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ABACBS (pron.ˈabəkəs) runs the Australian Bioinformatics Network

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Welcome to The Pipeline

...a blog for members of AustralianBioinformatics.net to share ideas, insights, questions...

Friday
Nov072014

ABiC 2014 and beyond... survey closes today

Just a quick note to say that you have until midnight tonight to shape the future of Australian bioinformatics (for today anyhow).

How can you shape the future of Australian bioinformatics?

Good question! Keep working hard for science. Be kind to each other. Maintain a healthy lifestyle... that sort of thing, I guess.

As for shaping the future of Australian bioinformatics conferences, you can do that by sharing your thoughts via this link.

The survey asks questions about ABiC 2014 (in a way we hope will capture views of participants and non-participants) and also solicits your ideas and preferences for an ABiC-style event next year.

Please help build and strengthen Australian bioinformatics by sharing your thoughts!

Thursday
Nov062014

Australian Bioinformatics: busy, busy, busy

Just some of the activity in Australian Bioinformatics over the past two-and-a-half yearsOne of the priveleges of running AustralianBioinformatics.net is that you get to see a fair slice (though not all) of the activity in Australian Bioinformatics.

This comes from posting and managing posts about jobs, events, training. (And by the way, anyone registered with AustralianBioinformatics.net can post to these blogs as well!)

All this information sharing is one of the main functions of the ABN, and we like to track how much information is getting shared.

And now, thanks to the miracle of content management, we can share that information with you! Just click here for the latest traffic report.

Cheers,
David 

Wednesday
Nov052014

Bob Kuhn connects hundreds to UCSC browser goodness!

Featuring nearly one hundred species and serving millions of requests each year, the UCSC Genome Browser is one of the world’s most popular bioinformatics resources.

This September, hundreds of Australian researchers had the chance to learn some of the key functions and inside tricks of the Browser from no less than the project’s Associate Director, Dr Bob Kuhn. Over two and a half weeks, Bob toured Australia delivering seminars, running workshops and meeting with scientists around the country, and even managed to fit in a little sightseeing along the way.

In total, nearly four hundred researchers in Brisbane, Sydney, Melbourne, Perth and Adelaide took the opportunity to benefit from Bob’s unique knowledge of the capabilities of the Browser. More than one hundred and twenty people participated in the hands-on workshops, while over two hundred and fifty attended his series of lectures and seminars or met with him individually. Bob's presentations were enjoyable, informative and engaging and widely appreciated by his audience, as summed up by Nigel Bennett from the University of Queensland: “His knowledge and enthusiasm made the workshop extremely interesting”.

As well as providing a great chance to find out more about the Browser, the roadshow also gave valuable exposure to the Genomics Virtual Laboratory and its Australian mirror of the UCSC Genome Browser. The GVL is a national project to deliver bioinformatics tools on the NeCTAR research cloud, and their copy of the Browser offers local scientists faster access and longer storage of custom tracks than the main instance. Bob used the mirror for all of his seminars and workshops, and also worked closely with the GVL team during his visit to optimise the performance of this local resource.

QFAB Bioinformatics and the ABN would like to thank all our colleagues around the country for hosting Bob throughout his tour – Helen Speirs from the Ramaciotti Centre, Jason Ellul and Maria Doyle at the Peter Mac, Shane Herbert of AGRF and Nathan Watson-Haigh from the Australian Centre for Plant Functional Genomics – as well as the GVL team for their great support.

Bob's visit was made possible by one of the ABN's Connection Grants, so a massive thanks goes out to Mark Crowe for siezing the initiative to apply for the Grant and for putting in a huge amount of work to coordinate the entire tour.

Last, but by no means least: thanks to the UCSC Genome Browser team and Bob Kuhn! Love your work!

 

 

Tuesday
Oct282014

The killer ninja skill in bioinformatics

"Hmmm... sed -n '1~4s/^@/>/p;2~4p' file.fq > file.fa
...while invisible..."
As usual, it was after the event that the deeper insights emerged...

Following a mind-expanding day of bioinformtics at InCoB 2014 earlier this year, we had repaired to a nearby restaurant for the conference dinner.

After discussing

  • (with Asif M Khan) how the major histocompatibility complex helps our immune system adapt in response to new diseases
  • (with Tin Wee Tan) how the Infiniband system used for high-speed data transfer inside supercomputers can be co-opted to provide insanely fast data transfer over tens of kilometres (e.g., across a city)
  • (with Asif and Tin Wee after some beers) plans for a pre-emptive intervention system for world peace

...talk turned to bioinformatics learning, education and training, following a lively discussion session (which I will be writing about soon) involving Vicky Schneider (TGAC, GOBLET), Michelle Brazas (bioinformatics.ca, GOBLET), a quartet of COMBINErs, and a roomful of enthusiasts.

So, what did we regard as the truly killer ninja skill in bioinformatics?

Was it

No.

We figured that the absolute killer ninja skill for bioinformaticians was:

the ability to learn stuff fast, and apply it well.

(OK, we may have to work on the phrasing a bit there, but it is still catchier than "metalearning".)

Like gene and protein expression, these sorts of opinions are time- and environment-dependent. However, on reflection, it speaks of one of the defining features of bioinformatics and bioscience these days: things change... fast.

...not so sure what is says about ninjas though.

Tuesday
Oct282014

ABiC 2014: We Salute You!

Q: What are all these people looking at?
A: Australian bioinformatics (quite possibly as presented by a bearded man in shorts)
This is to give a huge thank you to everyone who made the 2014 Australian Bioinformatics Conference an outstanding event on the Australian bioinformatics calendar, including

ABiC 2014 received support from The Australian Bioinformatics Network via one of this year's Connection Grants and I would like to thank Dr. Jovana Maksimovic, Dr. Katrina Bell, Dr. Dieter Bulach, Dr. David Goode, Dr. Alicia Oshlack and Dr. Torsten Seemann for making that pitch to the reviewers.

Just some of the words that survey respondents have already used to describe ABiC 2014Encouraging leaders and members of Australian Bioinformatics Communities

The ABN is about supporting and encouraging the kind of leadership shown by the ABiC 2014 Organisers. The ABN is also keen to help build on what has been started through ABiC and through The Australian Bioinformatics And Computational Biology Society (ABACBS, pron.ˈabəkəs) which is focused on the science and profession of bioinformatics and computational biology in Australia.

With that in mind, we are running a survey that is open not just to those who attended ABiC 2014, but also those who have an interest in an ABiC-style event next year. Already we have had a great response, and this post is to try increase the breadth of input from the community.

How can you shape the future of Australian bioinformatics?

Good question! Keep working hard for science. Be kind to each other. Maintain a healthy lifestyle... that sort of thing, I guess.

As for shaping the future of Australian bioinformatics conferences, you can do that by sharing your thoughts via this link.

The survey asks questions about ABiC 2014 (in a way we hope will capture views of participants and non-participants) and also solicits your ideas and preferences for an ABiC-style event next year.

Please help build and strengthen Australian bioinformatics by sharing your thoughts!