Archives

The Proteome Browser on R@CMon

Leave a reply

The Proteome Browser (TPB) is a web portal that integrates human protein data and information. It provides an up-to-date view of the proteome (the entire library of proteins that can be expressed by cells or organisms – like us!) across large gene sets to support human proteome characterisation as part of the Chromosome-centric Human Proteome Project (C-HPP). Pertinent genomic and protein data from multiple international biological databases are assembled by TPB in a searchable format supporting C-HPP’s global proteomics effort.

Screen Shot 2014-04-23 at 5.27.23 pm

TPB’s primary report of chromosome-ordered genes visualised using traffic light colour system.

TPB’s framework extracts biological data from numerous sources, maps it into the genome, and performs categorisation on the results based on quality and information content. The result (level of evidence) is presented by TPB using a simple point matrix coded by traffic light system (green – highly reliable evidence, yellow – reasonable evidence, red – some evidence is available or black – there is no available evidence). TPB uses hierarchical data types to group similar information from different experiment types.

Screen Shot 2014-04-23 at 4.06.09 pm

TPB’s summary report for the chosen chromosome.

TPB is supported by Monash University, Monash eResearch Centre (MeRC), Chromosome-centric Human Proteome Project (C-HPP), Australia/New Zealand Chromosome 7 Consortium and the Australian National Data Service (ANDS). Researchers are now using TPB in various proteomic-related discoveries.

The R@CMon cloud team recently provided assistance to migrate The Proteome Browser web service to be hosted on the Monash node of the NeCTAR Research Cloud. TPB is using persistent storage (Volumes) granted via a VicNode computational storage allocation to house its underlying database. TPB’s new home will ensure it has stable and scalable long-term hosting supported by the NeCTAR and RDSI federal research infrastructure programmes.

 

Beginnings of a new data service: Store.Synchrotron

Leave a reply

In line with the first day of eResearch Australasia, the Australian Synchrotron demonstrates its new data service – Store.Synchrotron with the upload of its first open experiment data.

Store.Synchrotron

The Store.Synchrotron service, built on the MyTardis data management system.

This is the first step in a partnership between the Australian Synchrotron and Monash University that leverages the leading Australian eResearch infrastructures of – MyTardis, R@CMon and VicNode, through the support of the NeCTAR and ANDS programs. The goal is to establish a data service, initially for the MX beam line, that captures all research beam line data for analysis, discoverability and re-use. The MX beam line alone means that approximately 1-2TB/month of research data is captured for collaborative use, and managed through the life cycle to the point where data behind important discoveries is one click away to being made open. The Store.Synchrotron pilot has been capturing data for several months, and as of today some collections have progressed from research collaborations to open through Creative Commons licenses.

Monash University is a recognized leader in the creation and management of large scale imaging for research. Store.Synchrotron is a user of the MyTardis service hosted by the Monash eResearch Centre under the leadership of the coordinator of the newly formed Monash Bioinformatics Platform – Steve Androulakis. MyTardis operates on a virtual machine at R@CMon and uses the computational volume storage that is part of the R@CMon/VicNode facility. As the data grows, infrequent data will spill over to vault storage, automating operational efficiencies.