A PLATFORM for SYSTEMS BIOLOGY
A growing set of tools to wrestle the complications of numerical solutions to complex dynamical systems,
such as
cycles and webs of biochemical reactions, optionally with
macro-molecules, spatial components and diffusion (plus, upcoming,
membranes.)
ONLY 1/2 OF THE BATTLE, is to offer functionality to set up and simulate the system...
The OTHER 1/2 OF THE BATTLE is a battery of tools:
- to tame numerical instabilities
- to throttle up/down the computational effort
- to visualize & analyze the results
- to provide helpful diagnostics
- to integrate high-performance computing
- to provide an API that is simple, convenient & intuitive
A collaboration of software engineering, data science, numerical methods, biochemistry & biology, among other fields
Examples
From experiment
macromolecules_1:
From experiment
A cycle of reactions:
From experiment
enzyme_1:
From experiment
variable_steps_1:
From experiment
negative_concentrations_1:
From experiment
impossible_1:
From experiment
large_time_steps_1:
From experiment
cycles_1:
From experiment
down_regulate_1:
From experiment
cascade_1:
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