Search Results for "linux utilities"
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Showing 32 open source projects for "linux utilities"
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Bowtie 2
A fast and sensitive gapped read aligner
Bowtie 2 is a fast, memory-efficient genomic read aligner used to map sequencing reads against long reference sequences such as mammalian genomes. It is especially effective for reads ranging from around 50 bases to hundreds or thousands of characters, and it supports modern sequencing workflows that require gapped, local, and paired-end alignment. The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs... -
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GROMACS
Public/backup repository of the GROMACS molecular simulation toolkit
GROMACS is a molecular simulation toolkit focused on high-performance molecular dynamics. It is widely used for biomolecular systems such as proteins, lipids, nucleic acids, solvents, and ligand interactions. The software is optimized for speed and supports modern CPU and GPU acceleration for large and demanding simulations. It includes tools for system preparation, running simulations, trajectory processing, analysis, and workflow automation. GROMACS is especially strong in computational... -
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Intrinsic Core
Local runtime, SDK, and hardware agnostic, real-time control framework
Intrinsic Core is an open, local robotics runtime and SDK for building industrial automation and AI-enabled robotic applications. It provides a preconfigured environment where core robotics services and capabilities are designed to operate together. Built-in functionality includes grasp planning, AI perception, digital twins, simulation, and hardware execution. A hardware-agnostic real-time control framework lets applications switch robot arms and grippers through a unified abstraction... -
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GNU SPICE GUI provides a GUI front-end for various freely available electronic circuit simulation engines ie. NG-SPICE and GNU-CAP. It's core function is to generate simulation engine instructions based on user input. However, it also offers extra functionality via applications and utilities developed by others. Electronic Design Automation (EDA) tool suites are used to provide schematic capture and editing, and schematic to netlist conversion. Waveform data viewers are used to display...
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QMCF2
Quantum Mechanical Charge Field - Molecular Dynamics
...The source includes force-field, electrostatics, constraints, thermostats, pressure control, water models, QMCF/QM-MM, external-QM interfaces, conversion tools, and analysis utilities. Interfaces are available for xTB, DFTB+, Gaussian, Turbomole, CRYSTAL, and ASE-based workflows. External programs must be installed separately. Installation: open the Code tab and download or clone the complete repository. On Linux, open a terminal in `qmcf2_installer` and run: `python3 qmcf2_installer.py3` Review the detected compilers, libraries, paths, and warnings, then start the build. ... -
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APTTools
A collection of utilities for atom probe tomography analysis
A collection of command-line tools for atom probe analysis including: * Point data XML scripting language, load, transform, resize and otherwise alter point data * Radial Distribution Function analysis tools * Level-set tools for simulating shape transformations during experiments -
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GridLAB-D is a new power system simulation tool that provides valuable information to users who design and operate electric power transmission and distribution systems, and to utilities that wish to take advantage of the latest smart grid technology. It incorporates advanced modeling techniques with high-performance algorithms to deliver the latest in end-use load modeling technology integrated with three-phase unbalanced power flow, and retail market systems. Historically, the inability...
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The FMI++ Library
A High-level Utility Package for FMI-based Software Development
The Functional Mock-up Interface (FMI) specification intentionally provides only the most essential and fundamental functionalities in the form of a C interface. On the one hand, this increases flexibility in use and portability to virtually any platform. On the other hand, such a low-level approach implies several prerequisites a simulation tool has to fulfill in order to be able to utilize such an FMI component. The FMI++ library addresses this problem for models and tools with... -
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xc3sprog is a suite of utilities for programming Xilinx FPGAs, CPLDs, and EEPROMs with the Xilinx Parallel Cable and other JTAG adapters under linux. Originally based on code written by Andrew Rogers (http://www.rogerstech.co.uk/ ).
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A reworking in C++ of KBMAG. A package and C++ library for computing automatic structures and confluent rewriting system for group and coset rewriting systems, and for computing with finite state automata
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A... -
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allink
Software for data analysis, image processing, simulations, solver.
Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the... -
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Piklab
IDE for PIC microcontrollers
Piklab is an integrated development environment for applications based on PIC and dsPIC microcontrollers. The GNU PIC Utilities, SDCC, PICC, PIC30 toolchain, ICD2 debugger, PICkit1, PICkit2, PicStart+, GPSim and most direct programmers are supported. -
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SL is a suite of C++ template classes that support geometric computation (specifically adapted to OpenGL). It includes many different kind of algorithms (linear algebra methods, coding/decoding tecniques, generalized data structures, utilities).
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FoxHive
Library and tools for storing and retrieving arbitrary metadata
FoxHive is a general purpose cross-platform library and utilities for storing and retrieving semantic meta-data associated with files. Where metadata is stored in: a special directory, extended file attributes, embedded e.g. XMP, nepomuk or xesam. -
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OpenPMU is a collaborative project developing a software defined Phasor Measurement Unit for Smart Grids and electrical utilities. This project is currently hosted by Queen’s University Belfast.
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General numerical simulation software in C++. Provides a basic and very general library to automate simulation housekeeping details such as configuration file managment. Utilities and examples are also planned. [[WE HAVE MOVED TO GITHUB http://github.com/tgrigera/glsim ]]
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The Sick LIDAR Matlab/C++ Toolbox offers stable and easy-to-use C++ drivers for Sick LMS and Sick LD LIDARs. It provides a Matlab Mex interface for streaming LIDAR returns directly into Matlab. Also included are config utilities, examples, and tutorials.
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Core program and associated utilities for building a machine translation system using the Example-Based paradigm, where previously-translated text is used to infer new translations of previously-unseen text.
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Many people have met the challenge of finding out their location, while not having a gps. We have developed a solution to this challenge. wLBS is the world's first completely open Wi-Fi geolocation system.
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Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
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BEDTools is a suite of utilities for comparing genomic features in BED format. These utilities allow one to quickly address tasks such as: 1. Intersecting two BED files. 2. Merge overlapping features. 3. Paired-end overlaps.
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Text Matrix implements a c++ library and corresponding utilities for text mining. Cross-platform execution are supported.
