Search Results for "simulation tools peptide" - Page 2
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Showing 70 open source projects for "simulation tools peptide"
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DWSIM - Open Source Process Simulator
Simulate chemical processes using advanced thermodynamic models
DWSIM is an open source, CAPE-OPEN compliant chemical process simulator for Windows, Linux and macOS systems. Written in VB.NET and C#, DWSIM features a comprehensive set of unit operations, advanced thermodynamic models, support for reacting systems, petroleum characterization tools and a fully-featured graphical interface. DWSIM Pro is a commercial sibling of DWSIM built on top of open-source software. It offers extended features, comes with private support, and is accessible in the... -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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Tellurium
Model, simulate, and analyze biochemical systems using one tool.
Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support. -
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SimFPGA
VHDL Verification and Simulation Tool
SimFPGA is a graphical user interface (GUI) tool designed to facilitate the simulation of VHDL projects. It enables users to select VHDL source files and testbenches, configure library and standard settings, and run simulations using GHDL. Additionally, it allows visualization of waveforms through GTKWave. SimFPGA elaborates the project files using GHDL and builds the VHDL project before simulating it. This ensures code verification without the need for additional compilation tools. ... -
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Code_TYMPAN
Open source software calculating industrial noise in the environment
Code_TYMPAN™ is an open source software for calculating industrial noise in the environment. It allows dealing with 3D realistic geometries and has a convenient Human Machine Interface to help engineers to build 3D models and to achieve analysis needed in environmental noise studies. Code_TYMPAN™ allows developing your own calculation method from basic components and geometrical solvers. It includes a solver based on ISO 9613 extended to industrial applications. In 4.2.x version, a Python... -
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Automated Interpretability
Code for Language models can explain neurons in language models paper
The automated-interpretability repository implements tools and pipelines for automatically generating, simulating, and scoring explanations of neuron (or latent feature) behavior in neural networks. Instead of relying purely on manual, ad hoc interpretability probing, this repo aims to scale interpretability by using algorithmic methods that produce candidate explanations and assess their quality. It includes a “neuron explainer” component that, given a target neuron or latent feature,... -
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GNNPCSAFT Chat
Chatbot with GNNPCSAFT
The GNNPCSAFT Chat is an implementation of our project that focuses on using Graph Neural Networks (GNN) to estimate the pure-component parameters of the Equation of State PC-SAFT. We developed this app so the scientific community can access the model's results easily. In this app, you can chat with LLM models (Gemini or Ollama) with GNNPCSAFT tools, allowing you to ask questions about the PC-SAFT parameters of various compounds, predict thermodynamic properties, and get insights into the... -
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GromacsProSuite
Graphical User Interface for Gromacs
...The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure stable performance during parallel processing. Beyond simulation execution, it includes advanced trajectory processing and analysis tools such as RMSD, RMSF, SASA, clustering, PCA, hydrogen-bond analysis, Ramachandran plots, and FEL mapping. With integrated visualization and plotting utilities, it offers a unified platform for researchers, educators, and students to perform complete MD workflows efficiently and reproducibly. ... -
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eCxx
A C++ library for AVR and NodeMCU
NOTE: This project is marked with 'Status: Abandoned' on SourceForge because not enough time can be dedicated to this project. However it may still get sporadic commits to the repository. eCxx is a library for AVR and NodeMCU tailored for micro LED displays and lighting effects. eCxx is utilizing Makefile build system. Java and Python based applications/tools are also included to ease the development and debugging process using the host PC. On one side, eCxx supports the original... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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AEA Framework
A framework for autonomous economic agent (AEA) development
agents-aea by Fetch.ai is a framework for building autonomous economic agents (AEAs) that can act independently, communicate, and transact on decentralized networks. It focuses on enabling AI-driven agents to participate in digital marketplaces and ecosystems. -
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ELECHEM & FARADAY (Electrochemical)
Simulation tool for electrochemical / electroplating parameters
FARADAY and ELECHEM are the two portable computer programs, find useful for electrochemical researchers, electroplating units, battery as well as supercapacitor industries, process engineers, materials scientists & engineers, electroplaters, hobbyists, and students to evaluate various electrochemical deposition parameters. These computational tools can be used to simulate various electrochemical deposition data or electroplating parameters for metals, alloys, composites as well as energy efficiency of the process. For more information, visit to project Home page: https://www.enote.page/2022/07/computer-simulation-electrochemical.html Designed by: Dr. M Kanagasabapathy, Asst. ... -
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MuJoCo-py
mujoco-py allows using MuJoCo from Python 3
...The library is compatible with MuJoCo version 2.1 and supports Linux and macOS, while Windows support has been deprecated. It provides utilities for loading models, running simulations, and accessing simulation states in real time, along with visualization tools for rendering environments. The project also includes interactive examples showcasing collision handling, texture randomization, state resetting, and robot control. By bridging MuJoCo with Python, mujoco-py enables rapid prototyping, training, and evaluation of AI agents in physics-rich environments. -
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ADFRsuite
Automated docking software tools from the Sanner lab at Scripps
the ADFRsuite provides a self contain python-based software environment with various tools for automated docking. visit ccsb.scripps.edu/adfr for more info -
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Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.
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OpenVCT
The Open-Source Virtual Clinical Trial Project
The OpenVCT project is designed to provide a common platform for performing Virtual Clinical Trials of medical imaging. OpenVCT provides tools for simulation of patient accrual and reader studies of medical imaging devices, simulating by simulating cohorts of patients and readers. OpenVCT uses common data standards, such as DICOM, to ensure inter-compatibility. -
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Makani
Makani was developed a commercial-scale airborne wind turbine
...This open-source repository contains the complete software stack that powered Makani’s research and flight systems, including the flight simulator, autopilot controller, avionics firmware, visualization tools, and ground control software. The software enables simulation, control, and analysis of the Makani M600 turbine system, designed to operate offshore and autonomously manage complex aerodynamic behaviors. Built primarily in C++ and Python, the codebase integrates real-time flight control, sensor fusion, aerodynamic modeling, and telemetry visualization. ... -
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Graph Nets library
Build Graph Nets in Tensorflow
Graph Nets, developed by Google DeepMind, is a Python library designed for constructing and training graph neural networks (GNNs) using TensorFlow and Sonnet. It provides a high-level, flexible framework for building neural architectures that operate directly on graph-structured data. A graph network takes graphs as inputs, consisting of edges, nodes, and global attributes, and produces updated graphs with modified feature representations at each level. This library implements the... -
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C++QED
A framework for simulating open quantum dynamics
C++QED is an application-programming framework for simulating open quantum dynamics in general. It has demonstrated the ability to simulate full Master equation of up to several thousand, and quantum trajectories of up to several hundred thousand dimensions. The basic idea is to allow users to build arbitrarily complex interacting quantum systems out of free subsystems and interactions (elements), and simulate their time evolution with a number of available time-evolution... -
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Neural MMO
Code for the paper "Neural MMO: A Massively Multiagent Game..."
Neural MMO is a massively multi-agent simulation environment developed by OpenAI for reinforcement learning research. It provides a persistent, procedurally generated world where thousands of agents can interact, compete, and cooperate in real time. The environment is inspired by Massively Multiplayer Online Role-Playing Games (MMORPGs), featuring resource gathering, combat mechanics, exploration, and survival challenges. Agents learn behaviors in a shared ecosystem that supports long-term... -
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ECommerceCrawlers
Collection of Python ecommerce and website crawler examples projects
ECommerceCrawlers is a collection of practical Python web crawler projects designed to gather data from a variety of ecommerce platforms, websites, and online services. It aggregates many independent crawler examples created by contributors and organized into separate subprojects that target specific sites or data sources. These examples demonstrate how to build and operate web scrapers capable of collecting structured information such as product listings, news content, job postings, social... -
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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
ParamIT is a toolkit aiding the development of molecular mechanical force field parameterization of small, drag like, molecules within CHARMM general force field (CGenFF) protocol. The developed toolkit helps the researchers in following ways: 1) automating the creation of multiple input files for quantum and molecular mechanics programs, 2) automating the output analysis and 3) substitute the use of full MM programs with a faster specialized one. The developed tools include: 1) generator of... -
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LaueTools
open source python packages for X-ray MicroLaue Diffraction analysis
LaueTools is an open-source project for white beam Laue x-ray microdiffraction data analysis including tools in image processing, peaks searching & indexing, crystal structure solving (orientation & strain) and data & grain mapping visualisation. Python 3 Code and new features are now at: https://gitlab.esrf.fr/micha/lauetools -
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TEACUP
TCP Experiment Automation Controlled Using Python
TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP... -
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
