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1 |
| -# directed-forgetting-network-dynamics |
2 |
| -Investigate the network dynamics underlying list-method directed forgetting |
| 1 | +# Network dynamics underlying contextually mediated intentional forgetting |
| 2 | + |
| 3 | +This repository contains data and code used to produce the paper ["_Network dynamics underlying contextually mediated intentional forgetting_"](ADD LINK) by Jeremy R. Manning. The repository is organized as follows: |
| 4 | + |
| 5 | +``` |
| 6 | +root |
| 7 | +└── code : all code used in the paper |
| 8 | + └── notebooks : jupyter notebooks for paper analyses |
| 9 | +└── data : all data used in the paper |
| 10 | + ├── raw : raw data before processing |
| 11 | + └── processed : all processed data |
| 12 | +└── paper : all files to generate paper |
| 13 | + └── figs : pdf copies of each figure |
| 14 | +``` |
| 15 | + |
| 16 | +I also include a Dockerfile to reproduce our computational environment. Instruction for use are below (copied and modified from [this project](https://github.com/ContextLab/sherlock-topic-model-paper)): |
| 17 | + |
| 18 | +## One time setup |
| 19 | +1. Install Docker on your computer using the appropriate guide below: |
| 20 | + - [OSX](https://docs.docker.com/docker-for-mac/install/#download-docker-for-mac) |
| 21 | + - [Windows](https://docs.docker.com/docker-for-windows/install/) |
| 22 | + - [Ubuntu](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/) |
| 23 | + - [Debian](https://docs.docker.com/engine/installation/linux/docker-ce/debian/) |
| 24 | +2. Launch Docker and adjust the preferences to allocate sufficient resources (e.g. > 4GB RAM) |
| 25 | +3. Build the docker image by opening a terminal in this repo folder and enter `docker build -t qwave .` |
| 26 | +4. Use the image to create a new container for the workshop |
| 27 | + - The command below will create a new container that will map your computer's `Desktop` to `/mnt` within the container, so that location is shared between your host OS and the container. Feel free to change `Desktop` to whatever folder you prefer to share instead, but make sure to provide the full path. The 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 |
| 28 | + - `docker run -it -p 9999:9999 --name qwave -v ~/Desktop:/mnt dffr ` |
| 29 | + - You should now see the `root@` prefix in your terminal, if so you've successfully created a container and are running a shell from *inside*! |
| 30 | +5. To launch any of the notebooks: `jupyter lab --port=9999 --no-browser --ip=0.0.0.0 --allow-root` |
| 31 | + |
| 32 | +## Using the container after setup |
| 33 | +1. You can always fire up the container by typing the following into a terminal |
| 34 | + - `docker start dffr && docker attach dffr` |
| 35 | + - When you see the `root@` prefix, letting you know you're inside the container |
| 36 | +2. Close a running container with `ctrl + d` from the same terminal you used to launch the container, or `docker stop dffr` from any other terminal |
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