biosoc.org
Analysis Software
various computational biology software tools, including their types, functionalities, and access to their project websites, source codes, and demos.
Aquarium
Analysis and comprehension tool leveraging the open-source statistical language, R. AMI and Docker images are available.
Resources
Copasi
A standalone program supporting SBML standard models, capable of simulating behavior using ODEs or the Gillespie stochastic simulation algorithm. It includes arbitrary discrete events in simulations.
Resources
Road Runner
A portable simulation engine for systems and synthetic biology models in SBML format. Written in C#, it incorporates C, C++, and Python APIs.
Resources
BioConductor
Analysis and comprehension tool using the open-source statistical language, R. AMI and Docker images are available.
Resources
Morpheus
A modeling environment for simulating cell-based models with ordinary differential equations and reaction–diffusion systems. It supports multiscale biological models defined in biological terms and mathematical expressions.
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Tinkercell
Incorporates a detailed diagram that can be mapped to models or experimental results, allowing various mathematical analyses to be run on those models.
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BioPSy
Performs guaranteed parameter set synthesis for ODE biological models expressed in SBML based on desired behavior expressed by time-series data.
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Pysces
Provides tools for analyzing cellular systems, including a human-readable model description language, a structural, and a bifurcation analysis module. Supports SBML and SED-ML.
Resources
gro
A programming, modeling, specifying, and simulating language for the behavior of cells in growing microcolonies of microorganisms.