generic scripting syntax for running tvb simulations

tvb-scripting is a simple set of tools that allow a range of tvb simulation scenarios to be run by simply supplying a short text file detailing the parameter values to be used.

The rationale is to try to separate code specifying how a simulation is run from code specifying the parameter values used. This is generally regarded as 'good practice' or 'desirable' in both simulation and data analysis research, and has a number of advantages.

(Most of these and more are summarized better by Andrew Davison, author of the Sumatra and PyNEURON libraries).

Less code needed to specify a simulation

As rules of thumb go, 'the less code the better' isn't a bad one.

My personal experience of scripting, especially sharing of scripts between multiple users and over long periods of time, is that a certain amount of 'drift' in cosmetic things like layout, variable names, etc. is inevitable. At best this is often unecessary; at worse this makes understanding something you didn't write a serious headfuck requiring a lot more time and brainpower than it should. It also makes 'real' version control (therefore long-term management, bux-fixing, reproducibility) exponentially harder than it needs to be.

Other reasons why less code is better include minimizing redundancy; less chance of silly-mistake bugs; being more easily human readable, etc. etc.

Plays well with databases

The json-type nested python dictionaries used by tvb-scripting lend themselves very well to databasing, as they effectively define database entries. In fact this is precisely what Sumatra does: log the input parameters in a database, and take a snapshot of the execution code using a version control system such as git. Whilst tvb-scripting is intended primarily for use with tvb-sumatra, it doesn't need to be, and the functionality was considered useful enough on its own to separate the two. The nested dictionary format isn't arbitrary - it follows the recommended format of the Parameters python library, which provides some other useful tools for dealing with data structures of this kind.

Plays well with Sumatra

ibid...

The command line usage is simple:

    python run_tvb_sims.py <PARAMETER FILE>

Examples

Parameter files matching several of the demo examples from the tvb-library repo are given in /examples/tvb_demos.