Search Results for "cell"
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Showing 36 open source projects for "cell"
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a... -
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The auditory modeling toolbox (AMT) is a Matlab/Octave toolbox for the development and application of auditory computational models. Over 50 auditory models implemented in Matlab, Octave, C, C++, and Python can be run from Matlab and Octave, on Windows and Linux. The AMT provides a well-structured in-code documentation, includes auditory data required to run the models. It integrates functionality to reproduce the model predictions. Model implementations can be evaluated in two stages,...
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atomes
Analysis, visualization, edition of 3D atomistic models
atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. atomes is a toolbox developed to analyze, to visualize and to create/edit 3D atomic scale models. atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K atomes is developed by Dr. Sébastien Le Roux, research... -
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The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.
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Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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PMCGPU
Parallel simulators for Membrane Computing on the GPU
Membrane Computing is a new research area (within Natural Computing) that aims to provide computing devices abstracted from the functioning and structure of living cells. These devices are called P systems. The objective of this project (PMCGPU) is to bring together all the researchers working on the development of parallel simulators for P systems, specially those using the GPU (e.g. CUDA, OpenCL, etc). Other parallel platforms are also welcome (multicore and manycore, FPGAs,... -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. ... -
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experix laboratory control system
instrument control, data acquisition display and analysis
...Interfaces accessible via commands and scripts: file i/o modelled on stdio and stdlib; usb control and bulk transfers; socket operations; webcam; graphics via framebuffer. Applications (not all available yet for download) include: cell poker (like an atomic force microscope); tissue mechanical tester; fluorescence photobleaching; alternating laser excitation fluorescence; fluorescence intensity distribution analysis; iverilog simulation analysis. -
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. ... -
Stop Cyber Threats with VM-Series Next-Gen Firewall on AzureGain integrated visibility across all traffic in a single pass. Deploy Palo Alto Networks VM-Series to determine application identity and content while automating security policy updates via rich APIs.
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ECMM
OMNET++ implementation of the Enhanced Community-based Mobility Model
This project enables the introduction of community-based mobility models into the OMNET++ simulation environment. These models provide many desired characteristics, such as socially influenced mobility decisions and are quite realistic. One specific model, namely the Enhanced Community-based mobility model, is very suitable for opportunistic routing research comparing to the others, because of its advanced properties. These include a pause period, conformance to the existing social ties and... -
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neuranep
Neural Network Engineering Platform
...NeuraNEP emulates a distributed processing environment capable of handling millions of microthreads in parallel, for example running neural networks with millions of spiking cells. Microthreads are general processing elements that can also represent non-neural elements, such as cell populations, extracellular space, emulating sensory activity, etc. NeuraNEP handles microthread scheduling, synchronization, distribution and communication. This project is a fork of SpikeOS (sourceforge.net/projects/spikeos) and represents a major update to that code base, including a scripting interface and low-level rewrite of several components. ... -
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OCIViz
Visualize data from the opencellid.org project
Open-Cell-Id-Visualization (OCIViz) ========================= Tools to visualize and analyze opencellid data. Create Googlemaps overlays and statistics. http://www.opencellid.org/ Contains (2013-06) >60million datasets of celltower information worldwide. This project wants to find out: * how much data was gathered where * quality of the coverage * what can you do with the data (localization etc.) -
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blutle
Small wireless board to control tiny DIY toys over bluetooth
Being powered with cell phone battery, this board can drive small toys - up to two DC motors, several input/output pins, discharge control. -
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Simulated annealing for cell tracking (assignment problem in 4D) with scheme for removing low energy nodes from consideration ("quenching").
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The project is a time domain correlator for the Cell Broadband Engine (Cell BE). It is the outcome of a master thesis conducted at the Swedish Institute of Space Physics (www.irfu.se). The project files can be found in the SVN repository.
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Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics.
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The CellBE Execution Framework (CEF) is designed to be used by anyone wanting to develop and use an algorithm executing on multiple SPEs of a Cell processor. It lets the developer concentrate on the algorithm and data.
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Forensic tool designed to extract 3GP video files (regular files, deleted or fragments), SMS (regular, erased or fragments) and address books (regular, erased or fragments) from memory dumps of motorola V3i, V3r and V3D&G cell phones.
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Cell Broadband Engine Processor optimized libraries and software from Georgia Tech, for a number of libraries for FFT, MPEG, compression, and encryption. This project also includes patches to accelerate R on the Cell Broadband Engine processor.
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This project implements the parallelized version of the LBG vector quantization algorithm on Cell Broadband Engine.
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Beam and it's follow-on I-Beam are sets of programs to produce coverage charts of radio sources. It has been used for RADAR, DME, VOR and various communications sources specific to aviation. However, it is also valid for cell phone, TV and radio towers
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You can use this Program to reconstruct images using measuring data of a new small animal PET apparatus (MedPET 2). The code is optimized for the Cell BE platform. No different types of Prozessor are supportet!
