Australian Fgenesh++ on Galaxy Service on Galaxy Australia

Terms of Use and Policies

Version 1.0 (published 5 September 2023)

1. Definitions

1.1 Fgenesh++ Software

Fgenesh++ is a pipeline for automatic prediction of genes in eukaryotic genomes based on proprietary gene finding software. The software package includes both public software and data [1] as well as copyrighted software [2] which is owned by the company, Softberry Inc. Fgenesh++ software can NOT be used, copied or distributed without a license from Softberry Inc.

1.2 Fgenesh++ on Galaxy Service

The “Fgenesh++ on Galaxy Service” (the Service) is offered by the Australian BioCommons [3] and a number of its Operational Partners as part of their collective mission to provide access to digital techniques, data and tools, used by environmental, agricultural and biomedical researchers.

The Service includes access to a licensed copy of Fgenesh++ and relevant gene finding matrices that are installed on a virtual machine for a set time period. The majority of the systems administration tasks are taken care of by the Operators of the Service, which allows Australian-based research groups to upload genome assemblies and supporting evidence files to be annotated using the software.

“Fgenesh++ on Galaxy Service” (the Service) refers to the complete service that is provided to its users. This includes: (a) an online application form to enable users to apply to use the software, (b) user support from Galaxy Australia team (and Softberry Inc. when required), (c) maintenance of the software and communications about the Service, (d) the creation and improvement of tutorials and documentation, (e) the development and/or delivery of training materials and/or events for Australian audiences and (f) operation of the Service is in accordance with Galaxy Australia Terms and Conditions (https://site.usegalaxy.org.au/about), where there is a conflict between these Terms of Use and Galaxy Australia Terms and Conditions, Galaxy Australia Terms and Conditions take precedence.

2. Terms of Use

Interaction with any of:

• The Australian Fgenesh++ on Galaxy Service Support website: https://www.biocommons.org.au/fgenesh-plus-plus, and
• Fgenesh++ software on Galaxy Australia.

Denotes agreement with the following terms:

2.1. Use of service

1. The Fgenesh++ on Galaxy Service is part of the Australian BioCommons suite of services that aim to provide fully subsidised access to publicly available services.
2. End Users affiliated with a recognised Australian academic or research institute (see Section 8) may choose to apply for access via the Fgenesh++ on Galaxy Service Application Form.
3. End Users interact with Fgenesh++ in accordance with the features described in our feature catalogue (Section 5).
4. Your access to the Fgenesh++ on Galaxy Service is provided under the condition that you abide by the Fgenesh++ on Galaxy Service Acceptable Use Policy (Section 6).
5. You indemnify and hold the Fgenesh++ on Galaxy Service Operational Partners free and harmless in connection with your use of the Service.
6. You agree to acknowledge the use of the Fgenesh++ on Galaxy Service in your research outputs using the format of our Fgenesh++ on Galaxy Service Acknowledgement Statement (Section 7).

2.2 Data hosting and analysis

1. The Fgenesh++ on Galaxy Service is designed to support the automated annotation of your genomes. If you choose to upload and host data in Galaxy Australia 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 End User to comply with these laws.
2. The Fgenesh++ on Galaxy Service is not designed to handle sensitive data, including potentially re-identifiable human-derived 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. The Fgenesh++ on Galaxy Service is designed for short-term access and does not provide any long term storage for any data, including your input genome assembly and output genome annotation data.
4. It is the responsibility of the End Users to ensure they have read, acknowledged and adhered to these Terms of Use.

2.3 Sharing / Downloading content

1. End Users accessing Fgenesh++ on Galaxy are the owners of any new data (content) generated through the use of the Fgenesh++ pipeline.
2. End Users can choose to delete their content at any time.
3. It is the sole responsibility of the End User to download a copy of all output files off Galaxy Australia. These files can NOT be recovered by the system administrator once purged from the service.

2.4 Termination

1. The Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy Service interferes with its operations or violates these Terms of Use or applicable laws.

2.5 Change of terms

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 Galaxy Australia home webpage and via email to users of the Service via their registered accounts.

2.6 Service maintenance and downtime

1. The Fgenesh++ on Galaxy Service is underpinned by resources at Galaxy Australia which is subject to scheduled and occasional maintenance downtime for updates that may impact the Service. Users will be notified prior to occasional scheduled maintenance downtime via email communication at the address provided by the user when joining the Fgenesh++ on Galaxy Service. 
2. In the event of a security breach, Fgenesh++ on Galaxy Service may need to perform urgent maintenance resulting in Service downtime at a time other than the scheduled maintenance windows. In this case, Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy 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 the Galaxy Australia support webpage.

3. Fgenesh++ on Galaxy Service Privacy Policy

The Fgenesh++ on Galaxy Service is operated through Galaxy Australia, and therefore compiles with the Galaxy Australia Privacy Policy and Data Collection Statement - https://site.usegalaxy.org.au/about#data-privacy policy.

3.1 Usage data

1. In order to monitor and enhance Fgenesh++ on Galaxy Service, the Fgenesh++ on Galaxy Service Operational Partners track and retain information about your interaction with the Service (i.e. IP addresses, cookies, pages visited, etc).
2. The Fgenesh++ on Galaxy Service Operational Partners may share log files of interactions with the service in aggregation with our Operational Partners. 
3. The Fgenesh++ on Galaxy Service Operational Partners may share debugging information with the Softberry [4] developers to improve their systems. When the Fgenesh++ on Galaxy Service Operational Partners do, the Fgenesh++ on Galaxy Service Operational Partners aggregate and anonymise this data to protect your privacy.
4. For promotional reasons and reporting to funding bodies, the Fgenesh++ on Galaxy Service periodically creates public usage reports. When the Fgenesh++ on Galaxy Service Operational Partners do, the Fgenesh++ on Galaxy Service Operational Partners aggregate and anonymise this data to protect your privacy.

3.2 Registration data

1. If you choose to register an account with Fgenesh++ on Galaxy Service, the Fgenesh++ on Galaxy Service Operational Partners collect registration data (i.e. email address, institutional affiliation and public name).
2. Fgenesh++ on Galaxy Service Operational Partners collects and stores your personal information for the administration of your use of Galaxy Australia and Fgenesh++ to support your research.
3. Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy Service policies.

4. Fgenesh++ on Galaxy 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 the Australian BioCommons, operational partners and funding partners.

3.3 Data you upload and share

1. You are prohibited from using Fgenesh++ on Galaxy Service to host or process sensitive data, including but not limited to potential re-identifiable or identifiable personal data.
2. The Fgenesh++ on Galaxy Service Operational Partners may examine the data you share through the service for alignment with our Fgenesh++ on Galaxy Service Acceptable Use Policy.

3.4 Support requests

1. Support is offered for users accessing the Fgenesh++ on Galaxy Service with two access points depending on your question:

1. For technical support:

1. Users can submit a request please contact us via the Galaxy Australia support webpage. This includes support with: accessing and using the service. When you submit a support request via the Galaxy Australia support webpage, the Fgenesh++ on Galaxy Service Operational Partners collect your email address and may ask for personal data as part of the support process.

2. For support related to bioinformatics and annotation:

1. The nominated End User can contact Softberry, Inc. at softberry@softberry.com during the duration of their access to the Instance.

3. For support related to Galaxy:

1. The nominated End User can contact the Galaxy Australia team at help@genome.edu.au.

3.5 Data location

1. All other data is stored and processed in Australia by our Operational Partners, and will not be provided to any third party unless
2. You choose to share content through the service, and;
3. The Fgenesh++ on Galaxy Service Operational Partners are required to do so by law.

3.6 Modifying and removing personal data

1. The personal information collected by Fgenesh++ on Galaxy Service for registered account holders includes name, organisation and email address associated with accessing the Fgenesh++ software. Optimally the Fgenesh++ on Galaxy Service Operational Partners may also store a user’s 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 contacting the Galaxy Australia support webpage.

4. Fgenesh++ on Galaxy Service Operational Partners

The Australian BioCommons operates Fgenesh++ on Galaxy Service in collaboration with and underpinned by resources provided by Galaxy Australia, Queensland Cyber Infrastructure Foundation and Bioplatforms Australia. The service is underpinned by computational resources provided by The University of Melbourne, QCIF, Pawsey Supercomputing Centre, AARNet and Microsoft Azure.

5. Fgenesh++ on Galaxy Service Feature Catalogue

5.1 Fgenesh++ on Galaxy Service features and quotas for End Users

End Users must be affiliated with a recognised Australian academic or research institute (see Section 8), and register using an email address from our list of Australian research institutions.

5.2 Best effort operations

The Fgenesh++ on Galaxy Service Operational Partners realise that the data and annotations you host with Fgenesh++ on Galaxy Service are important to you. For that reason, the Fgenesh++ on Galaxy 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 (i.e. Australian Eastern Standard Time). During those hours the Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy Service runs research-grade infrastructure contributed by the Fgenesh++ on Galaxy Service Operational Partners. Fgenesh++ on Galaxy Service’s reliability and capacity may be impacted if partner infrastructure unexpectedly becomes unavailable.

5.3 Service capacity

The Fgenesh++ on Galaxy Service is underpinned by significant compute and storage capabilities, allowing you to scale analysis beyond your desktop computer. The Fgenesh++ on Galaxy 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.

5.4 Service lifetime

The service will continue for the lifetime of the Australian BioCommons, which is currently funded until June 2024.

6. Fgenesh++ on Galaxy Service Acceptable Use Policy

You may use the Fgenesh++ on Galaxy Service to analyse and annotate life science data for the purposes of research.

1. You agree to interact with the Fgenesh++ on Galaxy 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.

2. The following uses of the Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy 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. The 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 Fgenesh++ on Galaxy Service Systems Administration team;
2. corruption of, or disruption to, data stored on the Fgenesh++ on Galaxy Service, or to the data of another user;
3. disruption to other users, and/or;
4. introduction or transmission of malware into the Fgenesh++ on Galaxy Service’s systems.

7. Fgenesh++ on Galaxy Service Acknowledgment Statement

The Australian Fgenesh++ on Galaxy Service is provided by the Australian Biocommons in collaboration with and underpinned by resources provided by Galaxy Australia, Queensland Cyber Infrastructure Foundation and Bioplatforms Australia.

When papers acknowledge the Australian Fgenesh++ on Galaxy Service, they support continued research infrastructure investments by institutions and governments. When you use the Australian Fgenesh++ on Galaxy 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 Fgenesh++ on Galaxy Service (biocommons.org.au/fgenesh-plus-plus) provided by the Australian BioCommons and Galaxy Australia."

8. List of Australian Research Institutions

The Fgenesh++ on Galaxy Service is for exclusive use by publicly funded Australian researchers, as described in the Galaxy Australia Feature Catalogue [5]. Access to the features and quotas is available to individuals registered using an email address from one of the Australian Research Institutions in the Galaxy Australia Feature Catalogue [5]. The Fgenesh++ on Galaxy Service Operational Partners acknowledge that this list may not be exhaustive. Please contact us via the Galaxy Australia support webpage to request the addition of your research institution to this list.

[1] Fgenesh++ package uses the following public software and data:

• NCBI BLAST+ blastp or BLAST blastall, bl2seq programs;
• NCBI NR database (non-redundant protein database);
• NCBI RefSeq database.

[2] Fgenesh++ package includes the following copyrighted software:

• Fgenesh - an accurate and fast HMM-based gene prediction program;
• Fgenesh+ - gene prediction program that uses similar protein information;
• gene finding parameters for Fgenesh and Fgenesh+;
• est_map - program for mapping known mRNAs to genome (genome alignment with splice sites identification) and mapping a set of available ESTs to improve the gene prediction accuracy and add 5' and 3'- noncoding sequences;
• prot_map - mapping protein database to genomic sequences;
• perl scripts.

[3] The Australian BioCommons initiative is hosted by The University of Melbourne.

[4] Softberry, Inc. own the software Fgenesh++. The Australian BioCommons currently hold a license for the use of Fgenesh++ to supply access to bona fide Australian researchers via the Australian Fgenesh++ on Galaxy Service. 

[5] Galaxy Australia Feature Catalogue, https://site.usegalaxy.org.au/institutions