User Workflow Overview
The relationship between experiment and simulation in computational
neuroscience is illustrated in the figure below.
Conducting experiments and running simulations are two iterative processes
connected by a feedback loop that uses interpretation of results to design new
experimental setups and model constructions. GENESIS supports the lower loop
within the system as shown above.
GENESIS User Workflow
The typical workflow within GENESIS has five basic steps, as the following figure
This workflow provides an organizing principle that guides the user experience
of GENESIS, for example, the GUI and tutorial documentation.
- Construct model: Simple models can be created directly within the
G-Shell by entering commands. More complex models can be imported
into the G-Shell from either the GENESIS model libraries or from
external model libraries. The model can also be explored, checked, and
- Design experiment: Set model parameter values specific to a given
simulation, the stimulus parameters for a given simulation run or
‘experiment’, and/or the variables to be stored for subsequent analysis.
- Run simulation: Configure runtime options, check, run, reset
simulation, and save model state. The model state can be saved
at any simulation time step to allow it to be imported into a
subsequent GENESIS session. Output is flushed to raw result storage
for subsequent data analysis.
- Output: Check simulation output and the validity of results to
determine whether simulation output exists in the correct locations.
Output can be analyzed either within GENESIS or piped to external
applications such as Matlab, Grace, or Mathematica.
- Iterators: Close the loop between output of results and model
construction in the GENESIS users workflow. Iterators connect
experimental results and model output and include for example,
automated construction of simulations and batch files, static parameter
searching, and active parameter searching using the dynamic clamp.