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The Australian Bioinformatics Network was initiated by

  AustralianBioinformatics.net

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...

Tuesday
Jun032014

Screen-scraping for bioinformatics with R 

...you know it's time to pull together information for Annual Reports when thoughts turn to screen-scraping...

...there's something for everyone

Sunday
Jun012014

See ABN grow

The Australian Bioinformatics Network kicked off on 1 July 2012, nearly two years ago.

Here's how it has grown since then:

This chart shows cumulative membership of AustralianBioinformatics.net and cumulative active membership the ABN Yammer. Alas, they are updated manually, and the membership of ABN.net lists some duplicates and dormant accounts. Still, they give us a sense of how things are growing.

Based on the ABS Population Clock's estimate of a population of 23,508,937 mid-2014, my guess is that there's probably about 1 bioinformatician for every 30,000 Australians.

Saturday
May312014

Questions that get to the heart of what the ABN is about

Perhaps there is a word in German for "questions that allow you to articulate important points", if so, let us know because this applies to an email we received from Lavinia Gordon, Bioinformatics Manager at the Australian Genome Research Facility (Australia's largest (and not for profit) provider of genomics services and solutions).

Click to read more ...

Wednesday
May282014

A vision for Australian Bioinformatics and Computational Biology

For some months now, Australian bioinformaticians and computational biologists have been meeting towards re-forming a national professional society.

This hasn't been "secret-bioinformaticians-business"... far from it: the committee is open to all and welcomes participation of anyone with a genuine interest in the science and profession of bioinformatics.

And the purpose of this post is to let you know that we have

  • arrived at a workable society name: ABACBS (pron ˈabəkəs)
  • figured out that an incorporated association is a good plan (the lawyers agree!)
  • drafted rules and an application for association
  • drafted a succinct statement of the society's aims and vision.

Click to read more ...

Friday
May232014

Big thumbs up for eRSA, axolotls, SAHMRI, and many more

By Friday most weeks, I think we all of a bit of a boost to eclipse all the crap that has accumulated since Monday. With that in mind, I want to give a big thumbs up following a trip to Melbourne yesterday to welcome EMBL Australia’s newest Group Leaders, David Lynn and Ville-Petteri Mäkinen.

Hooray for eResearch SA!Thumbs up to eResearch SA

After explaining to David and Ville the purpose of the Australian Bioinformatics Network and the Systems Biology Initiative, Sarah Boyd and I asked how things were going on the computational infrastructure side of things.

The gist of their response was: aside from the inevitable issues of getting started in a new lab, they greatly appreciated the practical and proactive support and engagement from eResearch SA.

I know that eResearch is a challenging gig: Australia’s national eResearch infrastructure is growing and evolving, and somehow in the midst of that dynamic landscape, Australian eResearch Organisations have to connect the “big iron” to the diversity of researchers who can benefit from it.

So “hurrah” for eResearch SA’s excellent connection with bioinformaticians!

Thumbs up to Mirana Ramialson and Nadia Rosenthal

…for blowing my mind with axolotls, antlers and Artemia.

As an electrical engineer whose been working in bioscience for a decade or so, I’m pretty well used to being amazed by the diversity and complexity of living organisms, but yesterday I scored a trifecta.

"You wanna bite me, mate?"I didn’t know that

  • Axolotls can regenerate whole organs and limbs. (Nadia told my they have to on account of how much time they spent biting bits off each other.)
  • Antlers grow from the tip. I just thought they were like big old horns or fingernails that grow from the base, but no, the tips are full of mesenchymal cells that let antlers grow at up to 3.8cm a week. You can even graft ‘em if you’d like a pair elsewhere (cf. current trends in tattooing)
  • Kids, just don't put 'em in a tank with your ZebrafishArtemia make a tasty snack for Zebrafish. Mirana showed me and Ville around the FishCore, one of the largest facilities of its kind in the Southern Hemisphere. So there’s Life from A to Z. My advice to ARMI is to not to communicate this to small children who own Sea- Monkeys.

One of the greatest assets of Australian science lies in the willingness of researchers to share and communicate why science matters. I think this can get lost in conventional forms of science communication (e.g., journals) and the media.

Mirana and Ville, moments before "the axolotl incident"I say a big thank you to Mirana and Nadia for taking the time to enlighten me (and now you) about three facets of life science relevant to regenerative medicine.

Thumbs up to SAHMRI and EMBL Australia

I think career opportunities and job security are stand out issues for Australian bioinformaticians. The positions that David and Ville hold, and the teams that they will build around them show that Australia can support longer term posts for bioinformaticians, computational biologists and quantitative bioscientists.

Here’s to SAHMRI and EMBL Australia for making these roles possible, and here’s hoping there can be more of this approach in the National Innovation System.

In closing

I hope this has given you a boost this Friday. If it has, pass it on.

Sure, it’s not about a cure for cancer or the common cold, but I think these things are no less a currency of optimism, and something that we can all celebrate.

Cheers,

David

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