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Thanks for making connections in 2013

The Australian Bioinformatics Network awarded three Connection Grants this year to support efforts that build and strengthen Australian bioinformatics, specifically, to support:

  • A visit from systems biology expert, Dr Mike Hucka ($3k)
    proposed by Sarah Boyd (SBI Australia)
  • Networking events for wheat bioinformaticians ($12k)
    proposed by Ute Baumann (ACPFG) with  Jen Taylor (CSIRO) and  Paula Moolhuijzen (Murdoch University)
  • Improving bioinformaticians' productivity through Software Carpentry ($10k)
    proposed by Nathan Watson-Haigh (ACPFG and BIG SA) with Greg Wilson (Software Carpentry), Ute Baumann (ACPFG),  Catherine Shang (BPA), Annette McGrath (CSIRO), Philipp Bayer (UQ)

This week, we caught up with some of the people whose energy, commitment and leadership made these activities possible.

Mike Hucka: "This work was made possible thanks to a great community"Making connections in Systems Biology                                

As part of spearheading the establishment of SBI Australia, the Australian Node of the Systems Biology Institute, Sarah has been active in fostering international linkages, including with Dr Mike Hucka, one of the pioneers of SBML – the Systems Biology Markup Language, co-founder of, the Systems Biology Graphical Notation (SBGN), the Systems Biology Ontology (SBO), COMBINE (the Computational Modeling in Biology Network) and HARMONY (the Hackathon on Resources for Modeling in Biology).

With support from the Victorian Government, The Walter and Eliza Hall Institute of Medical Research, St Vincent’s Institute of Medical Research, BioMelbourne, The Bio21 Cluster, CSIRO and The University of Sydney, as well as the ABN, audiences in Sydney and Melbourne got to hear from Mike on Computational Approaches to Systems Biology, How SBML and other tools are transforming computer models of life, Creating a new language to support open innovation, and Systems Biology Systems.

Our thanks go to Mike, of course, for sharing his perspectives and wisdom on developing software standards and infrastructure for scientific domains.

In addition, we want to acknowledge all the people who actually made Mike’s visit happen and put in the hard yards with logistics and organisation, including Sarah Boyd and colleagues, and organisers of the Sydney Computational Biologists’ Meetup.

Wheat... a bit like the TARDIS: bigger on the inside and all thatBioinformatics gets the ear of wheat researchers

The inaugural Wheat Bioinformatics Forum brought twenty-nine scientists from Australia’s leading wheat research institutions together in Adelaide for two days this August.

 Convened by Ute Baumann, Paula Moolhuijzen and Jen Taylor, the Forum aimed to strengthen connections between researchers dealing with the massive volume and complexity of genomic data from one of Australia’s most important crops.

Ute sets out the bioinformatics challenge: “The wheat genome is more than five times bigger than the human genome. A single chromosome of wheat can be larger than the entire rice genome! And most of it consists of repetitive sequences: these make it really difficult to assemble the genome sequence.”

There’s a lot of hype around “big data” at the moment and, to some extent, an impression that “big technology” is the answer. But what this Forum and seasoned data scientists recognize is that people are at the heart of understanding big data: there’s no substitute for getting together to discuss common interests and challenges. At the forum, these topics included wheat sequence resources, data quality and experimental design, genome and transcriptome assemblies, genotyping by sequencing and QTL mapping.

“It was fantastic to finally meet people face-to-face who we knew were working in the field but hadn’t met yet,” says Ute.

Even when people have met, the pace of research (and perhaps just modern life in general) means that get-togethers are vital.

“Because the meeting was quite focused, several collaborations spawned,” says Ute. “We’re now working with Stuart Stephen [author of BioKanga] and, through connections with Gabriel Keeble-Gagnere, we’re working towards a national annotation effort for Chromosome 7A.”

Our thanks go to all participants for ensuring a lively and productive Forum that looks set to reconvene in 2014.

Again, we want to give thanks to the people who made it happen. Ute, Paula and Jen: Australia’s (wheat) bioinformatics capability is even stronger thanks to your initiative, leadership and hard work.

This is not a holiday camp, this is a boot camp!Software Carpentry nails skills development

Programming and software are at the heart of bioinformatics and quantitative bioscience, but it is a constant challenge to keep up with good programming and software development practices, especially if your day job is to meet the massive demand for data analysis in the life sciences.

In September/October this year, Software Carpentry Bootcamps were held in Adelaide and Melbourne to help nail this challenge.

This was a huge undertaking, and it took a hugely talented team to pull it off: Nathan Watson-Haigh, Greg Wilson, Ute Baumann, Catherine Shang, Annette McGrath and Philipp Bayer did a great job… as Terry Bertozzi attests:

I recently attended the SWC bootcamp in Adelaide and found it incredibly useful. Sure there was a lot of information in a short amount of time but the topics covered were practical and very relevant to my daily work. Thanks must go to the presenters and organisers who kept things moving along brilliantly.

We asked Nathan if the bootcamps were worthwhile. “I have never had so many people coming up to express how positive and useful an event was,” he replied. “People were just really happy that someone took the initiative and time to hold a workshop targeted at bioinformaticians.”

“People found the content was spot on… things they’re heard about but not had time to put into practice,” says Nathan.

Anyone who has ever run hand-on training will tell you that setting up the computers and computing environment for participants is a lot of work.

“I was able to draw on experiences from Next-Generation Sequencing Hands-on workshops  with Catherine Shang (BPA) and Annette McGrath (CSIRO Bioinformatics Core) to set up virtual machine infrastructure,” said Nathan. The NeCTAR Research Cloud was key to this, enabling each trainee to access a specific virtual workstation. (This in turn, was the subject of a further workshop that Nathan ran.)

One added bonus of having Software Carpentry trainers in Australia was seized by Annette McGrath and Rob Lanfear (ANU) who convened a Software Carpentry R Bootcamp in Canberra, following the workshops in Melbourne and Adelaide.

Our sincere thanks go to the teams behind these events: thank you for all your hard work to deliver high quality, much appreciated training to Australian bioinformaticians.

A New Year’s wish

With Christmas nigh, we at the Australian Bioinformatics Network give thanks to everyone who has helped strengthen Australia’s many bioinformatics communities this year.

We appreciate your creative efforts, your enthusiasm and your selflessness!

We have lots of New Year’s wishes! But if we were to pick just one it would be this: that there be greater appreciation and support for the role of community and community builders in science.

We need our shining science stars, to be sure; we also need a firmament.

Merry Christmas!
from David, Benita and Candace