What is the Australian Fgenesh++ Service?

Fgenesh++ is a pipeline for automatic prediction of genes in eukaryotic genomes based on gene finding software. 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 (hosted byThe University of Melbourne) 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 Sign Up. To 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 notified of the reservation system to access Fgenesh++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 . 

How do I reserve my access to Fgenesh++?

Once you have signed in to the reservation system, you will be granted access and notified to view the schedule. 

You can then block out a time period of up to three weeks. To do this, you can:

before you can make a reservation on the portal.

How do I make a public key?

A public key available to access our Nimbus instances, if that is the system your requested application is on. 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/firstname_lastname_key

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/firstnamepawsey_lastnamersa_key 
 

Print your public key:

cat ~/.ssh/firstnamepawsey_lastnamersa_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 (hosted by The University of MelbourneBioCommons operates Fgenesh++ Service in collaboration with, and underpinned by resources provided by, Pawsey Supercomputing Centre and investment from the Australian Research Data Commons and  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