- What is Apollo Service?
Apollo software package is a web-based tool for visualising genomic contents and manually improving gene predictions. It allows researchers to work on a reference genome collaboratively. Apollo Service provides Australian researchers with customised, local instances of the Apollo software for their genome projects.
- How Can I Get an Apollo Instance?
Researchers from Australian-based research groups and research consortia <link to table of research institutes> can obtain an Apollo Instance by applying for an account at https://apollo-portal.genome.edu.au/signup. Further details can be found in the Getting Started tab.
- Can I trial Apollo before signing up?
To become familiar with the Apollo environment, please use the demonstration site created by the official Apollo developers, accessible via demo.genomearchitect.org with the credentials:
Further information about this demonstration site is available here.
- I am a Non-Australian based researcher, can I access the Apollo service?
The service is funded to support Australian-based research groups and consortia, and only Principal Investigators with an institutional email address from an Australian research institution may apply for a hosted Apollo instance. International collaborators are however very welcome to be invited to collaborate within an established instance, or view data. This is at the discretion of the instance managers.
- Can Apollo automatically annotate my genome?
No. Apollo is a tool to manually correct genome annotations that have already been produced from automated tools or pipelines. A non-exhaustive list of automated genome annotation tools are available in the table on this page.
- How can I get training to use Apollo?
Training for Apollo Portal Service is in development with plans to offer workshops or training to the Apollo Service in late 2021. Training announcements will be advertised to users through their email or via the Genome Annotation Google Group
Evidence data upload to your Apollo Instance is conducted in one of three ways
- Via the web interface (recommended for users with data files with a total size < XX GB)
- Via the command line (recommended for users with data files > XX GB confident in the use of command-line data transfers).
- Via CloudStor (recommended for users with data files > XX GB who are not confident in command line data transfer or uploads).
- How Can I Get an Apollo Instance?
Researchers from Australian-based research groups and research consortia <link to table of research institutes> can obtain an Apollo Instance by applying for an account at https://apollo-portal.genome.edu.au/signup. Further details can be found in the Getting Started tab <link to answer>.
Evidence data can only be uploaded to an Apollo Instance by the Principle Investigator or Project Administrator of that Instance. Further details can be found in the tutorial documentation <link to answer in documentation>
- How long will my Apollo Instance be around?
- Do I have to pay for my Apollo Instance?
No. The service is fully subsidised for Australian researchers and their collaborators thanks to: National Collaborative Research Infrastructure Strategy (NCRIS) investments made by Bioplatforms Australia and the Australian Research Data Commons (ARDC), investment from the Queensland Government’s Research Infrastructure Co-investment Fund and generous computational resourcing from the Pawsey Supercomputing Centre.
- Who will have access to my data on Apollo?
Control over the access to curate or view data is determined by the Project Administrator of the Apollo Instance. Access to data in your Apollo Instance is by default private with access for public view and restricted view granted by the Project Administrator.
- Can I publish my genomes using Apollo?
Yes. As the manager of an Apollo instance, just upload the genome, any associated aligned genomics data then make genomes and tracks viewable by the public.
- Is there a help desk I can contact?
Yes. To access help with your Apollo Instance please email support at firstname.lastname@example.org.
- What is the difference between Apollo and JBrowse?
JBrowse is a web-browser based genome browser that can be used to interactively view and explore a genome and any aligned genomics data (e.g. sequences reads of transcripts).
Apollo is a tool that is built on top of JBrowse that lets users view a genome, associated annotation file and any other aligned genomics data, but also enables trusted users to curate/correct the genome annotation files by making changes.
- Can I make my genomes available to view to the public?
Yes. As the manager of an Apollo instance you can choose to make genomes and tracks viewable by the public.
- Can I make my genomes private?
Yes. As the manager of an Apollo instance you can choose to make genomes and tracks private and only viewable (and editable if you like) by trusted collaborators.
- I have sensitive genomic data, can I use this Apollo Portal Service?
The Apollo Service is not designed to handle sensitive 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.
- Will my personal and genome data be shared?
Apollo Portal Service stores data which you provide to us voluntarily when you upload data or annotate data. You are prohibited from using Apollo Portal Service to host or process sensitive data, including but not limited to personal data. We may examine the data you share through the service for alignment with our Acceptable Use Policy <link>.
- Where is my genome data hosted?
All other data is stored and processed in Australia by our Operational Partners.
- How can I acknowledge the Apollo Instance that was built for me?
When you use Apollo Portal to support your publication or project, please cite its use using the following acknowledgement statement:
This work is supported by the Apollo Portal service provided by the Australian Biocommons and its partners. The service 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.