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organizing repo
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.gitignore

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# mypy
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.mypy_cache/
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.DS_Store
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*.aux
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*.out
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*.synctex.gz
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main.pdf

.gitmodules

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[submodule "paper/CDL-bibliography"]
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path = paper/CDL-bibliography
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url = https://github.com/ContextLab/CDL-bibliography.git

Dockerfile

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FROM debian:latest
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# Install necessary linux packages from apt-get
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RUN apt-get update --fix-missing && apt-get install -y eatmydata
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RUN eatmydata apt-get install -y wget bzip2 ca-certificates \
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libglib2.0-0 libxext6 libsm6 libxrender1 \
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git \
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libfreetype6-dev \
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swig \
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mpich \
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pkg-config \
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gcc \
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wget \
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curl \
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vim \
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nano \
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git-annex
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# Install anaconda
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RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
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wget --quiet https://repo.continuum.io/archive/Anaconda3-4.4.0-Linux-x86_64.sh -O ~/anaconda.sh && \
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/bin/bash ~/anaconda.sh -b -p /opt/conda && \
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rm ~/anaconda.sh
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# Setup anaconda path
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ENV PATH /opt/conda/bin:$PATH
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# Install gcc to make it work with brainiak
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RUN ["/bin/bash", "-c", "conda install -y gcc"]
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# update setuptools
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RUN conda update setuptools
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# install jupyter lab
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RUN conda install -c conda-forge jupyterlab
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# Install packages needed
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RUN pip install --upgrade git+https://github.com/IntelPNI/brainiak \
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hypertools \
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seaborn \
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scikit-learn \
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ffmpeg \
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scipy \
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supereeg \
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datalad \
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# add some useful directories as mirrors of directors in the same location on your computer
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ADD data /data
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ADD code /code
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ADD figs /figs
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# Finally, expose a port from within the docker so we can use it to run
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# jupyter notebooks
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EXPOSE 9999

README.md

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# directed-forgetting-network-dynamics
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Investigate the network dynamics underlying list-method directed forgetting
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# Network dynamics underlying contextually mediated intentional forgetting
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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:
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```
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root
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└── code : all code used in the paper
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└── notebooks : jupyter notebooks for paper analyses
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└── data : all data used in the paper
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├── raw : raw data before processing
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└── processed : all processed data
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└── paper : all files to generate paper
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└── figs : pdf copies of each figure
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```
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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)):
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## One time setup
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1. Install Docker on your computer using the appropriate guide below:
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- [OSX](https://docs.docker.com/docker-for-mac/install/#download-docker-for-mac)
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- [Windows](https://docs.docker.com/docker-for-windows/install/)
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- [Ubuntu](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/)
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- [Debian](https://docs.docker.com/engine/installation/linux/docker-ce/debian/)
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2. Launch Docker and adjust the preferences to allocate sufficient resources (e.g. > 4GB RAM)
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3. Build the docker image by opening a terminal in this repo folder and enter `docker build -t qwave .`
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4. Use the image to create a new container for the workshop
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- 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
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- `docker run -it -p 9999:9999 --name qwave -v ~/Desktop:/mnt dffr `
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- 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*!
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5. To launch any of the notebooks: `jupyter lab --port=9999 --no-browser --ip=0.0.0.0 --allow-root`
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## Using the container after setup
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1. You can always fire up the container by typing the following into a terminal
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- `docker start dffr && docker attach dffr`
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- When you see the `root@` prefix, letting you know you're inside the container
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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

paper/CDL-bibliography

Submodule CDL-bibliography added at bd3eb86

paper/main.tex

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\documentclass{article}
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\usepackage[utf8]{inputenc}
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\usepackage{geometry}
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\usepackage{natbib}
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\usepackage{pxfonts}
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\usepackage{graphicx}
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\usepackage{hyperref}
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\title{Network dynamics underlying contextually mediated intentional forgetting}
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\author{Jeremy R. Manning\\Dartmouth College, Hanover, NH\\[email protected]}
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\begin{document}
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\maketitle
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\begin{abstract}
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Abstract goes here...
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\end{abstract}
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Main text here...
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\section*{Acknowledgements}
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This work was supported in part by NSF EPSCoR Award Number 1632738. The content is solely my responsibility and does not necessarily represent the official views of my supporting organizations.
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\section*{Data and code availability}
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All analysis code and data used in the present manuscript may be found \href{https://github.com/ContextLab/directed-forgetting-network-dynamics}{\underline{here}}.
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\bibliographystyle{apa}
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\bibliography{CDL-bibliography/memlab}
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\end{document}

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