Monday, 15 June 2015

Is it a prop out of a sci fi movie?

So I posted a few weeks about Serious Equipment needing a Serious Crane. While the PacBioRSII is a cool piece of equipment, it basically looks like a big box. Nowhere near as cool looking as this crazy thing:
I think we got this from a Star Trek movie set

Or maybe its a steampunk thingie from Girl Genius

It seems to be looking at me

OK so these are pictures of the Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) instrument that has just been installed at UNSW. I was part of a team led by Mike Manefield and Federico Lauro that attracted funding for this instrument from the Australian Research Council. I'd never seen pictures of one until Federico showed me these, its truly a crazy looking thing. What this thing does is fire a pulsed beam of ions at a sample, and then it can identify the compounds present by collecting secondary ions produced by running them through a mass spec. It can thus produce a image map with a sub-micron resolution showing what chemicals are present. We hope to use it to analyze the metabolic activities of different bacteria within complex communities.

Tuesday, 26 May 2015

Australian Wine Research Institute

Yesterday, I flew down to Adelaide for the day and visited our collaborators at the Australian Wine Research Institute (AWRI). AWRI are our partners in the Australian node of the Yeast 2.0 synthetic biology project. While I was down there I gave a seminar and we had fun discussions over the progress of our collaborative project. The photos below show a couple of interesting scenes from labs at AWRI. Of course, a trip to AWRI wouldn't be complete without some wine consumption, so we ended the visit with a wine and cheese tasting.

It was a bit jarring to walk through labs and see wine bottles sitting around on lab benches

This was cool though- this is a GC-MS for detecting different metabolites in wine, on the very right hand side is a sniffer where you stick your nose, so you correlate specific wine aromas with the detected chemicals. One of the latest discoveries from AWRI is identifying the chemical that gives a peppery smell to wine, which turns out to be the same compound that gives a peppery smell to pepper!

Saturday, 23 May 2015

Death by Grant Review

This year I am serving on an NHMRC grant review panel, which means I will once again get to spend my birthday in wintery Canberra for the panel meeting. For some reason (more grants submitted? less panel members?) this year the mostly unpaid workload is much higher. I have 23 grants to review within the next week, which means I will spend pretty much every waking moment looking at grants. I do have a feline advisor in my lap at the moment to give her recommendation on each grant.

Not an actual view of my grants to review, since I do it all electronically

Friday, 22 May 2015

Kittybiome Update

The power of successful whining! Thanks to the efforts of Holly Ganz over at Kittybiome, they have worked out the required paperwork for international shipping of kitty poop from Australia to the USA, so Australian cats can now partake in the Kittybiome project. Of course now I'm trapped into having to increase my pledge support to allow sequencing of my cats microbiomes :)

Tuesday, 19 May 2015


A couple of years back I blogged about crowdfunding of science (and games). Yesterday, I came across a scientific project on kickstarter which I felt I had to support- Kittybiome! The microbiome is the collection of bacteria, fungi and other microorganisms that live in us and on us, and there is increasing evidence that these microbial communities play important roles in our health. Thus, Kittybiome aims to use modern DNA sequencing technologies to characterise the microbial communities that live on and in cats.

The combination of silly and serious questions Kittybiome seeks to address include-
  • How do grumpy cats compare to happy cats?
  • How do athletic cats compare to couch potato cats?
  • Does it matter if you feed your cat a paleo-mouse diet?
  • How do indoor and outdoor cats compare? 
  • What happens when your cat goes on antibiotics? 
  • How does the microbiome change during your cat's nine lives?

I would like to add the question- how do different cat breeds compare in terms of their microbiome?

I would have been happy to support at a level that allowed sequencing of the microbiomes of my cats Lyra and Chihiro, but sadly that was only an option if you live in the US or Europe. Since I live in the scientific third world, I can only support the sequencing of the microbiome of a shelter cat. Still it looks like Kittybiome is a kickstarter success as it is already over-subscribed with 22 days still to go. Go Kittybiome!

(Full disclosure- Kittybiome is co-founded by my friend and colleague Jonathan Eisen)

Lyra and Chihiro want to know why Australian cats are discriminated against by Kittybiome

Thursday, 14 May 2015

Serious technology needs a serious crane

In my copious spare time I serve on the Management Committee for the Ramaciotti Centre for Genomics. The Ramaciotti Centre provides technology and services for genomic research, particularly in the area of next-gen DNA sequencing. The Centre is based at the University of New South Wales, but is supported by a consortium of universities and research institutes around the Sydney area (including Macquarie).

Last year I was part of a team led by Marc Wilkins that attracted funding from the Australian Research Council for a new PacBioRSII sequencer. This sequncing instrument will extend our technical capabilities enabling the generation of very long DNA sequence reads compared with other technologies, as well as enabling the detection of methylated and other modified bases in DNA.

After purchasing the instrument, one technical hurdle that had to be overcome was actually getting it into the building, as the Pac Bio sequencer was too big to fit through the doors. The solution- get a big ass crane. Here's photos of the sequencing instrument being installed (Thanks to Marc Wilkins for the photos).

Seems to be happening at night- maybe to minimise the chance of dropping it on students

Ok it is a pretty sizeable piece of hardware

Thursday, 7 May 2015

About time for a gaming post

It's been a while since I've had a gaming related post. My friend Fraser sent me this link- The Fifty Best Strategy Games Ever Made. Sadly, I have only played 14 of them, Fraser tells me he has played 30 of them, putting me to shame (I have played most of the top ten at least).