sim2bids 1.1.2

App to preprocess and convert simulation data

SIM2BIDS: convert computational data to BIDS standard

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This app is created to convert computational data to BIDS standard as proposed by Michael Schirner and Petra Ritter. The specification proposes a data structure schema for neural network computer models that aims to be generically applicable to all kinds of neural network simulation software, mathematical models, computational models, and data models, but with a focus on dynamic circuit models of brain activity. Importantly, they not only propose suggestions for a BIDS schema for computer models, but they also propose extensions to the entire BIDS standard that solve several other problems.

Installation

Simply run the following command to get the app up and running:

pip install sim2bids

Alternatively, either fork or obtain the latest sim2bids version by running the following:

git clone https://github.com/dissagaliyeva/sim2bids

cd sim2bids

python setup.py install

Then, open up your notebook and import the following packages:

import param

import io
import panel as pn
import numpy as np
import pandas as pd

import sim2bids
from sim2bids.sim2bids import MainArea

import warnings

warnings.filterwarnings('ignore')
pn.extension('tabulator', 'ace', 'jsoneditor', 'ipywidgets', sizing_mode='stretch_width', notifications=True)

There are two options to proceed:

1. Run the app locally (yields the best user experience) by calling pn.serve(MainArea().view()). This will take you to a localhost page where you'll see the app.

2. Run the app inline (might have small differences in layout) by calling MainArea().view().servable().

Important ❗

• Provide SoftwareVersion, SoftwareRepository, and SoftwareName

The final conversion includes JSON sidecars for each file that is created. Some folders (param, eq, code, ts) require additional information on the software you're using to produce simulations.

In case you're using TVB (The Virtual Brain) workspaces, you can copy this snippet and paste before calling pn.serve(MainArea().view()) or MainArea().view().servable():

# set required fields
sim2bids.app.app.SoftwareVersion = 2.6
sim2bids.app.app.SoftwareRepository = 'https://github.com/the-virtual-brain/tvb-root/releases/tag/2.6'
sim2bids.app.app.SoftwareName = 'TVB'

# start the app
pn.serve(MainArea().view())

Alternatively, customize the above cells.

• Give your project a meaningful short description

All simulations are unique, that is why it will be much easier for everyone if you give a meaningful name to your work. There is an input field on the left-hand side in the Settings where you can supplement that information.

NOTE: make sure to give the description before picking the folder you need to convert.

Example:

• Provide additional information

Since there is a huge number of descriptions, parameters, and other variables, the app gives you the right to provide additional description. After the conversion, you can click on View Results and then JSON files tab to supplement user-specific input.

NOTE: Make sure to click on Update JSON button to update default values.

Example:

Resources

We want to ensure you have the best user experience. Therefore, on top of documentation page, we have included a presentation that covers the main functionality; it also includes a step-by-step image/video walk-through with different datasets. The link is right here.

Getting help

The app is still under active development, if you don't see the information you're looking for, please open a new issue or email me directly. I'll be happy to answer your questions! :)