Add BioShell context pages

Author: Mitchob

_data/sidebars/main.yml

@@ -1,6 +1,17 @@
 subitems:
   - title: Home
     url: /index
+  - title: Why BioShell?
+    url: /why-bioshell
+    subitems:
+      - title: What is a virtual machine?
+        url: /why-bioshell#what-is-a-vm
+      - title: Cloud vs HPC
+        url: /why-bioshell#cloud-vs-hpc
+      - title: Why BioShell?
+        url: /why-bioshell#why-bioshell
+      - title: BioShell and HPC
+        url: /why-bioshell#bioshell-and-hpc
   - title: Accessing BioShell
     url: /access
     subitems:

index.md

@@ -38,6 +38,9 @@ the BioCommons Training cooperative and
 
 ## Quick start guide
 
+> **Tip:** New to cloud computing or virtual machines? Read [Why use a cloud workspace?](why-bioshell)
+> first — it explains what BioShell is, how it compares to HPC, and whether it is right for your work.
+
 1. [Check you are eligible](access#eligibility) — confirm your project is life-science
    related and aligns with the five ABLeS principles.
 2. [Identify your access pathway](access#pathways) — most users apply through

pages/why-bioshell.md

@@ -0,0 +1,89 @@
+---
+title: Why use a cloud workspace for bioinformatics?
+description: An introduction to virtual machines, cloud computing, and why BioShell is a great starting point for life-science researchers and workshop participants.
+---
+
+If you are new to bioinformatics or planning a workshop, this page explains what cloud
+computing is, when to use it, and why BioShell makes it easy to get started.
+
+---
+
+## What is a virtual machine? {#what-is-a-vm}
+
+A virtual machine is a computer that runs inside another computer — delivered to you over the
+internet. You connect to it from your laptop or desktop, and it behaves like a full computer
+you have complete control over. You do not need to worry about your own hardware specs,
+operating system, or software installation.
+
+> Think of it like a fully-equipped lab bench that is always ready — you just sit down and
+> start working, then leave when you are done. The bench does not belong to you, but it is
+> set up exactly the way you need it.
+
+With a virtual machine you can:
+
+- Get more computing power than your laptop for data analysis
+- Share the same environment with colleagues or workshop participants
+- Run long jobs overnight without worrying about power outages or closing your laptop
+- Use a Linux environment even if you normally use Windows or macOS
+- Have administrator access to install software and configure the system
+- Host services such as databases or web servers
+
+---
+
+## Cloud vs HPC — which should I use? {#cloud-vs-hpc}
+
+Both cloud computing and High-Performance Computing (HPC) systems such as NCI Gadi are
+powerful research tools, but they suit different types of work.
+
+| | Cloud (BioShell) | HPC (e.g. NCI Gadi) |
+|--|-----------------|---------------------|
+| **Session type** | Interactive — work in real time | Batch — submit jobs and come back later |
+| **Interfaces** | JupyterLab, RStudio, CLI | CLI only (PBS/Slurm schedulers) |
+| **Setup required** | None — environment is preconfigured | Familiarity with job schedulers required |
+| **Best for** | Learning, workshops, exploratory analysis | Large-scale, tightly coupled, or long-running workloads |
+| **Scaling** | Flexible — choose your VM size on demand | Fixed allocations managed through project quotas |
+
+**Not sure which to use?** If you are learning bioinformatics, running a workshop, or
+exploring a new analysis, start with cloud. BioShell is the right choice. You can move to
+HPC later once your workflow is established and you need more compute power.
+
+---
+
+## Why BioShell? {#why-bioshell}
+
+Getting started on the command line is often the hardest part. Software installs break.
+Environments differ between computers. Trainers spend hours configuring machines instead of
+teaching. BioShell solves this.
+
+| Feature | What it means for you |
+|---------|----------------------|
+| **Ready to use** | Over 20,000 bioinformatics tools and reference datasets available — no setup required |
+| **Consistent everywhere** | The same environment works identically on Nectar and NCI Nirin |
+| **Training-ready** | Trainers can provision dozens of identical machines for a workshop in minutes |
+| **Multiple interfaces** | Access via SSH, or use JupyterLab and RStudio in your browser |
+| **Reproducible** | Containerised software means your analysis works the same way today, next year, and on a colleague's machine |
+| **Safe to explore** | You have administrator access to your own VM — mistakes only affect your own instance |
+
+---
+
+## How does BioShell fit with HPC? {#bioshell-and-hpc}
+
+BioShell is not a replacement for large-scale HPC — it complements it. Think of it as the
+place where you learn, develop, and test your workflows before scaling up.
+
+1. **Learn and explore on BioShell** — get comfortable with the command line, tools, and
+   your data in a low-pressure environment.
+2. **Develop and test your workflow** — build and validate your Nextflow or Snakemake
+   pipeline using BioShell's pre-installed tools and example datasets.
+3. **Scale up to HPC when ready** — once your workflow is confirmed and your data needs are
+   clear, move to NCI Gadi or another HPC system for large-scale runs.
+
+---
+
+## Ready to get started? {#get-started}
+
+BioShell is available to Australian life-science researchers, trainers, and developers
+through [ABLeS](https://australianbiocommons.github.io/ables/). Access is free — you just
+need to be affiliated with an Australian research organisation.
+
+[Check your eligibility and apply →](access#eligibility)