What is the Australian Fgenesh++ Service?

Fgenesh++ is a pipeline for automatic prediction of genes in eukaryotic genomes based on

gene finding software.

The Australian BioCommons are holders of the license to this software application, which is being held on a dedicated Nimbus instance for use by BioCommons users.

Ensure that you have:

Fgenesh++ is a software package that uses a combination of copyrighted and public software and data to automatically annotate genomes. The copyrighted software is owned by Softberry.

The Australian BioCommons offers Australian-based researchers fully subsidised access to the Fgenesh++ license with resources and service support underpinned by Pawsey Supercomputing Centre. If you would like to know more about the funding and operation of Fgenesh++ Service, please see our webpage.

How do I access it?

Researchers can apply to access Fgenesh++ via the Australian Fgenesh++ Service by completing the Fgenesh++ service signup. To be approved a user will need to be from an Australian research institute or university. Once you have completed the sign up form you will be notified within two business days. 

If you are a Pawsey user, you will be required to make a reservation on the portal -  https://reservation.pawsey.org.au. Once approved, details of logging in to the Fgenesh++ instance will be emailed to you. If you are new to Pawsey, a user account will be created for you before you can make a reservation on the portal.

How do I make a public key?

A public key is required to access the Fgenesh++ instance. If you have a public key, you may skip the following step.

To create a keypair, use the following commands on your local machine (the computer that you will be accessing the Pawsey resource from):

ssh-keygen -t rsa -f ~/.ssh/pawsey_rsa_key

This will create a new key pair named pawsey_rsa_key in your ~/.ssh directory, and will use the RSA algorithm for encryption. You will then be prompted to enter a passphrase, which is not your Pawsey password, but a passphrase to use for security of the generated key:

Generating public/private rsa key pair.
Enter passphrase (empty for no passphrase): [Type a passphrase]
Enter same passphrase again: [Type the passphrase again]

Change the permission of the private key:

chmod 600 ~/.ssh/pawsey_rsa_key  

Print your public key:

cat ~/.ssh/pawsey_rsa_key.pub

The output of the last command is the public key. Please note that you should never give out the private key, which is stored in ~/.ssh/ as above.

Who is funding and operating Australian Fgenesh++ Service?

The Australian BioCommons operates Fgenesh++ Service in collaboration with, and underpinned by resources provided by, Pawsey Supercomputing Centre and Bioplatforms Australia. The service is underpinned by computational resources provided by the Pawsey Supercomputing Centre.

How do I acknowledge this service in my publication?

You can use the following statement to acknowledge the use of this service:

"This work was supported by the Australian Fgenesh++ Service(biocommons.org.au/fgenesh-plus-plus) provided by the Australian BioCommons and thePawsey Supercomputing Centre."

Useful links

Softberry

Australian BioCommons

Bioplatforms Australia