Apollo Service Terms of Use and Policies

Table of Contents

Definitions

Terms of Use

Apollo Portal and Apollo Service Privacy Policy

Apollo Portal and Apollo Service Operational Partners

Apollo Service Feature Catalogue

Apollo Portal and Apollo Service Acceptable Use Policy

Apollo Service Acknowledgment Statement

List of Australian Research Institutions

Definitions

Apollo

Apollo ^[1] is a web application for visualising and sharing genome assemblies and annotations, and curating (i.e. manually improving) genome annotations.

Apollo Portal

The Apollo Portal is the website apollo-portal.genome.edu.au where researchers can access information about the Apollo Service, access public genome tracks, and apply for the creation of an Apollo Instance. Users can also find relevant documentation and guidelines regarding service support, funding, acknowledgement, tutorials, and frequently asked questions.

Apollo Service

The “Apollo Service” (the Service) is offered by Australian BioCommons ^[2] and a number of its Operational Partners as part of their collective mission to provide access to the digital techniques, data and tools, used by environmental, agricultural and biomedical researchers.

The Service includes hosted Apollo Instances where the majority of the systems administration tasks are taken care of by the Operators of the Service, allowingAustralian-based research groups to upload genome assembly, genome annotation and supporting evidence files, and focus on the annotation curation itself. Apollo Service is the complete Service that is provided to its users which includes the creation of an Apollo Instance, ongoing user support, maintenance of the instance, communications about the Service, the creation and improvement of tutorials and documentation, and the development and delivery of training materials and workshops.

Apollo Instance

An Apollo Instance is a virtual machine running the Apollo software that is used to host data owned by your research group or consortium created with the software package, Apollo ^[1] . The Apollo Instance, if granted, will be hosted on resources provided by the Apollo Service.

User Types

Due to the nature of how a hosted Apollo Instance can be created and managed through the Service, this document discerns between the following distinct user types and roles. Note that one individual may perform more than one of these roles.

Customer Roles

• Principal Investigators and Administrators (i.e. Project Administrators, Organism Administrators and Group Administrators), are considered to be the primary customers of the Apollo Service and must adhere to the Apollo Service Terms of Use and Policies.
• Principal Investigators and Administrators can invite or otherwise permit End Users or Viewers to interact with their hosted Apollo Instance, and as such are obliged to ensure End Users and Viewers adhere to the terms and conditions laid out in this document.

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Terms of Use

Interaction with any of:

1. The Apollo Portal website apollo-portal.genome.edu.au , or
2. Apollo browser workspaces hosted through the Apollo Service (these are denoted by URLs in the format https://YourHostName.genome.edu.au/apollo/annotator), or
3. JBrowse-based genome browsers hosted through the Apollo Service (these are denoted by URLs in the format https://YourHostName.genome.edu.au/apollo/jbrowse).

Denotes agreement with the following terms:

1. Use of service
   1. The Apollo Portal and Apollo Service are part of Australian BioCommons' suite of services that aim to provide fully subsidised access to publicly available services. At the discretion of an Apollo Administrator, anonymous use by Anonymous (public) Viewers of data is permitted.
   2. Principal Investigators affiliated with a recognised Australian academic or research institute may choose to register for an account via the Apollo Portal on behalf of their Research Group or a Research Consortium in order to access the features described in our feature catalogue .
   3. Administrators (including Project Administrators, Organism Administrators and Group Administrators) are authorised to add/remove data and End Users (Curators) and Viewers in accordance with the features described in our feature catalogue .
   4. End Users (Curators) are authorised to modify data in accordance with the features described in our feature catalogue.
   5. Your access to Apollo Portal and Apollo Service (no matter what role) is provided under the condition that you abide by the Apollo Portal and Apollo Service Acceptable Use Policy.
   6. You indemnify and hold the Apollo Service Operational Partners free and harmless in connection with your use of the service.
   7. You agree to acknowledge use of the Apollo Service in your research outputs using the format of our Apollo Service Acknowledgement Statement.
2. Data hosting and analysis
   1. The Apollo Service is designed to support visualising, curating, annotating and sharing genome assemblies and annotations. If you choose to upload and host data in the Service you shall ensure that you comply with applicable laws, including, but not limited to, privacy, data protection and intellectual property rights. It is the responsibility of the Principal Investigator and Project Administrator of an Apollo Instance to notify End Users of their responsibility to comply with these laws.
   2. The Apollo Service is not designed to handle sensitive data, including potentially re-identifiable data. You are prohibited from using the Service to store or process sensitive data, including but not limited to personally identifying genetic, genomic or medical data.
   3. Due to the incremental and long-term nature of manual genome annotation curation, the Apollo Service is designed for long term storage of genome assembly and annotation data. However, the overall Service is subject to storage quota limits, and it is necessary for Project and Organism Administrators, to routinely monitor the volume of large supporting data files (e.g. BAM) associated with each organism. Please only host large supporting data files for the period required for analysis/curation and then export/download supporting data files.
   4. If an Instance is underutilised, the Apollo Service Operational Partners reserve the right to reallocate the resources to other users.
   5. It is the responsibility of the Principal Investigator and Project Administrator to ensure all other Administrators, Curators and End Users have read, acknowledged and adhered to these Terms of Use.
3. Sharing content
   1. The Apollo Service is designed to support open science. Project and Organism Administrators may choose to share “content” (such as annotations).
   2. Principal Investigators, Project and Organism Administrators and any End Users (Curators) associated with each organism are the collective owners of this content.
   3. Principal Investigators, Project and Organism Administrators can choose to delete their content at any time.
   4. Download and use of content from the Apollo Portal and Apollo Service do not transfer any intellectual property rights in the content to you.
4. Termination
   1. The Apollo Service Operational Partners reserve the right, without notice, at its sole discretion and without liability:
      1. to alter, delete or block access to content that it deems to be inappropriate, and
      2. to restrict or remove access where it considers that your use of the Apollo Portal and Apollo Service interferes with its operations or violates these Terms of Use or applicable laws.
5. Change of terms
   1. These Terms of Use are subject to change at any time and without notice. Updates or modifications to the Terms of Use will be communicated on the apollo-portal.genome.edu.au/ website and via email to registered account holders.
6. Service maintenance and downtime
   1. The Apollo Service will have scheduled recurring and occasional maintenance downtime for updates and security patching of the Service. Recurring scheduled maintenance downtime will occur each Monday morning between 8:00 am and 9:00 am AEST. During these periods, the Service may become momentarily unavailable due to necessary and unavoidable maintenance and/or testing.
   2. Occasional scheduled maintenance downtimes will be reserved for larger upgrades, updates or testing, and will occur irregularly outside of the normal scheduled recurring maintenance timeframes. Users will be notified two weeks prior to an occasional scheduled maintenance downtime via email communication at the address provided by the user when joining the Apollo Service.
   3. In the event of a security breach, Apollo Portal and Apollo Service may need to perform urgent maintenance resulting in Service downtime at a time other than the scheduled maintenance windows. In this case, Apollo Portal and Apollo Service will make every effort to give the user/s as much advance notice as is possible to limit disruption.

If you have any questions or comments with respect to the Apollo Portal and Apollo Service, or if you are unsure whether your intended use is in line with these Terms of Use, or if you seek permission for a use that does not fall within these Terms of Use, please contact us via apollo-support@genome.edu.au.

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Apollo Portal and Apollo Service Privacy Policy

Apollo Portal and Apollo Service are committed to protecting your privacy. The Apollo Service Operational Partners do not collect, process, retain or share personal data other than for the purposes described below.

1. Usage data

   1. In order to monitor and enhance Apollo Portal and Apollo Service, the Apollo Service Operational Partners track and retain information about your interaction with the Service (i.e. IP addresses, cookies, pages visited, etc).

   2. The Apollo Service Operational Partners may share log files of interactions with the Service in aggregation with our Operational Partners.

   3. The Apollo Service Operational Partners may share debugging information with the Apollo ^[3] and JBrowse ^[4] developers to improve their systems. When the Apollo Service Operational Partners do, the Apollo Service Operational Partners aggregate and anonymise this data to protect your privacy.

   4. For promotional reasons and reporting to funding bodies, Apollo Portal and Apollo Service periodically create public usage reports. When the Apollo Service Operational Partners do, the Apollo Service Operational Partners aggregate and anonymise this data to protect your privacy.

2. Registration data

   1. If you choose to register an account with Apollo Portal and Apollo Service, the Apollo Service Operational Partners collect registration data (i.e. email address, institutional affiliation and public name).

   2. Apollo Portal and Apollo Service may contact registered account holders using the email address they provide for operational reasons, including:

      1. Checking user account security;

      2. Communicating service downtime;

      3. Communicating service improvements;

      4. Communicating actions the Apollo Service Operational Partners are taking with respect to data quotas, retention periods, and compute resource usage;

      5. Responding to support requests;

      6. Surveying existing and planned use in order to improve and promote the Service;

      7. Discussing breaches of these Terms of Use, and;

      8. Communicating updates to Apollo Portal and Apollo Service policies.

   3. Apollo Portal and Apollo Service may contact registered account holders using the email address they provide for promotional reasons, such as seeking consent and content for newsletters, annual reports or media releases by Australian BioCommons, operational partners and funding partners.

   4. Apollo Portal and Apollo Service list the names of Research Group/Lab or Consortium using the Service on this page.

3. Data you upload and share

   1. Apollo Portal and Apollo Service stores data that you provide to us voluntarily when you upload data or annotate data.

   2. You are prohibited from using Apollo Portal and Apollo Service to host or process sensitive data, including but not limited to potential re-identifiable or identifiable personal data.

   3. The Apollo Service Operational Partners may examine the data you share through the Service for alignment with our Apollo Portal and Apollo Service Acceptable Use Policy.

4. Support requests

   1. When you submit a support request with Apollo Service, the Apollo Service Operational Partners collect your email address and may ask for personal data as part of the support process.

   2. Data collected as part of a support request is stored in an instance of Freshdesk and is subject to the Freshworks Privacy Policy which can be found at https://freshworks.com/privacy.

5. Cookies

   1. Apollo Portal and Apollo Service use cookies to identify users/computers in order to maintain user sessions (e.g. to provide/maintain analysis results while you browse the website).

   2. Apollo Portal and Apollo Service cookies are not linked to your personal information.

   3. If you prefer not to receive cookies, you may set your browser to warn you before accepting cookies or you may also refuse all cookies by turning them off in your browser. Not accepting Apollo Portal and Apollo Service cookies will limit the functionality of the Service.

6. Data location

   1. Google Analytics uses cookies to generate data that may be transmitted and stored in Google servers outside Australia.

   2. User support data managed by Freshdesk may be stored outside Australia.

   3. All other data is stored and processed in Australia by our Operational Partners, and will not be provided to any third party unless

      1. You choose to share content through the Service, and;

      2. The Apollo Service Operational Partners are required to do so by law.

7. Modifying and removing personal data
   1. The personal information collected by Apollo Portal and Apollo Service for registered account holders includes name, organisation and email address associated with the Apollo Instance. Optimally the Apollo Service Operational Partners may also store a user's account name and GitHub account name.
   2. Registered account holders can modify collected information or request the removal of personal information at any time with effect for the future by emailing apollo-support@genome.edu.au.

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Apollo Portal and Apollo Service Operational Partners

Australian BioCommons (hosted by the University of Melbourne ) operates Apollo Portal Service in collaboration with Queensland Cyber Infrastructure Foundation with investment from the Queensland Government's Research Infrastructure Co-investment Fund (RICF) and Bioplatforms Australia. The Service is underpinned by computational resources provided by the Pawsey Supercomputing Centre.

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Apollo Service Feature Catalogue

Apollo Service features and quotas by account type

Principal Investigators must be affiliated with a recognised Australian academic or research institute, and register using an email address from our list of Australian research institutions.

Best effort operations

The Apollo Service Operational Partners realise that the data and annotations you host with Apollo Service are important to you. For that reason, the Apollo Service Operational Partners commit to making the best efforts to keep the Service as reliable and responsive as possible and to keep your data intact.

Our operational staff work normal Australian East Coast office hours. During those hours the Apollo Service Operational Partners aim to triage tickets, tool requests and reference data requests within one business day. Resolution of tickets, requests, outages and issues will take longer outside normal office hours, on weekends, and on public holidays.

The Apollo Service runs research-grade infrastructure contributed by the Apollo Service Operational Partners. Apollo Portal and Apollo Service's reliability and capacity may be impacted if partner infrastructure unexpectedly becomes unavailable.

Service capacity

The Apollo Service is underpinned by significant compute and storage capabilities, allowing you to scale analysis beyond your desktop computer. The Apollo Service Operational Partners periodically project capacity requirements, taking into account growth in users, jobs and community requests for new types of analysis that might need specialised hardware. From time to time the Apollo Service may reach capacity, resulting in delays in provisioning new Apollo Instances.

Service lifetime

The service will continue for the lifetime of Australian BioCommons, which is currently funded until June 2028. In case of closure of the Service, registered account holders can download their hosted data and content via Apollo's existing export mechanisms.

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Apollo Portal and Apollo Service Acceptable Use Policy

1. You may use the Apollo Service to visualise, manipulate, analyse and interpret life science data for the purposes of research.

2. You agree to interact with the Apollo Portal and Apollo Service Community (defined as other users of the service, technical support staff, operational staff, and those involved in the governance of the service) in a responsible and respectful manner at all times, consistent with the Australian BioCommons Code of Conduct.

3. The following uses of the Apollo Portal and Apollo Service are explicitly forbidden:

   1. The deliberate or reckless creation, transmission, storage, downloading, or display of any offensive or menacing images, data, metadata or other material, or any data capable of being resolved into such images or material;

   2. Use which constitutes an infringement of any intellectual property rights of another person or group;

   3. The creation of duplicate user accounts and/or double registration by a single user for the purposes of intentionally receiving increased quota on the Apollo Service;

   4. Attempt to circumvent the appropriate authentication or access control measures, security or restrictions on the use of a registered account, including the unauthorised distribution or use of tools of any kind for compromising security;

   5. The storage or processing of any sensitive data, including but not limited to potentially personally identifying genetic, genomic or medical data;

   6. Communications which would be actionable under the law of defamation;

   7. Use for private or business purposes other than scientific research, and;

   8. Deliberate or reckless undertaking of activities which seek to, or result in:

      1. the imposition of (or attempted imposition of) an unreasonable burden on the Apollo Portal and Apollo Service Systems Administration team;

      2. corruption of, or disruption to, data stored on the Apollo Portal and Apollo Service, or to the data of another user;

      3. disruption to other users, and/or;

      4. introduction or transmission of malware into the Apollo Portal and Apollo Service's systems.

Other uses of the Apollo Portal and Apollo Service are only permitted with the written permission of the Apollo Service Manager (contact via apollo-support@genome.edu.au).

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Apollo Service Acknowledgment Statement

The Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons (https://doi.org/10.47486/PL105), as well as Queensland Government RICF funding.

When papers acknowledge the Australian Apollo Service, they support continued research infrastructure investments by institutions and governments. When you use the Australian Apollo Service to support your publication or project, please cite its use using the following acknowledgement statement and web address:

This work was supported by the Australian Apollo Service https://apollo-portal.genome.edu.au/ provided by Australian BioCommons and Operational Partners.

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List of Australian Research Institutions

The Apollo Portal and Apollo Service are for use by publicly funded Australian researchers (and their international collaborators), as described in our feature catalogue. Access to the features and quotas is available to Principal Investigators registered using an email address from one of the Australian Research Institutions listed in the table below. The Apollo Service Operational Partners acknowledge that this list may not be exhaustive. Please contact us ( apollo-support@genome.edu.au ) to request the addition of your research institution to this list.

Australian research institution	Email domains
ANZAC Research Institute	@anzac.edu.au
Australia New Zealand Gynaecological Oncology Group	@anzgog.org.au
Australian Catholic University	@myacu.edu.au, @acu.edu.au
Australian Centre for Heart Health	@australianhearthealth.org.au
Australian Institute of Aboriginal and Torres Strait Islander Studies	@aiatsis.gov.au
Australian Institute of Marine Science	@aims.gov.au
Australian Museum	@nma.gov.au
Australian National University	@anu.edu.au
Australian Red Cross	@redcrossblood.org.au
Baker Heart and Diabetes Institute	@baker.edu.au, @bakeridi.edu.au
Bond University	@bond.edu.au
Burnet Institute	@burnet.edu.au
Calvary	@calvarymater.org.au
Cancer Council NSW	@nswcc.org.au
Cancer Council Queensland	@cancerqld.org.au
Cancer Council Victoria	@cancervic.org.au
Centenary Institute of Cancer Medicine and Cell Biology	@centenary.org.au
Central Adelaide Local Health Network Incorporated	@sa.gov.au
Central Australian Aboriginal Congress Aboriginal Corporation	@caac.org.au
Central Queensland University	@cqu.edu.au
Centre for Eye Research Australia	@cera.org.au
Charles Darwin University	@cdu.edu.au
Charles Sturt University	@csu.edu.au
Children's Medical Research Institute	@cmri.org.au
CSIRO	@csiro.au
Curtin University	@curtin.edu.au, @student.curtin.edu.au, @postgrad.curtin.edu.au
Deakin University	@deakin.edu.au
Ear Science Institute Australia Incorporated	@earscience.org.au
Edith Cowan University	@ecu.edu.au
Federation University Australia	@federation.edu.au
Flinders University	@flinders.edu.au
Florey Institute of Neuroscience and Mental Health	@florey.edu.au
Griffith University	@griffith.edu.au, @griffithuni.edu.au
Health Support Queensland	@health.qld.gov.au
Heart Research Institute	@hri.org.au
Hudson Institute of Medical Research	@hudson.org.au
Institute for Breathing and Sleep
James Cook University	@jcu.edu.au, @my.jcu.edu.au
La Trobe University	@latrobe.edu.au, @students.latrobe.edu.au
Ludwig Institute for Cancer Research	@ludwig.edu.au
Macquarie University	@mq.edu.au, @students.mq.edu.au, @hdr.mq.edu.au
Mater Research	@mater.org.au
Melanoma Institute Australia	@melanoma.org.au
Melbourne Health	@mh.org.au
Menzies School of Health Research	@menzies.edu.au
Metro South Hospital and Health Service	@health.qld.gov.au
Monash University	@monash.edu, @student.monash.edu
Murdoch Childrens Research Institute	@mcri.edu.au
Murdoch University	@murdoch.edu.au, @student.murdoch.edu.au, @ccg.murdoch.edu.au
Museum Victoria	@museum.vic.gov.au
National Acoustic Laboratories	@nal.gov.au
National Ageing Research Institute	@nari.edu.au
National Institute for Aboriginal and Torres Strait Islander Health Research	@lowitja.org.au
NSW Health Pathology	@health.nsw.gov.au
Peter MacCallum Cancer Centre	@petermac.org
Queensland University of Technology	@qut.edu.au
RMIT University	@rmit.edu.au, @student.rmit.edu.au
Royal Brisbane and Women's Hospital Foundation	@rbwhfoundation.com.au
South Australian Health and Medical Research Institute	@sahmri.com
South Australian Museum	@samuseum.sa.gov.au
Southern Cross University	@scu.edu.au, @student.scu.edu.au
St Vincent's Institute of Medical Research	@svi.edu.au
St Vincent’s Health Australia	@svha.org.au
Swinburne University of Technology	@swin.edu.au, @student.swin.edu.au
Sydney Local Health District	@health.nsw.gov.au
Telethon Kids Institute	@telethonkids.org.au
The Asbestos Diseases Research Institute	@adri.org.au
The Bionics Institute of Australia	@bionicsinstitute.org
Queensland Institute of Medical Research	@qimr.edu.au, @qimrberghofer.edu.au
The Garvan Institute of Medical Research	@garvan.org.au
The George Institute for Global Health	@georgeinstitute.org
The Olivia Newton-John Cancer Research Institute	@onjcri.org.au
The Prince Charles Hospital	@health.qld.gov.au
The Sax Institute	@saxinstitute.org.au
The University of Adelaide	@adelaide.edu.au
The University of New England	@une.edu.au
The University of Newcastle	@newcastle.edu.au
The University of Notre Dame Australia	@nd.edu.au
The University of Queensland	@uq.edu.au
Walter and Eliza Hall Institute	@wehi.edu.au
Torrens University Australia	@torrens.edu.au
Townsville Hospital and Health Service	@health.qld.gov.au
Trans Tasman Radiation Oncology Group	@trog.com.au
University of Canberra	@canberra.edu.au
University of Melbourne	@unimelb.edu.au, @student.unimelb.edu.au
University of New South Wales	@unsw.edu.au, @ad.unsw.edu.au, @student.unsw.edu.au
University of South Australia	@unisa.edu.au, @mymail.unisa.edu.au
University of Southern Queensland	@usq.edu.au
University of Sydney	@sydney.edu.au, @uni.sydney.edu.au
University of Tasmania	@utas.edu.au
University of Technology Sydney	@uts.edu.au, @student.uts.edu.au
University of the Sunshine Coast	@usc.edu.au, @student.usc.edu.au, @research.usc.edu.au
University of Western Australia	@uwa.edu.au, @student.uwa.edu.au, @research.uwa.edu.au
University of Wollongong	@uow.edu.au, @uowmail.edu.au
VCS Foundation	@vcs.org.au
Victor Chang Cardiac Research Institute	@victorchang.edu.au
Victoria University	@vu.edu.au
Wesley Medical Research	@wesleyresearch.com.au
Western Sydney Local Health District	@health.nsw.gov.au
Western Sydney University	@westernsydney.edu.au
Woolcock Institute of Medical Research	@woolcock.org.au

[1] Information about Apollo software and documentation can be found here and the article: Dunn et al, 2019 PLoS Comp. Biol.

[2] Australian BioCommons is hosted by the University of Melbourne.

[3] The Apollo Service uses the application Apollo, developed for genome annotation, curation and visual sharing, detailed here.

[4] The Apollo Service and Apollo use the platform technology JBrowse , built for the visualisation of biological data.

[5] DBPA - Decided by Project Administrator.

[6] Publish here is defined as making a track publicly accessible via URL to either a restricted viewer outside of the Apollo Instance or a public anonymous viewer outside of the Apollo Instance.