Search Results for "stochastic"
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Showing 8 open source projects for "stochastic"
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ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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StochPy - Stochastistic modeling in Python - is an easy-to-use package, which provides several stochastic simulation algorithms and unique analysis techniques, which can be used for stochastic simulations of biochemical systems.
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Stochastic Rule Builder (SRB)
Modeling framework for capturing positional and temporal dynamics
...All the possible actions are based on the current state of factors bound to the DNA. We developed a rule builder to automatically generate the complete set of biochemical interaction rules for any given DNA sequence. Off-the-shelf stochastic simulation engines can model the behavior of a system of rules and the resulting changes in the configuration of bound factors can be visualized. -
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Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
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NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
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Path Sim contains a collection of tools for analysing Biochemical pathways with respect to stochastic behavior and cell-to-cell variations.
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Hierarchical Stochastic Block Model
just a bunch of PhD projects
Development codes for hierarchical stochastic block models
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