diff --git a/README.md b/README.md index 79db7bf..906ae23 100644 --- a/README.md +++ b/README.md @@ -1,23 +1,37 @@ -# Geometric models reveal behavioral and neural signatures of transforming naturalistic experiences into episodic memories +# Geometric models reveal behavioural and neural signatures of transforming naturalistic experiences into episodic memories -This repository contains data and code used to produce the paper "[_Geometric models reveal behavioral and neural signatures of transforming naturalistic experiences into episodic memories_](https://www.biorxiv.org/content/10.1101/409987v3)" by Andrew C. Heusser, Paxton C. Fitzpatrick, and Jeremy R. Manning. The repository is organized as follows: +

+ Paper (Nature Human Behaviour) + + + Paper (Direct PDF link) + + + Behind the Paper (blog post) + +

-``` +This repository contains data and code used to produce the paper "[_Geometric models reveal behavioural and neural signatures of transforming naturalistic experiences into episodic memories_](https://rdcu.be/cfsYs)" by Andrew C. Heusser, Paxton C. Fitzpatrick, and Jeremy R. Manning. + +The repository is organized as follows: + +```yaml root -├── code : all code used in the paper +├── code : all analysis code used in the paper │ ├── notebooks : Jupyter notebooks for paper analyses -│ ├── scripts : python scripts used to perform various analyses on a cluster -│ │ ├── embedding : scripts used to optimize the UMAP embedding for the trajectory figure -│ │ └── searchlights : scripts used to perform the brain searchlight analyses -│ └── sherlock_helpers : package with assorted helper functions and variables for analyses -├── data : all data used in the paper -│ └── raw : raw data before processing +│ ├── scripts : Python scripts for running analyses on a HPC cluster (Moab/TORQUE) +│ │ ├── embedding : scripts for optimizing the UMAP embedding for the trajectory figure +│ │ └── searchlights : scripts for performing the brain searchlight analyses +│ └── sherlock_helpers : Python package with support code for analyses +├── data : all data analyzed in the paper +│ └── raw : raw video annotations and recall transcripts │ └── processed : all processed data └── paper : all files to generate paper - └── figs : pdf copies of each figure + └── figs : pdf copies of all figures ``` -We also include a Dockerfile to reproduce our computational environment. Instruction for use are below (copied and modified from the [MIND](https://github.com/Summer-MIND/mind-tools) repo): +We also include a `Dockerfile` to reproduce our computational environment. Instruction for use are below (copied and modified from the [MIND](https://github.com/Summer-MIND/mind-tools) repo): ## One time setup 1. Install Docker on your computer using the appropriate guide below: @@ -26,7 +40,7 @@ We also include a Dockerfile to reproduce our computational environment. Instruc - [Ubuntu](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/) - [Debian](https://docs.docker.com/engine/installation/linux/docker-ce/debian/) 2. Launch Docker and adjust the preferences to allocate sufficient resources (e.g. >= 4GB RAM) -3. To build the Docker image, open a terminal window, navigate to your local copy of the repo, and enter `docker build -t sherlock .` +3. To build the Docker image, open a terminal window, navigate to your local copy of the repo, and run `docker build -t sherlock .` 4. Use the image to run a container with the repo mounted as a volume so the code and data are accessible. - The command below will create a new container that maps the repository on your computer to the `/mnt` directory within the container, so that location is shared between your host OS and the container. Be sure to replace `LOCAL/REPO/PATH` with the path to the cloned repository on your own computer (you can get this by navigating to the repository in the terminal and typing `pwd`). The below command will also share port `9999` with your host computer, so any Jupyter notebooks launched from *within* the container will be accessible at `localhost:9999` in your web browser - `docker run -it -p 9999:9999 --name Sherlock -v /LOCAL/REPO/PATH:/mnt sherlock `