iBioSim

iBioSim

iBioSim has been developed for the modeling, analysis, and design of genetic circuits. It supports modeling and visualization support for multi-cellular and spatial models, importing and exporting models specified using the Systems Biology Markup Language (SBML), and is one of the first tools to also support the Synthetic Biology Open Language (SBOL).

Contributors

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Pedro Fontanarrosa

Graduate Researcher, Ph.D.

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Payton Thomas

Undergraduate Researcher

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Thomas Stoughton

Undergraduate Researcher

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Leandro Watanabe

Google, Software Engineer

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Zhen Zhang

Utah State University, Assistant Professor

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Curtis Madsen

Sandia National Laboratories, R&D S&E, Computer Science

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Tramy Nguyen

Raytheon BBN Technologies, Research Scientist/Software Engineer

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Hiroyuki Kuwahara

King Abdullah University of Science and Technology, Computational Bioscience Research Center Research Scientist

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Nathan Barker

Southern Utah University, Department Chair of Computer Science & Information Systems

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Nam-phuong Nguyen

Boundless Bio INC, Principal Scientist I

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Kevin Jones

Lockheed Martin, Senior Cyber Applied Research Scientist

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Tyler Patterson

Ever Accountable, President

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Jason Stevens

Amazon, Business Intelligence Engineer

Publications

  • Automated Generation of Dynamic Models for Genetic Regulatory Networks
  • A Computational Workflow for the Automated Generation of Models of Genetic Designs
  • iBioSim 3: A Tool for Model-Based Genetic Circuit Design
  • Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language
  • Technology mapping of genetic circuit designs
  • Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models
  • Hierarchical Stochastic Simulation of Genetic Circuits
  • Hierarchical stochastic simulation of genetic circuits
  • A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language
  • Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits
  • Dynamic Modeling of Cellular Populations within iBioSim
  • Design and Test of Genetic Circuits Using tt iBioSim
  • Modeling and Visualization of Synthetic Genetic Circuits
  • iBioSim: a tool for the analysis and design of genetic circuits
  • Representing Genetic Networks as Labeled Hybrid Petri Nets for State Space Exploration and Markov Chain Analysis