Intersect News #69 June 2014

5 Jun 2014

Back in the workshop: FAIMS round 2

Dr Adela Sobotkova testing the Android version of FAIMS against its predecessor early this year in Zagora, Greece.

The FAIMS application has the capability to radically improve the workflow of archaeology. The Federated Archaeological Information Management System (FAIMS) includes an Android application and Ruby server built by Intersect. It is a comprehensive information system, built for the digital collection and management of archaeological data, be it text, image, audio or video.

In late 2013 the FAIMS group was successful in attaining a LIEF grant from the Australian Research Council to deploy the tool Australasia wide, and the system has returned for a second year of development with Intersect. Take up in the field has Intersect creating modules for practising archaeologists. The android tool is also being used in other fields where off-line data collection is required, e.g by GNS Science, New Zealand, who are “keen to continue using it for subsequent sampling”.

The system allows data from field and laboratory work to be born digital using mobile devices, processed in local databases, extracted and exchanged online.  Key features of the mobile application include

  • offline multi-device recording
  • rendering locally stored maps
  • customised recording per research project
  • complete multimedia integration to the record level. More at

FAIMS acknowledges support from the NeCTAR project which is funded by the Australian Government through its Super Science initiative and financed by the Education Investment Fund.

Alveo Project launch/ hackfest / workshop

The UWS-led Virtual Laboratory for Human Communication Science named Alveo will be formally launched on 1 July at the University of Western Sydney. Intersect developed Alveo between Q2 2013 and Q2 2014. Alveo provides on-line infrastructure for human communication data sets and specialised tools for searching, analysing and annotating that data. Alveo is online here :

The launch will be preceded by an Alveo Hackfest for developers and testers, and a workshop for users, see Events in sidebar.

Alveo is remarkable amongst the NeCTAR Virtual Laboratories for being multi-disciplinary and broadly supported. Designed to be used by a range of researchers across the various disciplines, Alveo involves 13 universities, 3 organisations, and 47 key investigators. Importantly those involved are supporting it via cash and in-kind commitments to allow for new tools and corpora to be added in future. Alveo is expected to enable a quantitative and qualitative leap to increased capability, collaboration and output.

Alveo acknowledges support from the NeCTAR project which is funded by the Australian Government through its Super Science initiative and financed by the Education Investment Fund.

Infrastructure Progress Report


We have now approved 63 collections totaling 6.5 PB of storage and ingested over 600 TB of research data.

Dataset update: Melanoma

A dataset critical to cancer research is now being hosted on the Intersect research data node. Genome sequences from a large proportion of the melanoma patient cohort will soon be made available as a public resource to scientists and clinicians.

Melanoma represents a major unsolved public health challenge. It remains one of the leading cancer killers, especially of young and middle-aged adults. Access to the melanoma collection will support research into the cellular and molecular biology of melanoma and other cancers. It will be translatable into diagnostic, prognostic and predictive biomarkers for melanoma and new therapies for advanced melanoma.

There are currently 15 lead researchers from 8 research institutes nationally involved in the production of the collection. Once the embargo period is complete, the collection will be advertised on Research Data AustraliaMore…

Generation of the data was funded by Bioplatforms Australia through the Federal Government’s Education Investment Fund Super Science Initiative. Additional datasets within this collection were funded by Melanoma Institute Australia, the NSW State Government and Cancer Council NSW.
Photograph: Immunofluorescent staining of melanoma cells. Helen Rizos, Westmead Institute for Cancer Research.

NeCTAR Research Cloud

Intersect has completed evaluation of the responses to our RFQ for provision of the Intersect node of the NeCTAR Research Cloud. The Infrastructure Committee is reviewing the Evaluation Committee report and its recommendation will be put to the Intersect Board.


Orange itself continues to prove a stable platform for researchers and has had no recent unscheduled downtime. Orange has been under heavy load during the recent Raijin outage. The Panasas File System appliance has experienced some issues and we are working to improve reliability.


ANDS/Intersect data curation roundtable
Wed, 25 June, 1–5pm
Colleagues in ANDS partner and Intersect member organisations are invited to attend a face-to-face roundtable to discuss data curation. Participants are encouraged to bring questions and challenges they face to the group to talk through. Places are limited to 25. Please RSVP to:
Alveo Hackfest
Monday 30 June, 9.30-6pm
Alveo is the Virtual Laboratory for Human Communication Science, the Alveo Hackfest is for developers, programmers and testers. Numbers are strictly limited. Priority will be given to those affiliated with the project. Email by 11 June.

Alveo Workshop
Tuesday 1 July, 9.30-4pm
The Alveo Users Workshop is for researchers and end users.
Numbers are strictly limited. Priority will be given to those affiliated with the project. by 11 June.

Intersect Training

The following training courses will occur in the near future:

– 6 June: Excel Fu at SCU. Register at
– 23 June: FASS eResearch: Working with big data sets – data mining at USYD. Register at
– 25 June: ANDS/Intersect Research Data Management Roundtable at Intersect. Limited places, please RSVP.
– 9-10 July: Introduction to Unix for HPC at UTS.  Register at
– 11 July: Data Visualisation with Google Fusion Tables at UTS. Register at
– 11 July: Cleaning & exploring your data with Open Refine at UTS.  Register at
– 15 July: Cleaning & exploring your data with Open Refine at UTS.  Register at
– 15 July: Data Visualisation with Google Fusion Tables at UTS. Register at
For more information, see


Intersect CEO Dr Ian Gibson has been elected President of the Australian Access Federation at the recent AGM.Mr Rick Van Haeften (ACU) took the position of Secretary, and Mr Paul Sherlock (USA) is Treasurer.

Ms JoAnn Sparks, University Librarian of Macquarie University has joined the Intersect Board. We thank Professor Neal Ryan, Pro Vice Chancellor, Research, Southern Cross University for his service on the Board.

Tom Brierley has joined Intersect as a User Interface Designer.

Grants News

In May Intersect hosted a forum for NSW universities to discuss changes to ARC grant funding. Senior representatives from member grants offices shared their responses to recent ARC funding rule changes, in particular new requirements for researchers related to the management of their data.

Finding the meeting useful, participants intend to meet periodically to take the discussion forward.

If you work in a member grants office and would like to be involved, contact

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