Search Results for "simulation agents biology"
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Showing 275 open source projects for "simulation agents biology"
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Agents.jl
Agent-based modeling framework in Julia
Agents.jl is a pure Julia framework for agent-based modeling (ABM): a computational simulation methodology where autonomous agents react to their environment (including other agents) given a predefined set of rules. The simplicity of Agents.jl is due to the intuitive space-agnostic modeling approach we have implemented: agent actions are specified using generically named functions (such as "move agent" or "find nearby agents") that do not depend on the actual space the agents exist in, nor on the properties of the agents themselves. ... -
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agency-agents-zh
193 plug-and-play AI expert roles
agency-agents-zh is a framework focused on building and coordinating multiple AI agents, likely with a particular emphasis on Chinese-language environments or documentation. The project appears to explore the concept of agent collaboration, where different agents handle specialized tasks and communicate to achieve broader objectives. It is designed to simulate organizational workflows, enabling complex problem-solving through distributed intelligence rather than a single monolithic model.... -
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OpenScience
The open-source AI workbench for scientific research
...The workspace runs in the browser and includes a file tree, editor, terminal, session history, and scientific rendering for molecules, structures, genomes, and plots. It supports frontier, open-weight, and local models through bring-your-own-key provider configuration. The project includes research agents, domain specialists, critique agents, literature-review agents, and more than 290 scientific skills. OpenScience is especially useful for machine learning, biology, physics, chemistry, and research automation workflows that need tool use and provenance. -
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Meta Agents Research Environments (ARE)
Meta Agents Research Environments is a comprehensive platform
Meta Agents Research Environments (ARE) is a simulation and benchmarking platform. It is designed to evaluate AI agents in dynamic, evolving, multi-step tasks. Unlike static benchmarks, ARE supports environments where agents must adapt to changes over time and reason over sequences of actions. It interacts with applications and faces uncertainty. -
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Anything Analyzer
AI Agent/IDE | All-in-one protocol analysis toolkit
...It combines browser-based packet capture, MITM proxy capabilities, and JavaScript hooking into a unified interface for deep inspection of requests and responses. The tool supports fingerprint spoofing and behavioral simulation, allowing users to analyze how systems react under different conditions. It integrates AI-powered analysis to interpret captured data and provide insights into protocols and behaviors. The system is built to connect seamlessly with AI agents and development environments through MCP server integration. It is particularly useful for security research, debugging, and reverse engineering workflows. ... -
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ESPResSo
The ESPResSo package
ESPResSo is a simulation package for molecular dynamics and Monte Carlo simulations of soft matter systems. It is designed for coarse-grained and bead-spring models used in physics, chemistry, and molecular biology. The software can model systems such as polymers, colloids, liquid crystals, ferrofluids, DNA, lipid membranes, and other complex fluids. It includes a broad range of interaction potentials and algorithms for electrostatics, hydrodynamics, and coupled particle-field behavior. ... -
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Scientific Agent Skills
A set of ready to use Agent Skills for research, science, engineering
Scientific Agent Skills is an open-source collection of ready-to-use agent skills designed to turn AI coding assistants into stronger research, science, engineering, and analysis partners. It supports any AI agent compatible with the Agent Skills standard, including tools such as Cursor, Claude Code, Codex, and Gemini CLI. The repository includes 135 skills across scientific domains such as genomics, cheminformatics, clinical research, medical imaging, machine learning, physics, materials... -
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Claude Scientific Skills
A set of ready to use Agent Skills for research, science, engineering
Claude Scientific Skills is a large open source collection of ready-to-use scientific capabilities that extend AI coding agents into full research assistants. The project provides more than 170 curated skills covering domains such as genomics, drug discovery, medical imaging, physics, and advanced data analysis. Each skill bundles documentation, examples, and tool integrations so agents can reliably execute complex multi-step scientific workflows. The framework follows the open Agent Skills... -
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BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
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Gradient Bang
Gradient Bang is an online multiplayer universe
Gradient Bang is an experimental open-source project developed within the Pipecat ecosystem that reimagines AI interaction as a persistent, multiplayer simulation where users and large language models coexist inside a shared virtual environment. Rather than functioning as a traditional application or API, it is conceptualized as an “online multiplayer universe” in which participants can explore, trade, battle, and collaborate while interacting with AI agents as active entities within the system. ... -
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colleague-skill
Transform a cold separation into a warm Skill
colleague-skill is a specialized agent skill designed to simulate a collaborative teammate within AI-driven workflows, enabling agents to behave more like human colleagues in problem-solving scenarios. The project focuses on enhancing interaction quality by introducing role-based behavior, contextual awareness, and cooperative task execution. It allows agents to provide suggestions, feedback, and alternative approaches, mimicking real-world collaboration dynamics. The system likely... -
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Catalyst.jl
Chemical reaction network and systems biology interface
Catalyst.jl is a symbolic modeling package for analysis and high-performance simulation of chemical reaction networks. Catalyst defines symbolic ReactionSystems, which can be created programmatically or easily specified using Catalyst's domain-specific language (DSL). Leveraging ModelingToolkit and Symbolics.jl, Catalyst enables large-scale simulations through auto-vectorization and parallelism. Symbolic ReactionSystems can be used to generate ModelingToolkit-based models, allowing the easy... -
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Claw3D
Claw3D is an open source 3D engine built on OpenClaw
Claw3D is an experimental open-source platform that combines elements of 3D simulation, developer tooling, and AI orchestration by creating an interactive virtual workspace where AI agents can be visualized as active participants in a shared environment. It is designed as a 3D “virtual office” where users can observe, manage, and interact with multiple AI agents performing tasks such as coding, reviewing pull requests, and coordinating workflows in real time. ... -
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Sapiens
High-resolution models for human tasks
Sapiens is a research framework from Meta AI focused on embodied intelligence and human-like multimodal learning, aiming to train agents that can perceive, reason, and act in complex environments. It integrates sensory inputs such as vision, audio, and proprioception into a unified learning architecture that allows agents to understand and adapt to their surroundings dynamically. The project emphasizes long-horizon reasoning and cross-modal grounding—connecting language, perception, and action into a single agentic model capable of following abstract goals. ... -
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MiroFish
A Simple and Universal Swarm Intelligence Engine
MiroFish is a next-generation artificial intelligence prediction engine that leverages multi-agent technology and swarm-intelligence simulation to model, simulate, and forecast complex real-world scenarios. The system extracts “seed” information from sources such as breaking news, policy documents, and market signals to construct a high-fidelity digital parallel world populated by thousands of virtual agents with independent memory and behavior rules. Users can inject variables or conditions into this simulated environment from a “god’s eye view,” enabling iterative prediction of future trends under different assumptions, which can be useful for decision support, scenario planning, or creative exploration. ... -
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Rust Port
The Rust workspace under rust/ is the current systems-language port
Rust Port is an open-source reconstruction and experimentation framework derived from leaked or reverse-engineered versions of advanced AI coding agents, designed to replicate and extend the capabilities of agentic development systems. It functions as a programmable coding assistant that operates through autonomous workflows, enabling users to generate, modify, and analyze code with minimal manual intervention. The project emphasizes agent-based execution, where tasks are broken down into... -
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Recursive Language Models
General plug-and-play inference library for Recursive Language Models
...RLM also includes integration with popular simulation environments and benchmark suites, giving researchers a ready-made playground for algorithm comparison and performance tracking. -
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Habitat-Sim
A flexible, high-performance 3D simulator for Embodied AI research
Habitat-Sim is a high-performance 3D simulator for embodied AI research, designed to run photorealistic indoor environments at thousands of frames per second. It offers GPU-accelerated rendering and a flexible sensor suite—RGB, depth, semantic segmentation, and more—so agents can perceive and act in realistic scenes. The engine is written in C++ with Python bindings and integrates physics, navigation meshes, and shortest-path planners to support tasks like point-goal navigation,... -
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The Mars Simulation Project is an open source Java project to create a simulation of future human settlement on the planet Mars. See https://github.com/mars-sim/mars-sim for the LATEST issues/wiki/code change
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VectorizedMultiAgentSimulator (VMAS)
VMAS is a vectorized differentiable simulator
VectorizedMultiAgentSimulator is a high-performance, vectorized simulator for multi-agent systems, focusing on large-scale agent interactions in shared environments. It is designed for research in multi-agent reinforcement learning, robotics, and autonomous systems where thousands of agents need to be simulated efficiently. -
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PentestAgent
AI agent framework for black-box security testing
PentestAgent is an open-source autonomous security testing platform designed to help organizations identify vulnerabilities and assess security posture by simulating real-world attack scenarios without manual intervention. It brings a modular and automated approach to penetration testing by orchestrating a suite of tools and scripts that can emulate common exploitation techniques, reconnaissance workflows, and post-exploitation activities across targets. Users configure rules, policies, and... -
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Mobile Next
Model Context Protocol Server for Mobile Automation and Scraping
...It is built to integrate seamlessly with modern AI agents, enabling multi-step workflows such as automated testing, form filling, and user journey simulation. -
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CarlaAir
Fly Drones Inside a CARLA World
CarlaAir is an open-source robotics simulator that combines CARLA urban driving with multirotor drone flight inside one Unreal Engine environment. It is designed for research involving coordinated aerial and ground autonomous systems. Vehicles, pedestrians, drones, weather, and sensor streams can coexist within the same simulated world. Users can access both CARLA and AirSim-style Python APIs to control different agents and environments. The platform supports synchronized cameras, lidar,... -
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ManiSkill
SAPIEN Manipulation Skill Framework
ManiSkill is a benchmark platform for training and evaluating reinforcement learning agents on dexterous manipulation tasks using physics-based simulations. Developed by Hao Su Lab, it focuses on robotic manipulation with diverse, high-quality 3D tasks designed to challenge perception, control, and planning in robotics. ManiSkill provides both low-level control and visual observation spaces for realistic learning scenarios.