A mud crab. Photo taken in Cairns by David Clode. (Unsplash.)

20/04/2021

Aquaculture has been Queensland’s fastest growing primary industry over the past decade as global demand for seafood continues to rise along with growing awareness about ecological sustainability. 

While Australians are well-acquainted with buying locally-farmed fish, the country’s aquaculture industry for crustaceans — prawns, crabs, crayfish and lobster — is still in its infancy with significant potential for expansion, particularly in regional areas. 

Acknowledging the growing interest in the genomics of crustaceans to assist the aquaculture industry, USC bioinformatician and software developer Dr Cameron Hyde created an online database that allows researchers to look up crustacean gene expression across tissues and life stages and enables them to upload their own data sets.

Named CrustyBase, the platform uses QCIF’s cloud compute service, QRIScloud (the Queensland node of the national ARDC Nectar Research Cloud), as the server for the website. 

Cameron’s aim with CrustyBase is to increase the public accessibility and sharing of crustacean transcriptome data sets around the world. 

It all started when he had a great data set that he really wanted to share — a transcriptome series providing novel insights into arthropod development and the unique life history of the rock lobster. 

“Transcriptome data is a highly utilised resource at the current time, but without better tools these data are challenging to share between researchers,” he said. 

The project was conceived in 2018 when Cameron was halfway through his PhD, with development beginning shortly afterwards. 

USC IT specialist Peter Embleton steered Cameron towards QRIScloud as a no-cost, trustworthy resource for him to use (QRIScloud is free for Australian researchers). 

As Cameron said: “Free cloud servers and storage for testing and production? What’s not to like about that?!”

He added: “I had no idea how to set up and run a cloud server, and little funding to ‘experiment’ with commercial servers.  

“Access to Nectar [QRIScloud] servers gave me lots of room to tinker and play with cloud servers and taught me a huge amount about computing within the Linux environment. I even run my personal computer on Linux now (it’s great).”

Although proficient in IT himself, Cameron called upon the QRIScloud Help Desk for some assistance in setting up the server. “Stephen [Service Desk Manager Stephen Crawley] was always quick to respond and offered practical, intelligent solutions,” said Cameron. 

CrustyBase uses two virtual machines via QRIScloud for its staging and production web servers, the latter being a 4-core machine with 8 GB of memory. 

CrustyBase has also been allocated 100 GB of virtual disk storage for its data sets, enabling the database to expand in the future as users upload more data.

Cameron uses USC’s own high-performance computer server to process data set uploads from CrustyBase users. “Once the processing is complete, the rendered data is sent back to the CrustyBase web server on QRIScloud and becomes available for the world to view and search.” 

CrustyBase was originally funded through an Australian Research Council grant and indirectly via Cameron’s PhD scholarship and grants awarded to his supervisor Dr Tomer Ventura. Some funding for maintenance and new features will also be allocated through the ARC Research Hub for Sustainable Onshore Lobster Aquaculture, a national initiative to foster crustacean aquaculture in Australia.

“As long as QCIF is willing to provide the web server, we are willing to maintain the resource. We may also pursue funding to expand this application to a broader range (potentially all) species. This would require an upgrade in infrastructure to make it more scalable but would be a valuable asset for the global genomics community,” said Cameron. 

QCIF is indeed willing to continue to support this important resource for crustacean genomics researchers. QCIF is also open to discussions with all other Australian researchers about supporting their projects.

In general, access to QRIScloud’s services (virtual machines, volume storage and object storage) is at no cost to Australian researchers or research communities and is made through the Nectar dashboard. Researchers can log into the dashboard via AAF using their institutional credentials. 

With QRIScloud, researchers can begin with a small project trial allocation and can request additional resources to support their project, with Linux virtual machines ranging in size from a single vCPU and 1 GB of RAM through to 32 vCPUs and 128 GB RAM.

Please contact the QRIScloud Help Desk if you have any queries about using QCIF’s cloud compute service in your research project. 

In brief:

Researcher: 
Dr Cameron Hyde
School of Science, Technology and Engineering
USC

Research communities:
Bioinformatics and computer science

Resources used:

  • Two virtual machines via QRIScloud, 4-cores, 8 GB memory
  • 100 GB virtual disk storage.