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‎_data/sidebars/main.yml‎

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url: /access#pathways
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- title: Access duration and renewal
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url: /access#duration
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- title: What does access include?
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url: /access#quotas
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- title: Acceptable use policy and service terms
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url: /aup
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subitems:
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- title: Acceptable use
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url: /aup#acceptable-use
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- title: Service commitments
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url: /aup#service-commitments
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- title: Privacy and data collection
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url: /aup#privacy
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- title: Choosing an environment size
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url: /flavours
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subitems:
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- title: About
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url: /about
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subitems:
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- title: How to cite
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- title: How to cite and acknowledge
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url: /about#cite
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- title: Contributors
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url: /about#contributors

‎index.md‎

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@@ -13,13 +13,11 @@ BioShell is a ready-to-use cloud bioinformatics environment designed to get you
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results with as little setup as possible. Rather than spending time configuring software on
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your own machine, you connect to BioShell and find a fully equipped workspace already waiting
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for you — with the tools, compute power, and interactive environments you need to run analyses
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that would be impractical on a laptop.
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that would be impractical on a laptop.
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BioShell is available through NCI Nirin and ARDC Nectar Research Cloud and is designed for
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researchers and learners at all stages. Whether you are a higher degree student running your
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first bioinformatics analysis, a trainer delivering a national workshop, or a researcher who
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needs a consistent and reproducible environment to share with collaborators, BioShell removes
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the technical overhead so you can focus on your science.
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Whether you are a higher degree student running your
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first bioinformatics analysis or a trainer delivering a national workshop, BioShell removes
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the technical overhead so you can focus on delivering science.
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This guide walks you through requesting access, choosing the right environment for your work,
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and using BioShell's built-in tools and support features. It assumes you are comfortable
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*Fig 1. Overview of the BioShell access and use flow: from submitting an access request
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through to connecting, choosing a flavour, loading tools, and launching interactive
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environments.*
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---
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## Operational partners
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BioShell is delivered through a collaboration between Australian BioCommons, the Sydney
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Informatics Hub at the University of Sydney, ARDC Nectar Research Cloud, and the National
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Computational Infrastructure.
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<div style="display: flex; flex-wrap: wrap; gap: 2rem; align-items: center; margin: 1.5rem 0;">
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<img src="{{ '/assets/img/Australian-Biocommons-Logo-Horizontal-RGB.png' | relative_url }}" alt="Australian BioCommons" style="max-height: 48px;">
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<img src="{{ '/assets/img/University%20of%20Sydney%20logo%20lockup%20-%20Sydney%20Informatics%20Hub%20-%20mono.png' | relative_url }}" alt="Sydney Informatics Hub, University of Sydney" style="max-height: 48px;">
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<img src="{{ '/assets/img/ARDC_Nectar_Research_Cloud_RGB.png' | relative_url }}" alt="ARDC Nectar Research Cloud" style="max-height: 48px;">
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<img src="{{ '/assets/img/NCI%20logo.png' | relative_url }}" alt="National Computational Infrastructure" style="max-height: 48px;">
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</div>

‎pages/about.md‎

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description: How to cite this guide, contributor acknowledgements, and references.
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---
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## How to cite this guide {#cite}
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## How to cite and acknowledge {#cite}
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If you use this guide in your research or training, please cite it as:
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### Acknowledging BioShell in outputs
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Acknowledge use of BioShell in relevant research, training, and innovation outputs using:
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> *"This work is supported by BioShell, a service provided by Australian BioCommons and its
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> partners. The service receives NCRIS funding through Bioplatforms Australia as well as
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> The University of Sydney."*
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and cite:
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> O'Brien M, Jaya F, Xue W, Al Bkhetan Z, Botting A, Gustafsson J. Samaha G (2026).
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> **BioShell how-to guide**. Australian BioCommons.
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> [AUTHOR TO SUPPLY — Zenodo DOI once minted]
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[AUTHOR TO SUPPLY — add bio.tools entry URL once registered]
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[AUTHOR TO SUPPLY — add WorkflowHub entry URL once registered]
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If you're a researcher, you're BioShell access has been provisioned through the ABLeS programme. Please also consider including:
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> *"The authors acknowledge the provision of computing and data resources provided by the
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> Australian BioCommons Leadership Share (ABLeS) program."*
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And cite ABLeS as:
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> Gustafsson et al. (2023). Enabling national step changes in bioinformatics through ABLeS,
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> the Australian BioCommons Leadership Share (3.0). Zenodo.
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> [https://doi.org/10.5281/zenodo.10139651](https://doi.org/10.5281/zenodo.10139651)
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---
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The authors acknowledge the support of Australian BioCommons which is enabled by NCRIS via
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Bioplatforms Australia funding.
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This guide makes use of the [ELIXIR toolkit theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme).
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{% include image.html file="elixir-toolkit-theme_logo.svg" alt="Elixir Toolkit Theme logo" max-width="15em" %}
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This guide is part of the [ABLeS programme](https://australianbiocommons.github.io/ables/),
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which supports life science research computing across Australian national infrastructure.
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BioShell is available through [ARDC Nectar Research Cloud](https://ardc.edu.au/services/ardc-nectar-research-cloud/)
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and [NCI Nirin](https://nci.org.au/our-systems/cloud-computing).
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BioShell is available through [ARDC Nectar Research Cloud](https://ardc.edu.au/services/ardc-nectar-research-cloud/) and [NCI Nirin](https://nci.org.au/our-systems/cloud-computing).
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---
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1. Gustafsson J, et al. (2023). Enabling national step changes in bioinformatics through
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ABLeS, the Australian BioCommons Leadership Share (3.0). Zenodo.
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https://doi.org/10.5281/zenodo.10139651
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2. CernVM-FS documentation. https://cvmfs.readthedocs.io/en/stable/
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3. Singularity Registry HPC (SHPC) documentation.
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https://singularity-hpc.readthedocs.io/
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4. BioContainers registry. https://biocontainers.pro/registry
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5. Galaxy Project CVMFS repositories. https://galaxyproject.org/admin/cvmfs/
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6. Nextflow documentation. https://www.nextflow.io/docs/latest/
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7. nf-core community. https://nf-co.re/
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8. FastQC. https://bio.tools/fastqc
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9. samtools. https://bio.tools/samtools
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10. plink. https://bio.tools/plink
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11. bwa. https://bio.tools/bwa
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12. STAR. https://bio.tools/star
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13. SPAdes. https://bio.tools/spades
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14. GATK. https://bio.tools/gatk

‎pages/access.md‎

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4. Your project should support collaboration and sharing of outputs where appropriate.
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5. You must comply with all relevant facility policies.
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For full eligibility criteria, see the [ABLeS eligibility page](https://australianbiocommons.github.io/ables/eligibility).
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For full eligibility criteria, see the [ABLeS eligibility page](https://australianbiocommons.github.io/ables/eligibility). By submitting an access request you agree to the [BioShell acceptable use policy and service terms](aup).
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### Who can apply?
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| Self-paced learning | Independent exploration and learning; no training event required |
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| Training projects | Nationally delivered or institutional life-science training activities |
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### What does access include? {#quotas}
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| | Training | Research | Development |
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|---|---|---|---|
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| Data analysis and visualisation | Yes | Yes | Yes |
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| Interactive interfaces (JupyterLab, RStudio) | Yes | Yes | Yes |
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| SSH CLI access | Yes | Yes | Yes |
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| Storage quota | 0 GB | 100 GB | 100 GB |
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| Allocation period | Training period | 3 months | 3 months |
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| Renewal | Not applicable — event bound | Yes, subject to review | Yes, subject to review |
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> **Note:** Storage quotas are enforced at the infrastructure level — it is not possible to
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> exceed your allocation. If you need more storage, contact the BioShell helpdesk. Requests
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> are subject to availability and review and cannot be guaranteed.
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## Your access pathway {#pathways}

‎pages/aup.md‎

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---
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title: Acceptable use policy and service terms
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description: The BioShell acceptable use policy, service level agreement, and privacy statement.
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---
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Submission of a BioShell access request, and use of the BioShell service following provisioning, denotes agreement with the [Australian BioCommons Services Acceptable Use Policy and Conditions of Use](https://portal.access.services.biocommons.org.au/terms/biocommons) in addition to the terms below.
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---
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## Acceptable use {#acceptable-use}
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1. **Sensitive data restrictions:** You are prohibited from using BioShell to host or process personal or sensitive data, including but not limited to personally identifying genetic, genomic, or health data.
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2. **Data hosting and retention:** BioShell is a compute environment, not a long-term data hosting service. You should only retain data for the period required for analysis, then export or download your results. Data are subject to the retention periods described in the [service commitments](#service-commitments).
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3. **Partner infrastructure compliance:** BioShell uses infrastructure provided by ARDC Nectar Research Cloud and the NCI Nirin Cloud. Your access to and use of BioShell is strictly conditional upon your compliance with the respective terms of use of those infrastructures as detailed in the [ARDC Nectar Research Cloud Terms of Use](https://dashboard.rc.nectar.org.au/terms/) and the [NCI Terms and Conditions of Access](https://nci.org.au/users/nci-terms-and-conditions-access). A breach of any partner infrastructure policy constitutes an immediate breach of this AUP.
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4. **Unacceptable use:** The following uses of BioShell are explicitly forbidden:
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- The deliberate or reckless creation, transmission, storage, or display of any offensive or menacing material, or any data capable of being resolved into such material.
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- Deliberate or reckless activities which seek to or result in:
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- Disruption to other users or to BioShell operations and support teams
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- Corruption of or disruption to data stored on BioShell or infrastructure partner systems
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- Introduction or transmission of malware into BioShell or partner infrastructure
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- Circumvention of quota enforcement or resource allocation mechanisms
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---
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## Service commitments {#service-commitments}
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### Best-effort operations
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We recognise that the work you do on BioShell is important to you. For that reason, we commit to making best efforts to keep the service as reliable and responsive as possible, and to keep your data intact.
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Our operational staff work normal Australian East Coast office hours (AEST/AEDT). During those hours we aim to triage support tickets within one business day. Resolution of tickets, outages, and issues will take longer outside normal office hours, on weekends, and on public holidays.
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BioShell runs on research-grade infrastructure contributed by our computational partners (ARDC Nectar and NCI Nirin). BioShell reliability and capacity may be impacted if partner infrastructure unexpectedly becomes unavailable. Users should monitor the relevant infrastructure status pages in the first instance:
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- ARDC Nectar: [https://status.rc.nectar.org.au/](https://status.rc.nectar.org.au/)
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- NCI Nirin: [https://nci.org.au/our-systems/status](https://nci.org.au/our-systems/status)
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### Service capacity
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BioShell provisions dedicated virtual machine environments for each approved project. Storage quotas are enforced at the infrastructure level — it is not possible to exceed your allocated storage quota. Additional storage cannot be guaranteed and must be requested through the BioShell helpdesk, subject to availability and review.
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No backup of VM data is provided by BioShell or its infrastructure partners. Users are responsible for ensuring their data is exported and stored appropriately.
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### Service lifetime
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BioShell operations are currently funded for the duration of the current Australian BioCommons funding period of 30 June 2028. Any extension or closure of the service will be communicated to registered users no less than 3 months prior to end-of-service.
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In the case of service closure, registered users will be notified with instructions on how to export and download their data before de-provisioning occurs.
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### Maintenance
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The maintenance and administration of BioShell is a balance between service uptime and the health of the service. From time to time the service may become unavailable during planned or unscheduled maintenance events.
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BioShell defers to its infrastructure partners for planned maintenance scheduling. Maintenance notices will be published by NCI and ARDC on their respective maintenance pages:
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- ARDC Nectar: [https://status.rc.nectar.org.au/outages/](https://status.rc.nectar.org.au/outages/)
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- NCI Nirin: [https://opus.nci.org.au/spaces/Help/pages/399802963/System+Maintenance+and+Notices](https://opus.nci.org.au/spaces/Help/pages/399802963/System+Maintenance+and+Notices)
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BioShell will communicate any platform-level maintenance affecting provisioning to registered users via the helpdesk email channel, with notice periods meeting or exceeding those provided by infrastructure partners. For unscheduled maintenance, BioShell will make every effort to give users as much advance notice as possible to limit disruption.
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### Managing storage quotas
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BioShell is a compute environment, not a long-term data storage service. You should only retain data for the period required for your project, and export or download your data before your allocation ends.
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Storage quotas are fixed at provisioning and enforced at the infrastructure level. You cannot exceed your allocated quota. If additional storage is required, submit a request to the BioShell helpdesk. Requests are subject to resource availability and review and cannot be guaranteed.
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At the end of your allocation period, you will be notified via email two weeks prior to de-provisioning with instructions on how to download your data and submit a renewal request if required. Data remaining on a de-provisioned VM cannot be recovered.
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---
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## Privacy and data collection {#privacy}
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BioShell is committed to protecting your privacy. We do not collect, process, retain, or share personal data other than for the purposes described below.
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**Usage data**
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In order to monitor and maintain BioShell, we may track and retain information about your use of the service, including login frequency and session activity, resource consumption and VM activity logs, and helpdesk interactions. Usage data collected by BioShell operational staff may be shared with Australian BioCommons for reporting purposes. When shared, data is aggregated and anonymised to protect your privacy.
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**Registration and onboarding data**
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When you submit a BioShell access request, we collect registration data including your name, institutional email address, organisation, and project details. This data is used to assess eligibility, provision access, and administer your project allocation.
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BioShell may contact registered users using the email address provided for operational reasons, including confirming your access request and provisioning details, communicating service downtime or maintenance, notifying you of actions being taken with respect to your allocation or data retention period, responding to your support requests, and communicating updates to BioShell policies.
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**Data you upload and store**
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BioShell stores data which you provision or upload to your VM environment voluntarily. You are responsible for ensuring your data complies with the Acceptable Use Policy. BioShell operational staff may examine data stored on provisioned VMs for the purposes of monitoring, troubleshooting, and verifying compliance with our Acceptable Use Policy.
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**Operator access to your VM environment**
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The BioShell operations team retains administrative access to provisioned VMs for the purposes of monitoring service health and providing technical support. This access will only be exercised where necessary for operational or support purposes.
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**Support requests**
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When you submit a support request to BioShell, we collect your email address and any additional information you provide as part of the support process. Support request data is stored in our instance of Freshdesk; please refer to the [Freshworks Privacy Policy](https://www.freshworks.com/privacy/) for further information. Note that Freshdesk data may be stored outside Australia.
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**Analytics**
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BioShell does not currently use third-party analytics tools. Aggregate usage statistics may be generated from infrastructure logs for reporting and service improvement purposes. When shared publicly, this data is anonymised.
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**Data location**
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All BioShell VM environments and associated storage volumes are hosted on Australian infrastructure provided by NCI and ARDC Nectar. Data stored on your VM does not leave Australia except in the following circumstances:
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- Support request data managed via Freshdesk may be stored outside Australia
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- Any data you choose to export or share externally is your own responsibility

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