Category Archives: VicNode Service

SONAS degraded Vault service notice for Saturday, April 29.

On Saturday, April 29, the Monash operating centre will be installing an expansion cabinet with 1000 slots for media on the Automated Tape Library (ATL). We have established the expansion can be executed under a degraded service rather than requiring a service-wide outage. Some technical detail is provided here to demarcate affected parts of the service. This upgrade enables an additional 4PB of tape media capacity, where new media cartridges will be added later as part of normal operations without additional interruption to services.

Recalls from Tape Vault Suspended on Saturday, April 29, 10am to 4pm.

The ability to recall data from tape will be temporarily suspended from 10am to 4pm, Saturday April 29, to accommodate this installation. Data can continue to be written as normal, and will be queued for backup/HSM within the normal business procedures that day. Any data already on the Vault disk cache will also be readily available for read and rewrite. Only data that has not been accessed in the last week and has been migrated to tape will be temporarily unavailable.

The effect of the suspension will be to stall user file read opens for files not in the cache until full service is resumed. Users expecting to have work in progress over the weekend can request the recall of the required Vault data prior to the upgrade, to maintain their workflow.

Data Custodians with Collection allocations that use Vault at the Monash operating centre have been contacted via email to their registered contact email addresses.

Happy Holidays from VicNode

VicNode would like to thank you all for another successful year. We hope you have a wonderful holiday season and look forward to working with you in 2017.

The VicNode office team will be breaking for the year on Friday 23 December returning on Tuesday 3 January 2017. There is no out of hours or holiday support for VicNode users during this time.

Integrating Gene Sequencers with the Cloud at VicNode Monash Operating Centre

The Monash Bioinformatics Platform, MyTardis, the Characterisation Virtual Laboratory and the R@CMon teams have joined forces to pioneer the “instrument integration” agenda into gene sequencing. MyTardis is unique in that it allows all three – researchers, storage/institutions and facility managers – to govern and automate data produced by instruments, whilst maintaining data provenance and durability.

The new MyTardis-seq benefits gene sequencing facility managers and researchers alike by providing an automated and structured method to capture, store and share the results of sequencing runs with associated quality reports and metadata.

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It was developed for and deployed at the Monash Health Translational Precinct Genomics sequencing facility (http://www.mhtpmedicalgenomics.org.au/) in partnership with the discipline specific data services of RDS. MyTardis-seq runs on the NeCTAR cloud and stores its raw data on the RDS-funded VicNode @ Monash storage. The MyTardis open-source software has been largely funded by the ANDS, NeCTAR and RDS projects.

Users of the facility can access their raw data and quality reports online in real-time. Data is provided securely in the web or via secure FTP.

MyTardis-seq’s instrument integration pipeline from data generation to capture.

Facility managers are provided with a holistic view of all gene sequencing data production, quality reporting and statistics collection.

A paper has been written on the MyTardis.org web site that discusses our solution and its use for other gene sequencing facilities: http://www.mytardis.org/news/mytardis-for-genomics

For more information please contact Steve Androulakis

University of Melbourne Digitisation Centre and Humanities Research Data Storage

The VicNode Culture and Community engagement officers, Tyne Sumner and Meredith McCullough, recently toured the Melbourne University Digitisation Centre (UDC) as part of VicNode’s ongoing commitment to supporting the humanities, arts and social sciences research disciplines. These disciplines, which underpin culture and communities, hold datasets that form important parts of our cultural heritage. There are many such datasets, but they are typically small in size. They are also typically heterogeneous, but capable of being linked and connected.

In aiding the digitisation these datasets, prior to the storage, analysis and dissemination of them through VicNode, the UDC provides a range of digitisation services to the University community. These services range from general advice, to digitisation of Library collection items, training and support.

As well as the primary business of digitising Collections assets, the UDC provides tailored services to researchers. The services include:

  • consultations to improve understanding of how digitisation of research records and assets can facilitate research;
  • guidance in meeting record-keeping obligations; and,
  • quotes for digitisation to facilitate grant applications

UDC has the capability to digitise a wide range of 2D materials and some 3D objects through the use of book scanners, document scanners, photography and more. Outputs range from digital preservation images to access formats like Jpeg and Pdf.Scanner2Scanner4

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Information on the scanners used can be found at https://digitisation.unimelb.edu.au/services/scanning/book_scanning

For University of Melbourne researchers, these services are either fee-for-service or self-service, where you can use professional equipment with established workflows in a supported environment. Value adding services include Optical Character Recognition (OCR) to facilitate searching text and forms design to improve data gathering in a range of applications.

For further information or general enquiries:

Phone: +61 3 8344 6161
Email: digitisation-enquiries@unimelb.edu.au
Website: digitisation.unimelb.edu.au

DaRIS capability available at VicNode

VicNode supports the DaRIS (Distributed and Reflective Informatics System) capability for managing bio-medical imaging and offers a DaRIS service.  DaRIS is built with the Mediaflux platform, which is also a core VicNode capability.

The DaRIS system has many functions (e.g. see here for more information). However, basically it provides:

  • A managed, secure, searchable repository to hold collections of data
  • Data organisation by Project, Subject, Study and DataSet and allows the addition of meta-data to provide better research context
  • Management of users permissions for each Project through roles (project admin, user, guest)
  • The means to upload directly from scanners (e.g. DaRIS is at the heart of data operations at the Melbourne Brain Centre imaging unit) or via other clients (e.g. upload my data from my desktop)
  • The means to directly send data (with format conversion e.g. DICOM to NIFTI)  to destinations (e.g. a high-performance computing environment) for analysis.
  • The means to share data with external users via shareable links.
  • The means to hold primary (raw) and processed data
  • Substantial inter-operability with other systems, especially (but not only) those dealing in DICOM data.  For example, it provides an OAI-PMH layer to harvest meta-data to collection registries (e.g. ANDS RDA).
  • A redundancy capability for your data in a separate location

Whether your collection has been aggregated from many places, and needs to now be secured and uploaded into a managed environment, or is being collected now at one specific scanner, the data can be managed with DaRIS and your research processes and outcomes enhanced.

Please contact VicNode if you would like to explore using DaRIS to manage your data.