Issue 07  13 February 2017

 February news

Already the year has started with lots of activity and we hope to sustain that throughout 2017.

The report to the Executive from the ISAG was welcomed last month and it was affirming to see a number of our already identified strategic goals were endorsed by them. A primary goal is to build the relationships with international bioinformatics efforts and get some more tangible outcomes for our Nodes, by way of demonstrating how EMBL-ABR is meant to work. We are happy to report that already, now with Vicky being co-located at EBI, we have a number of new developments across training, data, tools and standards. The first involves working with EMBL-EBI to extend the impact of Australia's Antibiotic Resistant Pathogens project. The full story is published today. 

Training remains vital to any country's bioinformatics' efforts and the needs spread across all stages of the data life cycle. So our goal for 2017 is to choose opportunities and platforms which enable existing and new training tools to be as open and scalable as possible. Linking in with EBI training will also help us to reach our training goals.

At the end of this newsletter there is a list of resources now on our website. The data from last year's survey of bioinformatics and computational biology needs in Australia is freely available for use by all
 Australian institutions, and we hope that it is valuable information for their own planning. In a year where our focus is on Open Science, we think this is a good way to bring evidence-based decision-making to our community.

Participants and Faculty at the 2-day BIO:INFO Conference held as part of GAMe 2017.

Finally, thank you to all the people who contributed to our very successful Galaxy Australasia meeting last week. A full report is available below.

Andrew Lonie, Director
Vicky Schneider, Deputy Director


GAMe 2017 Wrap up

The EMBL-ABR Hub has just wrapped up the Galaxy Australasia Meeting 2017 (GAMe 2017) hosted at VLSCI, the University of Melbourne, from 3-9 February. Bringing together current and future Galaxy users and administrators from nine different countries, the meeting had a fantastic community feeling and resulted in many ideas for carrying plans forward in our region.
Galaxy is an open, web-based platform for data intensive biomedical research that aims to make data-intensive biology accessible to everyone. The opportunity to collaboratively identify and address the needs of the local community and to interact directly with the international Galaxy team was enthusiastically taken up by 80 participants. Founding developer of the Galaxy platform, James Taylor (Johns Hopkins University) and Head of the Freiburg Galaxy Project, Björn Grüning (University of Freiberg) provided keynote presentations and were joined in Melbourne by members of the Galaxy Core Team including Nate Coraor (Penn State University), Enis Afgan (Johns Hopkins University), and Ross Lazarus (Sydney, Australia).

Read the full report here.

Key Areas Coordinators' update

The group has had its first call for 2017 aimed at priorities for the year. These are being based upon feedback from the All Hands workshops held late last year. All related documents are constantly being updated on the website.
Link to all Key Areas Coordinators Group updates
Interview series: Richard Edwards, UNSW

On 3 February we released an interview with Richard Edwards, the developer of SLiMSuite, an open source bioinformatics tool for the prediction of short linear motifs (SLiMs) and related sequence analysis. In this interview Richard reflects on bioinformatics in Australia as well as the realities of building a sustainable model for the development and maintenance of useful bioinformatics tools such as his.       
Full interview
2016 Survey data now available
In order to gain a snapshot of the bioinformatics and computational biology needs among life scientists and medical researchers across Australia, we conducted a survey over July to September 2016. Replies were received from 123 people spread across the country who comprised a useful mix of post-graduate students, researchers and research managers. Feel free to share with your institutions and to draw your own conclusions!
Survey summary and data
Research Software Workshop, a report

Vicky recently participated in JISC Workshop in Cambridge, UK, on Research Software Management, Sharing and Sustainability. The workshop was collaboration between JISC, Software Sustainability Institute (SSI) and University of Cambridge (Cambridge) among others, and was aimed at researchers interested in and passionate about developing or using research software who were keen to participate in a workshop on this subject. 

Slides from the morning keynotes are now available:

Neil Chue-Hong (SSI):
Is my research right? Surviving in a post-expert world 
Stephen Eglen, Cambridge: Towards standard practice for managing and sharing code.
You can link here to Cambridge's
Rosie Higman's excellent blog post about the event and  all presentations and discussions from the afternoon focus groups.    
The presentations have valuable links and information on resources, so it is worth browsing these.

On learning about Cambridge's Data Champions - local experts on research data management and sharing who provide advice and training within their departments - Vicky came away from the workshop keen to explore and discuss this model within the EMBL-ABR network. Further, these Champions are discipline-specific and readily to speak at local meetings about research data. Link here to see the
Cambridge Directory of Data Champions.

Research software and data management and sharing are definitely subjects for further discussion across the Nodes in the future and Richard Edwards comments about software in his interview (at left) is timely. Richard, we hope you have time to get involved in these discussions!

Send in your own agenda items for discussion around these topics
Training opportunities

Early in February Vicky met with EMBL-EBI Training Programme Manager Sarah Morgan and Scientific Training Officer (e-learning) Melissa Burke to devise a Collaborative Training Programme in Bionformatics for Australia. They are currently exploring:
·  how to promote, advertise and work across time barriers to facilitate accessibility for Australia of EMBL-EBI's existing online training including a forum for gathering questions and problems that the Australia Bioscience community has, with the aim of getting the most out of publicly available biological data 
·  greater collaboration on training materials where EMBL-ABR contributes to actual online courses in Train online, bringing specific case studies of relevance to Australian biosciences
·  potential methods for increasing training capacity for EMBL-EBI resources to increase their use across Australia.
We look forward to hearing how this develops in the coming months.

Microbial Genomics workshops

In late November the EMBL-ABR: UWA Node hosted a 2-day COMBINE workshop facilitated by Simon Gladman and Anna Syme from the EMBL-ABR: VLSCI Node. The workshop aimed to teach how to use Nectar resources, Galaxy, genome assembly and annotation, variant calling and RNA-Seq analysis for doing microbial genomics. 

The workshop was funded by AGTA with matched funding by VLSCI and was one of a series held in a number of States. Feedback from the 31 participants was very positive: 

I thought this was an excellent workshop, I found the information highly relevant and extremely easy to understand – definitely would recommend, PhD Student, School of Women’s and Infants’ Health, UWA. 

The course was excellent even for first time people to use new software. 

Great that the ‘why’ of everything was explained – not just the ‘how to’. 

EMBL-ABR: Monash Node

Monash University is a leading centre of activity in bioinformatics. Embedded in the Clayton Innovation Precinct, Monash holds key expertise in genomics, proteomics and imaging informatics, develops bioinformatics tools and platforms for Australian researchers, and is a leading participant in national and international bioinformatics initiatives. The Monash bioinformatics community is led, coordinated and underpinned by the Monash Bioinformatics Platform and the Monash Node will contribute high level training activities, sophisticated imaging and instrument platforms and high performance compute to the EMBL-ABR network.


Monash is improving bioinformatics practice through establishing best practice around data analysis life-cycles, tool and training material development. The development of guidelines relating to community best-practices, technical leadership, implementation of infrastructure, development and delivery of training will benefit bioinformaticians and biologists facing the challenges of data intensive science.

Coordinated deployment and training in the Characterisation Virtual Laboratory (CVL) will be facilitated by the EMBL-ABR network. The CVL integrates imaging instruments with cloud-based computing and data storage, provides online environments for data analysis and visualisation, and makes a wide variety of data processing tools and techniques more easily accessible to a wide cohort of imaging users.

A share of the MASSIVE facility will be available to the bioinformatics community through EMBL-ABR. MASSIVE is a unique Australian facility with a focus on fast data processing, including processing data in-experiment, large-scale visualisation, and analysis of large-cohort and longitudinal research studies.

Resources for all Australian students, researchers and their institutions

The website is growing as a resource, and below are those focussed on the Australian bioinformatics community. They are not comprehensive, we invite anyone to contribute further by emailing 
Christina Hall:
BIOINFORMATICS TRAINING IN AUSTRALIA, OVERVIEW 2016 see who did what kind of training in 2016

TRAINING OPPORTUNITIES FOR 2017 local, national and international search options
AUSTRALIAN BIOINFORMATICS FACILITIES AND GROUPS - be listed here to raise your international profile
AUSTRALIAN BIOINFORMATICS TOOLS: TOOLSAU - have your tools searchable on this global resource
REPORT ON THE LEVEL OF AWARENESS OF AUSTRALIAN BIOINFORMATICS FROM ISMB & ECCB 2016 - a glimpse into what do our overseas counterparts know or don't know about Australian bioinformatics
2016 EMBL-ABR SURVEY OF BIOINFORMATICS AND COMPUTATIONAL NEEDS IN AUSTRALIA - useful data for institutional, State and National projections and reporting

AUSTRALIAN BIOINFORMATICS TRAINING MATERIALS (STM) - This Search for Training Materials is a web-based tool using a custom Google search engine to find bioinformatics training materials from various organisations both in Australia and worldwide. 
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