResearchMaster is a tool that you can trust to help with organization, multitasking, and research. ResearchMaster provides a place to capture your fleeting thoughts and ideas, and it allows you to hit-the-ground-running on projects. -
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OSTIS - Open Semantic Technology for Intelligent Systems. This is an open project focused on mass semantic technology creation used in component-based design of various intelligent systems.
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SimpleAstroCapture
Serial Camera Trigger and Dithering by PHD for use in astrophotography
This program allows users to control their camera triggers via the bulb function and a serial cable trigger. The program has a manual mode (start and stop exposure with a button), a timer mode (program exposure time, number, and delay between exposures) and dither mode (program exposure time, number, and dither between shots using PHD guiding). More options may be added in the future. Currently uses an intuitive Graphical User Interface. -
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sfunctioner is a GUI wizard written in PyQt for creating Matlab Simulink sfunctions quickly and efficiently. It helps creating a fully functional sfunction within a few minutes.
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psignifit is a toolbox to fit psychometric functions and test hypotheses on psychometric data. This is version 3 which will now predominantly support python.
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting... -
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IMAGINE
Biological image viewer and processor
Detection, enumeration, and sizing of biological organisms by image analysis. -
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MicroView is a 2D/3D image viewer and analysis tool. It is written in Python and uses VTK for all of its graphical capabilities.
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PyBrella
Python script to automate umbrella sampling with AMBER
PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package. -
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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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AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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theZoo
A repository of LIVE malwares for malware analysis and security
theZoo is a project created to make the possibility of malware analysis open and available to the public. Since we have found out that almost all versions of malware are very hard to come by in a way which will allow analysis, we have decided to gather all of them for you in an accessible and safe way. theZoo was born by Yuval tisf Nativ and is now maintained by Shahak Shalev. theZoo’s purpose is to allow the study of malware and enable people who are interested in malware analysis (or maybe...
