Open Source Scientific/Engineering Software - Page 14
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Scientific/Engineering Software
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Visual Test Shell for BACnet
BACnet Tester
Visual Test Shell (VTS) is an application for testing the BACnet functionality of devices used in building automation systems. -
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GenX
X-Ray and Neutron Reflectivity Modeling
GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program. -
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Neuroph is lightweight Java Neural Network Framework which can be used to develop common neural network architectures. Small number of basic classes which correspond to basic NN concepts, and GUI editor makes it easy to learn and use.
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XSCHEM
Schematic circuit editor for VLSI and Mixed mode circuit simulation.
Xschem is a schematic capture program, it allows to create a hierarchical representation of circuits with a top down approach . By focusing on interconnections, hierarchy and properties a complex system (IC) can be described in terms of simpler building blocks. A VHDL, Verilog or Spice netlist can be generated from the drawn schematic, allowing the simulation of the circuit. Key feature of the program is its drawing engine written in C and using directly the Xlib drawing primitives; this gives top speed performance, even on very big circuits. I have succesfully managed to simulate complete VLSI projects with this tool, both digital (Verilog / VHDL) and analog (Spice). Schematics can be printed in SVG, PNG, PDF, formats. XSCHEM runs on Linux or other Unix-likes with Xorg server and on Windows with the Cygwin layer and required tools installed. Can be found also on github: https://github.com/StefanSchippers/xschem -
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FLASH
Merge mates from fragments that are shorter than twice the read length
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies. -
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Finite Element Method Magnetics
Finite element analysis of electromagnetic devices
Solves low frequency magnetic, electrostatic, heat flow, and current flow problems on 2D and axisymmetric domains via the finite element method. -
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NAVeGIS
GPS navigation software for Windows Mobile & WinCE devices.
NAVeGIS is a WinCE/Windows Mobile navigation application. -
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Qalculate! is a multi-purpose desktop calculator for GNU/Linux (now ported to Mac via MacPorts). It is small and simple to use but with much power and versatility underneath. Features include customizable functions, units, arbitrary precision, plotting, and a user-friendly interface (GTK+). Qalculate! has now moved to GitHub (https://github.com/Qalculate). Get the latest version from http://qalculate.github.io/downloads.html.
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System Stability Tester is a multi platform open source clone of SuperPI and comes with a GUI and a CLI. It can be used for CPU and RAM burning, stressing and benchmarking.
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AUDio MEasurement System
PC based Oscilloscope and Spectrum analyzer using sound card
AUDio MEasurement System - a multi-platfrom system for audio measurement through sound card in the PC. It contains: generator, oscilloscope, audio spectrum analyzer (FFT) and frequency sweep plot. Compiles and works under Linux, Windows and MacOS. Source code is available in "git" and as ZIP snapshot. For more information see README.md -
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Java Midlet to use OpenStreetMap data on a J2ME ready Mobile. Displays a moving map using external or internal GPS, shows the street name on which you are. There is Navigation support for car drivers, bicyclists and pedestrians plus many more ...
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A2L Build for MCD - AutoExtractGui
Build A2L from ELF for Automotive MCD tool (e.g. INCA)
1. A2L Builder : AutoExtractGui This tool is to help Measurement & Calibration people (e.g. INCA users) create their own A2L easily. - Please describe the MEMORY SEGMENT : this is mandatory part. - Optionally you may describe formula / min / max / unit / ... for variables. - Optionally you may describe communication specification like XCP, CCP, CAN BPS, ... - Press "Build New A2L" button to make a new A2L for the given ELF file. As a reference, you may see how this tool works with the given sample files (sample AEC, ELF, A2L). 2. ProF Builder This tool is to help people who need to make their own ProF script to FLASH their controllers through INCA. You can utilize "template" of XCP or UDS when you need to make a new ProF script. 3. INCA Instrument SDK Sample Project As a sample, I upload an Instrument project - displaying bar graph. 4. A2L Hint Help you easily read/browse A2L file, also give you some hints. -
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GLPK for Windows
Windows binaries for the GNU Linear Programming Kit (GLPK)
GLPK 4.65 (GNU Linear Programming Kit, http://www.gnu.org/software/glpk/) is a solver for large-scale linear programming (LP), and mixed integer programming (MIP). This project supplies the most recent Windows executables - 2018-03-17. Linux and OSX users should download the source distribution from http://ftp.gnu.org/gnu/glpk -
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CARLA Simulator
Open-source simulator for autonomous driving research.
CARLA has been developed from the ground up to support development, training, and validation of autonomous driving systems. In addition to open-source code and protocols, CARLA provides open digital assets (urban layouts, buildings, vehicles) that were created for this purpose and can be used freely. The simulation platform supports flexible specification of sensor suites, environmental conditions, full control of all static and dynamic actors, maps generation and much more. Multiple clients in the same or in different nodes can control different actors. CARLA exposes a powerful API that allows users to control all aspects related to the simulation, including traffic generation, pedestrian behaviors, weathers, sensors, and much more. Users can configure diverse sensor suites including LIDARs, multiple cameras, depth sensors and GPS among others. Users can easily create their own maps following the OpenDrive standard via tools like RoadRunner. -
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves, surface and volume mesh generation, spatial searching, alpha shapes, geometry processing, and many more. The use of these result in beautiful, visually complex and accurate representations. -
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Digital-Logic-Sim
A minimalistic digital logic simulator
Digital-Logic-Sim is an interactive simulation tool designed to help users understand digital logic circuits through a visual and hands-on environment. It allows users to build circuits using basic logic gates such as AND, OR, and NOT, and observe how signals propagate through the system in real time. The project emphasizes education, making it easier for beginners to grasp concepts like binary logic, combinational circuits, and signal flow. It provides a visual interface where components can be connected and tested dynamically, reinforcing learning through experimentation. The simulation engine handles signal updates and interactions efficiently, ensuring that circuit behavior is accurately represented. It is particularly useful for students and hobbyists interested in computer architecture and electronics. Overall, Digital Logic Sim serves as an accessible platform for exploring and understanding the fundamentals of digital systems. -
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ESP8266Audio
Arduino library to play MOD, WAV, FLAC, MIDI, RTTTL, MP3
Arduino library for parsing and decoding MOD, WAV, MP3, FLAC, MIDI, AAC, and RTTL files and playing them on an I2S DAC or even using a software-simulated delta-sigma DAC with dynamic 32x-128x oversampling. ESP8266 is fully supported and most mature, but ESP32 is also mostly there with built-in DAC as well as external ones. For real-time, autonomous speech synthesis, check out ESP8266SAM, a library that uses this one and a port of an ancient format-based synthesis program to allow your ESP8266 to talk with low memory and no network required. All this code is released under the GPL, and all of it is to be used at your own risk. If you find any bugs, please let me know via the GitHub issue tracker or drop me an email. The MOD and MP3 routines were taken from StellaPlayer and libMAD respectively. The software I2S delta-sigma 32x oversampling DAC was my own creation and sounds quite good if I do say so myself. -
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JAX
Composable transformations of Python+NumPy programs
With its updated version of Autograd, JAX can automatically differentiate native Python and NumPy functions. It can differentiate through loops, branches, recursion, and closures, and it can take derivatives of derivatives of derivatives. It supports reverse-mode differentiation (a.k.a. backpropagation) via grad as well as forward-mode differentiation, and the two can be composed arbitrarily to any order. What’s new is that JAX uses XLA to compile and run your NumPy programs on GPUs and TPUs. Compilation happens under the hood by default, with library calls getting just-in-time compiled and executed. But JAX also lets you just-in-time compile your own Python functions into XLA-optimized kernels using a one-function API, jit. Compilation and automatic differentiation can be composed arbitrarily, so you can express sophisticated algorithms and get maximal performance without leaving Python. -
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Vedo
A python module for scientific analysis of 3D data
A lightweight and powerful python module for scientific analysis and visualization of 3d objects. Inspired by the vpython manifesto "3D programming for ordinary mortals", vedo makes it easy to work with 3D pointclouds, meshes and volumes, in just a few lines of code, even for less experienced programmers. vedo is based on VTK and numpy, with no other dependencies. Import meshes from VTK format, STL, Wavefront OBJ, 3DS, Dolfin-XML, Neutral, GMSH, OFF, PCD (PointCloud). Export meshes as ASCII or binary to VTK, STL, OBJ, PLY formats. Analysis tools like Moving Least Squares, mesh morphing and more. Tools to visualize and edit meshes (cutting a mesh with another mesh, slicing, normalizing, moving vertex positions, etc..). Split mesh based on surface connectivity. Extract the largest connected area. Calculate areas, volumes, center of mass, average sizes etc. Calculate vertex and face normals, curvatures, feature edges. Fill mesh holes. -
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OnScreenProtractor
Simple on-screen protractror.
On-Screen Protractor is a simple java application that allows to measure an angle on the screen. Originally the program was conceived to assess the angle between north and a given point on any map open on the screen, therefore the background of the application window is transparent and the angle is measured from the positive y-axis and clockwise. The application allows to move the origin of reference axes and to rotate the axes as needed. OnScreenProtractor works correctly only in Windows context. In linux 'OnScreenProtractor_v0.7.exe' can be started with 'Wine' -
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XMedCon
medical image conversion utility
a medical image conversion utility & library; hereby hoping to lower at least one barrier in medical research projects. -
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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GPlates
Interactive visualization of plate tectonics.
GPlates is a plate-tectonics program. Manipulate reconstructions of geological and paleo-geographic features through geological time. Interactively visualize vector, raster and volume data. PyGPlates is the GPlates Python library. Get fine-grained access to GPlates functionality in your Python scripts. -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
MAGeCK2 is here: https://github.com/davidliwei/mageck2 Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support from Claudia Adams Barr Program in Innovative Basic Cancer Research and NIH/NHGRI to develop MAGeCK. -
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foam-extend
Open Source CFD Toolbox
The foam-extend project is a fork of the OpenFOAM® open source library for Computational Fluid Dynamics (CFD). The goal of this project is to integrate community contributions to the foam-extend CFD simulation toolbox. It is an open project welcoming and integrating contributions from all users and developers.
