This Genomics Workshop was held at Sydney University on 3rd June 2019 Pascal Tampubolon and Mike Lake attended the event. Present were the NSW Chief Scientist and leaders of various Genomics institutes in Australia.
The University of Sydney are developing a 1-5 year infrastructure roadmap to enable excellence in genomics-based research and a strategy to extend this across other institutions in Australia. This workshop showcased some outstanding genomics research being done Australia. A panel discussion by leaders in the genomics and genomics infrastructure followed.
Common and major technical issues raised by attendees were: requirements for increased space on /scratch on HPCs and long compute times, problems with I/O bottlenecks in sharing data with collaborators, and the responsibilities and costs of storing genomics data. After an ARC grant has finished who stores the data and who pays for the data to be stored?
Common and major technical issues raised by attendees were: storage requirements for research data (compute and archival purposes), long HPC compute and queue times, I/O bottlenecks in sharing data with collaborators, and the responsibilities and costs of storing genomics data.
A number of institutions are "bursting into cloud" for compute and they want to move the compute to where the data is. Though no one suggested how this could be done. Some users of the Syd Uni HPC are looking to migrate pipelines to AWS.
The ongoing problem of data curation was also raised as well as the repoducibility of re-running analyses. Using PiGx for reproducible pipelines across different infrastructure was mentioned.
Tony Papenfuss from the Walter and Eliza Hall Institute mentioned that they were using more GPU cards for processing jobs and that purchasers of new sequencers are required to specify compute and data storage requirements prior to purchasing.
Jon Smillie from NCI told us about the use of Crypt4GH, an encrypted file format, from the Global Alliance for Genomics and Health (GA4GH).
Andrew Gilbert, General Manager, Bioplatforms Australia spoke about the newly formed Australian Bioinformatics Commons and specifically drew our attention to the "BioCommons Principles".
Attendance was valuable to us in order to meet other researchers and managers of genomics institutes, to be aware of shared problems and possible future strategies.
Mike Lake & Pascal Tampubolon
eResearch