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+# Plotly
+
+To make plotly plot shows up in jupyterlab:
+
+$ jupyter labextension install jupyterlab-plotly
+
+# Reactome Setup Guide
+
+The following are the instructions to get Reactome running on Ubuntu 18.04. For other OS, please refer to the official Neo4j documentation.
+
+### 1. Install Java 8
+
+Neo4j specifically requires Java 8 to be installed. If you don't have Java installed, you can install it with the command below:
+```bash
+$ sudo apt install openjdk-8-jdk
+```
+Otherwise validate that you have Java 8 installed:
+```bash
+$ java -version
+openjdk version "1.8.0_181"
+```
+
+### 2. Install Neo4j Community Edition
+
+[Linux Installation - Neo4j Reference](https://neo4j.com/docs/operations-manual/current/installation/linux/debian/?_ga=2.249168388.2041192375.1507250087-893468657.1507250087).
+
+Run the following commands to install Neo4j Community Edition 3.4.6:
+```bash
+$ wget -O - https://debian.neo4j.org/neotechnology.gpg.key | sudo apt-key add -
+$ echo 'deb https://debian.neo4j.org/repo stable/' | sudo tee -a /etc/apt/sources.list.d/neo4j.list
+$ sudo apt-get update
+$ sudo apt-get install neo4j=1:3.4.6
+```
+Later version of Neo4j can also be used, as long as it is version 3 (version 4 seems to have problems with Reactome database).
+
+Verify that Neo4j is running:
+```bash
+$ sudo service neo4j status
+```
+From the status above, you can see that $NEO4J_HOME is located at `/var/lib/neo4j`. 
+If Neo4j is not running, start it:
+```bash
+$ sudo service neo4j start
+```
+
+Once it's running, [set the initial password](https://stackoverflow.com/questions/47530154/neo4j-command-failed-initial-password-was-not-set-because-live-neo4j-users-wer) to whatever you prefer.
+```bash
+$ curl -H "Content-Type: application/json" -X POST -d '{"password":"WHATEVER THE PASSWORD IS"}' -u neo4j:neo4j http://localhost:7474/user/neo4j/password
+```
+
+### 3. Install Reactome database
+
+See https://reactome.org/dev/graph-database
+
+Download the Reactome database. Extract and move it to `$NEO4J_HOME/data/databases`.
+```bash
+$ wget https://reactome.org/download/current/reactome.graphdb.tgz
+$ tar xvzf reactome.graphdb.tgz
+$ sudo mv graph.db /var/lib/neo4j/data/databases
+$ chown -R neo4j:neo4j /var/lib/neo4j/data/databases/graph.db
+```
+Edit the config file at either `$NEO4J_HOME/conf/neo4j.conf` or `/etc/neo4j/neo4j.conf`. 
+Change ```dbms.active_database``` to ```dbms.active_database=graph.db``` if necessary.
+
+Check that the neo4j service is running with the following command. If it is not running, start it.
+```bash
+$ sudo service neo4j status
+```
+
+For graph database connection in PALS, be sure to set the following environmental variables:
+- `NEO4J_SERVER`: your Neo4j server (default: bolt://localhost:7687)
+- `NEO4J_USER`: your Neo4j user name (default: neo4j)
+- `NEO4J_PASSWORD`: your Neo4j password (default: neo4j)
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