Search Results for "matrix structural analysis" - Page 4
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Showing 152 open source projects for "matrix structural analysis"
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Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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Open Cezeri Library
Effective Linear Algebra and Computer Vision Library with JAVA
OCL stands for Open Cezeri Library (yet another linear algebra and matrix library). This library provides rapid coding as matlab ease of use. To learn for library please try to use test examples at OpenCezeriLibrary\test\test. It is originally developed at el-cezeri laboratory of Siirt University, in order to establish generic framework of reusable components and software tools for machine vision, machine learning, AI and robotic applications. Currently, it holds following main concepts 1-... -
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beam3d
3d beam FEM structural analysis
3D FEM structural analysis using the beam element. It works with macro preprocessor and system pipes. -
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Universal Java Matrix Package
sparse and dense matrix, linear algebra, visualization, big data
The Universal Java Matrix Package (UJMP) is an open source Java library which provides sparse and dense matrix classes, as well as a large number of calculations for linear algebra such as matrix multiplication or matrix inverse. Operations such as mean, correlation, standard deviation, replacement of missing values or the calculation of mutual information are supported, too. The Universal Java Matrix Package provides various visualization methods, import and export filters for a large... -
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EDM Calibration Baseline Fitting
EDMFit is an adjustment tool to estimate EDM calibration parameters.
An EDM calibration baseline is used to derive specific instrument errors of the electronic distance measurement (EDM) unit of a total station. EDMFit is a simple adjustment tool to estimate the EDM calibration parameters (addition constant and/or scale parameter). The adjustment process is according to ISO 17123-4. The parameters are checked for significance, to avoid an overestimation. Based on two classical hypothesis testing, EDMFit provides a reliable outlier detection. For... -
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CoGA
R package for differential co-expression analysis
CoGA (Co-expression Graph Analyzer) is an R package to identify differentially co-expressed gene sets between two phenotypes. The software infers gene regulatory networks from gene expression data, and compares structural properties of the inferred networks based on their spectrum distributions. It also compares the networks in terms of their gene centralities, clustering coefficients and shortest path lengths. In addition to the differential co-expression analyses, the tool provides graphical interfaces for network visualization, ranking of genes according to their "importance" in the network, and the standard single gene differential expression analysis. -
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QuantitativeT2
Glioblastoma in mouse brain analyzed by QuantitativeT2
...It is written in XCode. The MRI data was acquired using Bruker 9.4T, 128 T2 echoes were collected for 128x128 image matrix. -
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand... -
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Copy Number Explorer
Interactive Copy Number Analysis for Cancer Genomics
Deployed online at: https://arraycgh.shinyapps.io/Copy_Number_Explorer/ https://arraycgh.shinyapps.io/Copy_Number_Explorer_Survival/ Copy Number Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes. Huge volumes of genomics data from nearly every cancer type are now freely available and several online databases have begun to collate and store this information. However, current tools focus on individual gene queries rather than... -
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ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.
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MARKOS Project
The MARKet for Open Source
MARKOS developed a prototype of a service and an interactive application providing an integrated view on the Open Source projects available the on web, focusing on functional, structural and licenses aspects of software code. -
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MSP: a 3D flocking boids simulator
A highly flexible 3D flocking boids simulator, conceived as a tool for
...The simulator delivers a 3D visual interface and provides as an output file all the instantaneous microscopic information related to each boid (positions and velocities over time), allowing in this way subsequent analysis, such as searching for synthetic and higher-level descriptions of collective behaviors, relying for instance on global network and meta-structural properties. -
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Gen3D
A tool for 3D genome and chromosome structural model construction
Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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ArchNURBS
NURBS-based elastic and limit analysis of masonry arches in MATLAB
ArchNURBS is a MATLAB tool for the analysis of planar curved structures, with a particular attention to masonry arches. As in CAD softwares, the geometry of the model is defined by a NURBS representation of the structure. Indeed, the user can upload geometries imported from a CAD environment. Based on such a representation, ArchNURBS performs the elastic isogeometric finite element analysis and the collapse limit analysis of the structure. -
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DynamicRoots
Software for the Reconstruction and Analysis of Growing Plant Roots
This is a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of... -
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CNV Explorer
Interactive Copy Number Analysis for Cancer Genomics
CNV Explorer for Gene discovery: https://arraycgh.shinyapps.io/CNV_Explorer/ CNV Explorer for survival analysis: https://arraycgh.shinyapps.io/CNV_Explorer_Survival/ CNV_Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes that happen in cancer genomes. Huge volumes of genomics data from nearly every cancer type are now freely available and several online databases have begun to collate and store this information. ... -
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igafem
Open source 3D Matlab Isogeometric Analysis Code
Isogeometric analysis (IGA) is a fundamental step forward in computational mechanics that offers the possibility of integrating methods for analysis into Computer Aided Design (CAD) tools and vice versa. The benefits of such an approach are evident, since the time taken from design to analysis is greatly reduced leading to large savings in cost and time for industry. The tight coupling of CAD and analysis within IGA requires knowledge from both fields and it is one of the goals of the... -
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fedtool
Tool to aid factorial design analysis of in vitro experiments.
...An Excel-spreadsheet tool steps the user through specifying factor names and entering the design and data from the experiment. The tool deconvolutes the data into a matrix which can be pasted into data visualisation and / or data analysis software. -
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YAFEMS
Yet Another Finite Element Method Solver
YAFEMS (Yet Another Finite Element Method Solver) is a FEM solver for Linux and WIndows that reads a MED mesh file produced by Salome (http://www.salome-platform.org/) with certain groups created into the mesh, and with the help of an input text file (.yaf), performs a 3D or 2D plane stress or plane strain analysis and creates results in plain text format and in MED format. This way a complete analysis can be carried inside Salome, where a mesh file can be created, exported and read by... -
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OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability analysis and elements of experimental design.
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PyInteraph
analysis of interaction networks in structural ensembles of proteins
...These graphs can be thoroughly analyzed using included network analysis tools, which are able to point out the most important features of the network for the discovery of paths of structural communication in proteins. The tool works best together with the xPyder PyMOL plugin ( http://xpyder.sourceforge.net ), which allows for further analysis and easily understandable representation of the calculated networks and graphs. -
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BoneSlicer
Experimental G-Code-Generator for variable density infill in FFF parts
BoneSlicer is an experimental G-Code-Generator written in Java that allows creating load-adapted infill for 3D printed (FFF) parts, inspired by the adaptive structures of trabecular bone tissue. It uses a simple structural Finite Element Analysis to determine the distribution of mechanical stress within the part and offers tools to generate an infill structure consisting of multiple subareas of varying infill density. Subdivision of the infill area can be based on a broad spectrum of FEA result parameters. BoneSlicer relies on the Open Source software GMesh and Calculix for meshing and FEA analysis. ... -
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MatrixUser
A Multi-functional GUI-based Program for Image Processing and Analysis
...Those images can be saved as multidimensional matrices in Matlab thanks to Matlab's powerful support of multidimensional data representation. However, within Matlab, most of image manipulation functions are limited or tailored for processing two-dimensional matrix. The MatrixUser is a software package which features functions designed and optimized specifically for manipulating multidimensional real or complex data matrix. MatrixUser provides a nice graphical environment for easily performing image analysis tasks including multidimensional image display, matrix (image stack) processing and rendering etc. ... -
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QUDeX-MS
Hydrogen/deuterium exchange estimation for isotopic fine structure MS
Hydrogen-deuterium exchange coupled to mass spectrometry permits analysis of structural dynamics, stability, and molecular interactions of proteins. Resolving isotopic fine structure during mass spectrometry has been recently demonstrated to allow direct detection and quantification of deuterium incorporation distinct from peaks corresponding to non-deuterium incorporated natural abundance heavy isotopomers.
