Open Source Scientific/Engineering Software - Page 89
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Scientific/Engineering Software
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The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs. -
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TheoDORE
Theoretical Density, Orbital Relaxation and Exciton analysis
The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a general purpose program suite for the analysis of excited states obtained from quantum chemical excited state calculations. Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole, ...) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities. Code development moved to github: https://github.com/felixplasser/theodore-qc -
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The Time2 Java library provides generic time series with configurable time domains.
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Tkgames is a site for games written using the powerful tcl/tk language. These include my original tesselation puzzle Polypuzzle, and recent additions Hearts, Spider, Yahtzee and the tooo addictive, Tktk.
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TopoCad France
French Geographic Information System
topography oriented GIS for cadastre maintenance fully configurable and totally autonomous (can be transfered to USB key) . -
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TopoGen is a small PyGTK application which will make a topographic image overlay for Google Earth using the given coordinate boundaries.
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Turing and Post Machines: C++ Simulators
Turing and Post Machines' C++ Simulators
The C++-programs simulate : Nondeterministic/Deterministic Multitape Turing & Post Machines, Universal Turing Machine, Turing Machine with faults, failures and recovery. -
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Ultrashort Pulse Propagator
A powerful simulation for designing femtosecond lasers and amplifiers.
This is a simulation package developed for numerical simulation of ultrashort pulse propagation in optical media and pulse generation from mode-locked lasers. Although the code is primarily intended for investigations of fiber links, fiber amplifiers and fiber lasers, it can be applied to any other setting for which the governing equiations are valid. The physics included in the code is based on a generalized nonlinear Schrödinger equation, including higher order dispersion, stimulated Raman effect, gain with bandwidth limitation and saturation, loss, and saturable absorption. Disclaimer: The simulation code is provided free of charge for the use of the academic community only. We kindly ask the users to acknowledge use of the code in academic settings. We do not accept responsibility for any errors or omissions that may be present. Çağrı Şenel, Punya Prasanna Paltani, Fatih Ömer Ilday -
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Ump is an easy to use math program that plots in both 2D and 3D. Ump also handles complex numbers, matrices, arbitrary sized integers and ratios.
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Uranie
Uranie is CEA's uncertainty analysis platform, based on ROOT
Uranie is a sensitivity and uncertainty analysis plateform based on the ROOT framework (http://root.cern.ch) . It is developed at CEA, the French Atomic Energy Commission (http://www.cea.fr). It provides various tools for: - data analysis - sampling - statistical modeling - optimisation - sensitivity analysis - uncertainty analysis - running code on high performance computers - etc. Thanks to ROOT, it is easily scriptable in CINT (c++ like syntax) and Python. Is is available both for Unix and Windows platforms (a dedicated platform archive is available on request). Note : if you have downloaded version 3.12 before the 8th of february, a patch exists for a minor bug on TOutputFileKey file, don't hesitate to ask us. -
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VHDL Notepad++ Plugin
VHDL Plugin for the Notepad++ Editor
VHDL plugin based on http://sourceforge.net/projects/nppvhdlplugin/ This version is enhanced to include: - Insert Instantiation - Insert Signals - Create Test Bench Framework - Insert Component - Make comments Doxygen compliant - Create New Behavioral/Structural Entity Template - Create New Package File Template - Insert Synchronous Process - Insert Asynchronous Process - Insert a Default Header The default header is set in the vhdlConfig.txt file. -
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Statistical program, somewhat like shareware DataFit. You may provide a custom template (or exchange the template library with your friends or Internet including sf.net) and test your tabled data. Calculates F-ratio.
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VariabilityAnalysisInNetworks
An R package for identifying biologically perturbed networks
The VAN package enables an integrative analysis of (i) gene expression data with protein-protein interaction networks or (ii) gene and microRNA expression data with microRNA-gene interaction networks to identify biologically perturbed networks. -
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WaveAnalizer is a tool, that extracts all the data from a wave-file to a readable ascii-textfile. Now one can analyze this data with gnuplot or other programs.
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WiimoteCommander is a tool for connecting a wii remote or "wiimote" (with extensions) to a PC (Windows or Linux) or a MAC. You can then see up to 7 wiimotes and extensions in order to manage them (events, rumble, speaker, LEDs, and 3D viewer).
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XISMuS
X-Ray Imaging Software for Multiple Samples
ATTENTION: Cumulative update 2.5.0 has been released!! The update works for any previous 2.x.x version. If upgrading from version v1.x.x, please download and install v2.0.0 first. IMPORTANT FIXES in respect to base v2.0.0 version: v.2.5.0 introduces the Differential Attenuation and Cube Viewer utilities, and migrates user database to *.json files v2.4.3 fixes a with K element in the fit-approx method v2.4.3 fixes and issue where saving plots with fit-approx or a auto-wizard could freeze the software v2.4.2 introduces Image Viewer to Mosaic v2.4.1 fixes an issue in merging H5 or EDF datasets with Mosaic Full changelog at https://linssab.github.io/history X-Ray Fluorescence Imaging Software for Multiple Samples is an open source software to manipulate and study macro-X-Ray Fluorescence (MA-XRF) datasets. XISMuS also works as a sample management tool, where you can easily change between datasets (samples) and compare, cross-interact and normalize them. -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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Zhu3D is an interactive OpenGL-based mathematical function viewer. You can visualize functions, parametric systems and isosurfaces. The viewer supports special effects like animation, morphing, transparency, textures, fog and motion blur.
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beben - DICOM to STL
builds a 3D model based on a contours from a DICOM RTStructures file
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bmrblib
The BMRB library
Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format. -
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cafe
CAFE: Computational Analysis of gene Family Evolution
CAFE: Computational Analysis of gene Family Evolution -
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Spreadsheet Template for Structural Engineering (FEA Analysis for beams, trusses, 2D-frames). It makes possible to create your own parametric models.Templates for engineering calculation (fatigue, concrete plates, etc)
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csv4students
This repository is a data storage backup for my students.
这个仓库是我为学生开设的一个数据存储备份，在没有本地数据的时候，这个数据备份是一个最好的选择. This repository is a data storage backup that I run for my students and is a great option when local data is not available. -
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ctqa-cp
Automatic analysis of CT images of the CatPhan600/504 phantom
Hosted at google code, for latest version please go to: https://code.google.com/p/ctqa-cp/ Automatic image quality analysis of computed tomography images of the CatPhan? phantom. CTQA is a software package to aid in quality assurance of image quality for CT scanners. The software currently only supports analysis of CT-images of the CatPhan600? phantom. Other phantoms may be supported upon request. The purpose of CTQA-cp is twofold: 1) To handle and analyze image sets consisting of a few thousand images that is commonly obtained from image quality assurance protocols on CT scanners. 2) Easily provide results that can be copied to your favorite word or spreadsheet processor, or be saved to disk.