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Showing 622 open source projects for "mx-linux"
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miRDiana
MATLAB package to find the miRNAs targeting a list of genes
To select miRNA target genes we developed software in MATLAB® (MathWorks®) called miRDiana that collects the union of mouse validated targets from the TargetScan, MicroCosm, mirTarBase and miRWalk 2.0 databases. Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database. Next, for... -
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ebfformat
An Efficient Binary data Format
EBF, which stands for Efficient Binary Format, is a binary file format for reading and writing binary data easily. Reading writing routines are currently available in C,C++,Fortran,Java, Python, IDL, MATLAB. A program called ebftkpy which has a set of utility functions to work with the .ebf files , e.g., viewing the contents and getting a summary, is also provided. The EBF specification is designed to be concise and easy to understand to make it easier for others to write their own code... -
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Relative Overestimation VOP
VOP compression for MRI with overestimation control
**** This work is outdated! For better compression and speed use these: ***** https://sourceforge.net/projects/enhanced-sar-compression/ Virtual Observation Points SAR compression. Contains multiple Algorithms: Compression according to Eichfelder et al. and Lee et al. The Lee algorithm is enhanced by including overestimation control to reduce maximum relative overestimation. All algorithms are implemented in Matlab and were optimized for enhanced speed. Needs Matlab R2016b at least.... -
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PRMLT
Matlab code of machine learning algorithms in book PRML
This Matlab package implements machine learning algorithms described in the great textbook: Pattern Recognition and Machine Learning by C. Bishop (PRML). It is written purely in Matlab language. It is self-contained. There is no external dependency. This package requires Matlab R2016b or latter, since it utilizes a new Matlab syntax called Implicit expansion (a.k.a. broadcasting). It also requires Statistics Toolbox (for some simple random number generator) and Image Processing Toolbox (for... -
Choose from a complete set of software solutions across EHSQ that address all aspects of top performing Environmental, Health and Safety, and Quality management programs.
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TauFactor
MatLab App for calculating the tortuosity factor of microstructure
Please contact the author at sjc08@ic.ac.uk for any questions or if you wish to cite this application in a academic study. Journal paper available here: http://www.sciencedirect.com/science/article/pii/S2352711016300280 TauFactor is a MatLab application for efficiently calculating the tortuosity factor, as well as volume fractions, surface areas and triple phase boundary densities, from image based microstructural data. The tortuosity factor quantifies the apparent decrease in... -
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A2RMS Algorithm
Implementation of the A2RMS Algorithm in Matlab
Implementation of the A2RMS Algorithm for univariate densities defined for real values. -
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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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OpenFace
A state-of-the-art facial behavior analysis toolkit
OpenFace is an advanced facial behavior analysis toolkit intended for computer vision and machine learning researchers, those in the affective computing community, and those who are simply interested in creating interactive applications based on facial behavior analysis. The OpenFace toolkit is capable of performing several complex facial analysis tasks, including facial landmark detection, eye-gaze estimation, head pose estimation and facial action unit recognition. OpenFace is able to... -
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Phenalysis
Analyze agronomic plant research plots in aerial orthomosaic images.
A graphical user interface to import, analyze and export plots from orthomosaic images of agronomic trials. Please cite the following reference in your work if you use Phenalysis: Khan Z and Miklavcic SJ (2019) An Automatic Field Plot Extraction Method From Aerial Orthomosaic Images. Front. Plant Sci. 10:683. doi: https://doi.org/10.3389/fpls.2019.00683 This tool is being developed through the sponsorship of the Australian Research Council's Industrial Transformation Research Hub on... -
It protects your internal resources such as behind-the-firewall applications, teams, and devices.
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PsPM
A matlab suite for Psycho-Physiological Modelling
PsPM is a powerful tool for psychophysiological modelling. It includes linear convolution models and non-linear models for SCR, and allows for modelling of other signals, too. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although... -
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FeRaL
Finite Element Rapid Analysis Lab
FEMM procedures to analyse rotating machines. -
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TracTrac
Massive Object Tracking Software (Matlab/Python)
TracTrac is a Particle Tracking Velocimetry (PTV) software which is extremely fast (more than 10k points tracked per second, 100k under python) and accurate (up to 0.01 pixel resolution), forming thus a good concurrent to the state-of-the art PIV/PTV algorithms. It allows to track anything that moves: birds, ants, grains, water flows... It runs on Python (v2&3) or Matlab (>2012a with Image Processing toolbox). Give it a try ! Get the last sources on GitHub:... -
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A symbolic framework for C++, Python and Octave implementing automatic differentiation by source code transformation in forward and reverse modes on sparse matrix-valued computational graphs.
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DSeg software
A MATLAB program to segment filamentous bacteria and hyphae structures
The analysis of microscopy image has been the basis to our current understanding of the cellular growth and morphogenesis. The quantitative evaluation of morphological changes in the biological processes is therefore important to characterize cell structures. Here we present an image analysis tool DSeg to overcome the difficulties in finding complicated elongated cell shapes by using time-lapse data and cell morphological constraints. A fast binary level-set based algorithm is implemented... -
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Liberal Learning Seminar
Code for a freshman seminar in animal behavior
At Winston-Salem State University, 'Liberal Learning Seminars' are freshman seminars that teach skills such as critical thinking and oral communication. This code is for one such seminar, called Why Animals Do It, which will be offered at WSSU beginning in 2016. The program will combine several simulation models and allow students to alter parameters and use computers to study animal behavior. All student interactions will be through a friendly user interface -- no coding is required by students. -
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Sensitizer
A toolset to automate STOP analysis with Zemax OpticStudio
SENSITIZER is an ESO software toolset written in Matlab and Mathematica aiming at automating some Structural/Thermal/Optical Performance (STOP) sensitivity analyses with Zemax OpticStudio (ZOS). The core code of SENSITIZER runs in MATLAB and drives ZOS in the background through the ZOS-API interface, based on .NET. The output is saved in the MATLAB file format and can be post-processed using MATLAB and/or Mathematica routines. The optical system to analyze is defined in a normal Zemax lens... -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) -... -
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ADiGator
A MATLAB Automatic Differentiation Tool
ADiGator is a source transformation via operator overloading tool for the automatic differentiation of mathematical functions written in MATLAB. Given a user written file, together with information on the inputs of said file, ADiGator uses forward mode automatic differentiation to generate a new file which contains the calculations required to compute the numeric derivatives of the original user function. Furthermore, these calculations are written entirely in the native MATLAB language,... -
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CorThiZon
Cortical Thickness of brain by Zones
CorThiZon is a Matlab toolbox. MRI 3D T1 images are treated to estimate cortical thickness by zones in native and normalized space. It uses a Laplace-based technique following brain segmentation. Results can be easily reported in Excel files for further statistical analysis. If you use this toolbox, please reference: ‘Early diagnostic of Alzheimer’s disease using cortical thickness: impact of cognitive reserve', Querbes O, Aubry F, Pariente J, Lotterie JA, Démonet JF, Duret V, Puel M,... -
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SegyMAT is a set of Matlab/Octave m-files to read and write SEG Y data following SEG Y Revision 0 and 1
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Advanced Vehicle Simulator
Advanced vehicle simulator
This project holds the latest releases for canonical versions of the ADVISOR® Software and "Advanced Vehicle Simulator". ADVISOR is a MATLAB/Simulink based simulation program for rapid analysis of the performance and fuel economy of light and heavy-duty vehicles with conventional (gasoline/diesel), hybrid-electric, full-electric, and fuel cell powertrains. New features are developed under the title "Advanced Vehicle Simulator". Periodically, stable versions of Advanced Vehicle Simulator will... -
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iTides
an internal tide generation GUI (in Matlab)
With the support of the NSF and ONR over the past few years we have developed a MATLAB tool that calculates the internal wave field generated by barotropic tidal flow of a nonlinearly stratified fluid past any arbitrary two-dimensional topography of finite extent You can download a recent version as a .zip file or get up-to-date version via the svn version (svn checkout svn://svn.code.sf.net/p/itides/svn/trunk itides-svn). -
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OpenOCL Matlab
Optimal control, trajectory optimization, model-predictive control.
The Open Optimal Control Library is a software framework in Matlab/Octave for modeling optimal control problem. It uses automatic differentiation and fast non-linear programming solvers. It implements direct methods. In the backend it uses CasADi and ipopt. -
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ATLAS_mPBPK
Modeling and Simulation of mPBPK models
ATLAS mPBPK is a MATLAb-based tool for modeling and Simulation of minimal Physiology Based Pharmacokinetic (mPBPK) models of small and large molecules. The tool enables the users to perform: i) PK data visualization, ii) simulation, iii) parameter optimization, and iv) local sensitivity analysis (SA) of mPBPK models in a simple and efficient manner. -
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