https://github.com/int-brain-lab/paper-behavior

The International Brain Laboratory et al. (2020) A standardized and reproducible method to measure decision-making in mice. bioRxiv, 909838
https://github.com/int-brain-lab/paper-behavior

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The International Brain Laboratory et al. (2020) A standardized and reproducible method to measure decision-making in mice. bioRxiv, 909838

• Host: GitHub
• URL: https://github.com/int-brain-lab/paper-behavior
• Owner: int-brain-lab
• License: mit
• Created: 2019-09-15T22:27:06.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-01-10T11:25:57.000Z (12 months ago)
• Last Synced: 2024-01-10T12:39:01.567Z (12 months ago)
• Language: Jupyter Notebook
• Homepage: https://doi.org/10.1101/2020.01.17.909838
• Size: 19.3 MB
• Stars: 11
• Watchers: 31
• Forks: 6
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Authors: authorship/Authorship and contribution for IBL behavior paper.ipynb

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README

        
# paper-behavior

This repository contains code to reproduce all figures of the behavior paper by the International Brain Laboratory. If reusing any part of this code please cite the [bioRxiv paper](https://www.biorxiv.org/content/10.1101/2020.01.17.909838v2) in which these figures appear. 

### Installation

These instructions require anaconda (https://www.anaconda.com/distribution/#download-section) for Python 3 and git (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)

In an Anaconda prompt window:

1. Clone or download the paper-bahavior repository

2. Install the other dependencies by running `pip install -r requirements.txt`

To call the functions in this repo, either run python from within the `paper-bahavior` folder or

add the folder to your python path: 

```python

import sys

sys.path.extend([r'path/to/paper-behavior'])

```

### How to run the code

All the scripts start with the name of the figure they produce. The figure panels will appear in the `exported_figs` subfolder.  When running the scripts for the first time the required data will be downloaded to ./data

NB: Since December 2023 our DataJoint servers were retired and some scripts no longer execute, however the main figure scripts should still work.

### Questions?

If you have any problems running this code, please open an issue in the [iblenv repository](https://github.com/int-brain-lab/iblenv/issues) where we support users in using the IBL software tools.

You can read more about the [IBL dataset types](https://docs.google.com/spreadsheets/d/1ieLXRPLLSgUKcLvFkrqizfZl5HjdfE6bQ2KLBCRmjQo/edit#gid=1097679410) and [additional computations on the behavioral data](data.internationalbrainlab.org), such as training status and psychometric functions.

### Known issues

The data used in this paper have a number of issues.  The authors are confident that these issues

do not affect the results of the paper but nevertheless users should be aware of these

shortcomings.

  

1. NaN values may be found throughout the data.  These resulted from failures to either produce

 an event (for example the go cue tone wasn't played) or to record an event (e.g. the stimulus was

 produced but the photodiode failed to detect it).

2. Some events violated the task structure outlined in the paper.  For example during some sessions

 the go cue tone happened much later than the stimulus onset.  Although this conceivably

 affected the reaction time on some trials, it did not occur frequently enough to

 significantly affect the median reaction times.