Search Results for "simulation agents biology"
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Showing 235 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... -
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Gym
Toolkit for developing and comparing reinforcement learning algorithms
Gym is a toolkit for developing and comparing reinforcement learning algorithms. It supports teaching agents, everything from walking to playing games like Pong or Pinball. Open source interface to reinforce learning tasks. The gym library provides an easy-to-use suite of reinforcement learning tasks. Gym provides the environment, you provide the algorithm. You can write your agent using your existing numerical computation library, such as TensorFlow or Theano. It makes no assumptions about... -
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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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SkyAGI
SkyAGI: Emerging human-behavior simulation capability in LLM
SkyAGI is a python package that demonstrates LLM's emerging capability in simulating believable human behaviors. Specifically, SkyAGI implements the idea of Generative Agents and delivers a role-playing game that creates a very interesting user experience. Different from previous AI-based NPC systems, SkyAGI's NPC generates very believable human responses. The interesting observations in this demo show a huge potential for rethinking game development in many aspects, such as NPC script writing. -
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters...
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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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Biogenesis is an artificial life program that simulates the processes involved in the evolution of organisms. It shows colored segment based organisms that mutate and evolve in a 2D environment. Biogenesis is based on Primordial Life.
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Biogenesis Color Mod
Mod for evolution simulation and artificial life program Biogenesis
You can download the Color Mod at the Biogenesis main site too (included in the main download now). You also find the sourcecode there. If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. Original project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ Includes Tyler Colemans "Features Mod": https://sourceforge.net/projects/biogenesisfeatu/ Biogenesis discussion forum: https://sourceforge.net/p... -
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DEVS-Suite Simulator
Component, CA, and CCA models; superdense time, DB repo, testing, etc.
Integrated component-based and cellular automata (CA) Parallel DEVS simulator: https://acims.asu.edu/devs-suite/ OFFERS: 1) synchronized execution & animation, 2) run-time linear/superdense I/O & state trajectories, 3) Action Level Real-Time modeling & simulation, 4) model checking, 5) ABM, 6) CA & composable CA playback, 7) KIB interaction modeling, 8) hierarchical model libraries, 9) Black-Box testing & debugging, 10) PostgreSQL repository, 11) FMU (OpenModelica), 12) OSATE (AADL... -
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Galatea: Multi-agent simulations
DEVs with Multi-agent Simulation Platform
GALATEA: Glider with Autonomous, Logic-based Agents, TEmporal reasoning and Abduction. GALATEA is a family of languages to model multi-agent systems to be simulated in a DEVS, multi-agent platform. GALATEA is software to model and simulate multi-agent systems. It is the product of two lines of research: simulation languages based on Zeigler's theory of simulation and logic-based agents. There is, in GALATEA, a proposal to integrate, in the same simulation platform, conceptual and concrete... -
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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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CyberUnits
Class library for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. -
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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This project introduces a simulation tool to study complex multi-agent systems in social context. The individual-level model is extended based on the well-known social force model, and it mainly describes how agents/particles interact with each other, and also with surrounding facilities including obstructions and passageways. Most importantly, we introduce a set of arrays to define social relationship of agents/particles in a quantitative manner. Opinion dynamics is integrated with force-based...
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EcoLab is a C++ based Agent Based Modelling system, with emphasis on high performance computing for scaling to large simulations.
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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Easy Agent Simulation
Java-based agent simulation platform
EAS is a Java-based simulation platform, developed as part of a research project at the Karlsruhe Institute of Technology. It comes with a broad range of pre-developed simulation scenarios, ranging from virtual agents acting in abstract environments to agents with a spatial representation in 2D or 3D. It is built upon a novel architecture using a separate "plugin layer" to communicate between the simulation engine and the simulated model. This allows to flexibly add or remove non-simulation... -
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Zarja
Agent-based simulation toolkit
It is an open source scientific library that is focused on multi-agent simulations on graphs. It prepares basic toolkit for agents, models, timers, graphs, nodes and edges. It is also accompanied with tools for data processing. -
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DBSolveOptimum
The software for systems biology/pharmacology modeling
DBSolveOptimum is a stand-alone software tool for the construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling techniques... -
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The Mobility Open Architecture Simulation and Tools (MOAST) framework aids in the development of autonomous robots. It includes an architecture, control modules, interface specs, and data sets and is fully integrated with the USARSim simulation system.
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Simultra
Multiagent simulator of road traffic in Qt/C++ and OpenStreetMap.
Simultra is an open-source, hybrid road traffic simulator designed to handle large roadmaps in real-time. It combines microscopic and mesoscopic simulations into one multiagent hybrid simulator. The large-scale maps are modelled mesoscopically in real-time, and the complex traffic interactions benefit from detailed agent-based microscopic simulations. To resolve the concurrency issues within the maps representation and the meso-micro transitions, Simultra combines an event-based mesoscopic... -
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The Teachingbox uses advanced machine learning techniques to relieve developers from the programming of hand-crafted sophisticated behaviors of autonomous agents (such as robots, game players etc...) In the current status we have implemented a well founded reinforcement learning core in Java with many popular usecases, environments, policies and learners. Obtaining the teachingbox: FOR USERS: If you want to download the latest releases, please visit: http://search.maven.org/#search|ga|1...
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This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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A Java library to facilitate SED-ML support for systems biology applications to read, validate, edit, and write SED-ML documents in compliance with MIASE guidelines. Also contains modules to execute simulation tasks and produce outputs. This project also contains the SED-ED editor application for SED-ML.
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KMC-KaiC
Kinetic Monte Carlo simulation of the in-vitro Kai Circadian clock
... clock", which is freely available at the open access journal PLOS Computational Biology: https://doi.org/10.1371/journal.pcbi.1005415 *UPDATE* We made a fully reversible version of our model, including the inverse reactions for ATP hydrolysis. This makes it possible to run the model at thermodynamic equilibrium. This version of the model can be downloaded under KMC_KaiC_Rev.zip. If you like to use our model for your own research, please cite our PLoS Computational Biology paper.