Search Results for "matrix structural analysis" - Page 5
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Showing 152 open source projects for "matrix structural analysis"
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
...PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level. -
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piv_clustering
structural clustering of atomic trajectories based on PIV
...Alternatively, also the SPRINT topological coordinates can be employed, that are particularly suited for nanostructures. The output is a partitioning of the trajectory into a few structural clusters (i.e., sets of frames), allowing for simpler analysis and visualization. Please read and cite Gallet & Pietrucci, J. Chem. Phys. 139, 074101 (2013) -
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ExafsArchitect
A tool kit for EXAFS/XAS/XES Analysis
ExafsArchitect helps you to create molecular models (or grids of molecular models) that allows you, by systematically varying the coordinates of ligands relevant to Chemistry and biology, to easily calculate and evaluate structural effects in EXAFS/XAS and XES spectra using FEFF and/or ORCA. -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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TikzCivilEng
Useful set of Tikz drawings for Civil Engineers
This project aims to build a big set of Tikz Drawing, that are useful for the creation of Reports in Civil Engineering. The main topics are: Structural Analysis and Geomechanics at the moment, since those are the kind of drawing I need at the time (I am still studying). -
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DNAA is the DNA analysis package, for analyzing next-generation post-alignment whole genome resequencing data. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.
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Fast Matrix for Java
General purpose matrix utilities for Java in Parallel Computing
Fast Matrix for Java (fm4j) is a general-purpose matrix utility library for computing with dense matrices. fm4j encapsulated different underlying implementations and select the optimal one in run-time depending on the size of the input matrix. Moreover, fm4j employs Java (Tm) Concurrency to take advantage of the computation power of multi-cor processors. -
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SymSAP
SymSAP - A Symbolic Structural Analysis Program
SymSAP is a little program, written in Maxima language, to perform symbolic matrix analysis of structures. SymSAP aims to become a powerful didactic tool to help students learn structural analysis. -
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THE tool for monitoring traceability between requirements and Java code. Create a traceability matrix using annotations. Report format: HTML.
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Component for structural analysis (graph-based concept and entity linking, segmentation and alignment of comparable texts)
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SecStAnT
Secondary Structure Analysis Tool for data selection and statistics
SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only... -
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TextProcessor
A Java package to preprocess text datasets for posterior text analysis
The TextProcessor Java package is a text processing toolkit, which provides some frequently used text processing functions such as stemming, removing stop-words, generating a term vocabulary, and calculating the term-doc frequency matrix. Basic topic mining models such as LDA and sparse NMF are also supported. The package can also generate feature files from a given text dataset with LDA and LIBSVM format for posterior procedures such as classification or clustering. The toolkit is also being extended for more advanced text analysis tasks based on natural language processing techniques. -
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ParaSim
Parallelized calculation of molecular similarities
Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently... -
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NAL Numerical Analysis Library
NAL Numerical Analysis Library
NAL is a numerical analysis library made of template-based c++ files. The library can be compiled as a static library, dynamic library or linked directly with other programs. Each module may also be used as a stand-alone component. -
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Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data. -
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SketchStruct
Structural analysis for Google Sketchup
This is a plugin written for Google Sketchup to perform structural analysis. Currently the plugin is limited to pin jointed trusses but the fully developed version of the plugin will include rigid jointed 3d frames with various loading conditions -
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X3DBio2
A visual analysis tool for biomolecular structure comparison
A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) protein structures. X3DBio2 is a visual analysis tool for 3D biomolecular structure comparison that allows for a clear comparison between similar structures from various species, for elucidation of structural effects of mutations, and for assessment of snapshots from molecular dynamics trajectories. -
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PeabraiN
A PIPE Extension for Performance Estimation and Resource Optimisation
PeabraiN tool is a collection of PIPE (Platform Independent Petri net Editor) modules for computing bounds, resource optimisation, and more bizarre properties on the Petri nets. Namely, the feature supported by PeabraiN are, namely: Performance Estimation, Resource Optimisation, Structural Enabling, Structural Marking, Visit Ratio Computation, and SPN Simulation Analysis. For more details, see the project website at http://webdiis.unizar.es/GISED/?q=tool/peabrain -
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The neuroimaging in python (NIPY) project is an environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).
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PyPedal is a Python module that provides tools for the manipulation of pedigrees, simple visualization of pedigrees, and the calculation of measures of genetic diversity from pedigrees.
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Phenex is an application for annotating taxa and phenotypes in character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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The Xtal System is a comprehensive suite of small molecule structural solution, refinement and analysis software, supporting both X-ray, neutron and electron diffraction data. It runs on both Unix and MS Win32 platforms and uses tcl/tk graphics.
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The TIMTAM (Target Information Management Tracking And More) system implements a secure knowledgebase supporting the management, tracking, and analysis of experimental data associated with structural biology projects.
