CWL integration of Showcase 3

Description

This project is about the integration in CWL of the Mouse TVB Model notebook that can be found at: https://wiki.ebrains.eu/bin/view/Collabs/public-3species-tvbadex-eitn-fallschool/Drive

This is a CWL Workflow consisting of 3 steps (CommandLineTools).

This workflow builds and executes an AdEx mean-field TVB model, plots the results and pushes these results to an EBRAINS Collab Bucket

Pre-defined inputs can be found in the workflow_info.yaml file.

Inputs

• bvals: adaptation values
• simname: label for each of the bvals
• output_dir_name: name of the output directory where to store the results
• run_sim: total time of the simulation (in ms)
• cut_transient: transient time (in ms) to cut from the simulation
• token: user's token for the data proxy (clb_oauth.get_token())
• bucket_id: Your bucket id. You should have read and write access to that Bucket
• folder_root and synch_root: auxiliar folders, they should not be changed and should be left as 'result' and 'synch' respectively

Outputs

• fig_PSD.png: final plot containing the PSD of the simulated traces for all nodes under given conditions
• fig_traces.png: final plot containing the traces of the simulation for all nodes under given conditions

Steps

Step 1: Running Simulation

Runs the simulation of the TVB model

Step 2: Plotting Results

Plots the results from the simulations

Step 3: Pushing files to bucket

Pushes the figure to the given Collab Bucket