Please complete the prerequisites before arriving

Most importantly, download the Docker images in advance, the conference venue's Wi-Fi may be slow and unreliable. Looking forward to meeting you — Mitchell Shiell, Ontario Institute for Cancer Research, mshiell@oicr.on.ca

IBC Workshop Prerequisites

This workshop has been developed as part of the 19th Annual International Biocuration Conference, it will guide you through building a foundational data discovery portal for tabular CSV data using Elasticsearch, Arranger, and Stage.

👋 Say hello

If you're attending, feel free to drop a quick introduction before the day, this helps tailor the session to the room. Entirely optional.

Objectives:

1. Deploy a functional data discovery portal using Elasticsearch, GraphQL, Arranger, and Stage
2. Configure search interfaces and indices tailored to tabular datasets
3. Gain familiarity with the tools needed to adapt this portal to your own data
4. Understand deployment options for making portals accessible on institutional networks and beyond

Prerequisites

The following software should be installed and verified before the workshop:

1. Git git --version returns a version number

Download from git-scm.com if the command is not recognised.

2. Docker Desktop (28.0.0 or later)

• macOS / Windows: Download from docker.com/products/docker-desktop
• Linux: Follow the Docker Engine install guide

Once installed, open Docker Desktop → Settings → Resources and set:

• CPUs: 4+ cores (8 recommended)
• Memory: 8 GB minimum
• Disk: 10 GB+ available

Please ensure docker --version and docker compose version both return version numbers, and Docker Desktop is running with 4+ CPUs and 8 GB+ memory allocated

3. Docker images pre-downloaded Most time-consuming step, run these before the workshop

Pull the required Docker images now to avoid slow downloads during the workshop:

docker pull alpine/curl:8.8.0
docker pull postgres:15-alpine
docker pull docker.elastic.co/elasticsearch/elasticsearch:7.17.27
docker pull ghcr.io/overture-stack/arranger-server:4919f736
docker pull ghcr.io/overture-stack/conductor:171d9ce
docker pull node:18-alpine

Verify all six downloaded:

docker images | grep -E "alpine/curl|postgres|elasticsearch|arranger-server|conductor|node"

You should see all six images listed.

4. Repository cloned: git clone -b IBCworkshop https://github.com/overture-stack/prelude.git

The prelude repository contains everything needed for this workshop: Docker Compose configuration, the Conductor wrapper script, and sample data. Clone it once before the workshop and you won't need internet access for the hands-on portion.

git clone -b IBCworkshop https://github.com/overture-stack/prelude.git

5. (Windows only) WSL2 configured with Docker Desktop integration enabled

1. Install WSL2
2. Use Ubuntu or another Linux distribution within WSL2
3. Enable Docker Desktop's WSL2 integration (Docker Desktop → Settings → Resources → WSL Integration)
4. Run all workshop commands from a Bash terminal inside WSL2, not PowerShell or Command Prompt. To open one, search for your Linux distribution (e.g. "Ubuntu") in the Start menu.

Optional Prerequisites

These are not required but will make the workshop easier to follow:

6. (Optional) Elasticvue: browser-based Elasticsearch GUI

Elasticvue is a browser-based Elasticsearch GUI useful for inspecting indices, browsing documents, and troubleshooting. It is not required but helpful for understanding what's happening inside Elasticsearch during the workshop.

Install it as a browser extension or standalone app.

7. (Optional) PostgreSQL GUI client

A PostgreSQL GUI client is useful for browsing the database during the workshop. It is not required but helpful if you want to inspect the Postgres data directly.

OS	Recommended client
macOS	Postico
Windows	pgAdmin
Linux	pgAdmin

8. (Optional) Bring your own data: CSV file

If you have a tabular dataset you'd like to use during or after the workshop, bring it as a CSV file. During the workshop we will use demo data, but the final section covers adapting the portal to your own dataset.

Schedule

Venue: Pacific 2

Time	Section	Description
2:00–2:20	Introduction & Overview	Workshop objectives, run the pre-built demo, and architecture walkthrough
2:20–3:30	Building Your Portal	Prepare data, generate configurations, wire up Docker, Launch & Load data
3:30–3:40	Break	Stretch break
3:40–4:00	Wrap-Up	Customize the portal, discuss next steps, and Q&A

Support

During the workshop	A link with Slack Channel support will be provided
Before or after	community support channels or contact@overture.bio
Bug reports	GitHub Issues

Facilitator: Mitchell Shiell, Ontario Institute for Cancer Research, mshiell@oicr.on.ca

Verification Checklist

Before the workshop, confirm:

1. git --version returns a version number
2. docker --version returns 28.0.0 or later
3. docker compose version returns a version number
4. Docker Desktop is running with 4+ CPUs and 8 GB+ memory allocated
5. All six Docker images are downloaded (docker images) — this is the most time-consuming step, do it before the day
6. The repository is cloned and you can cd into it
7. (Windows only) WSL2 is configured and Docker integration is enabled

Troubleshooting: If you run into issues before the workshop, reach out via the community support channels or email mshiell@oicr.on.ca.