Monday, 31 March 2014

News from San Diego

Well, its the start of baseball season in the US, and my beloved San Diego Padres just beat the hated Los Angeles Dodgers in their first game of the season. Yay!

While trying to get a news article about this game from the San Diego Union Tribune, I coincidentally came cross the latest genomic news. Craig Venter (who is famous for many things- sequencing the first bacterial genome, creating the first synthetic bacterium, sequencing his genome as the human genome, sequencing his poodle's genome, sequencing the world's oceans from his yacht, etc) has just announced raising $70 million to form a new genomics company- Human Longevity Inc. This company will be sequencing a hundred thousand human genomes each year as well as sequencing microbial communities living in/on people.

This should bring us closer to personalized medicine, where healthcare decisions can be tailored according to a patients genetics (and potentially the makeup of their microbial communities).

Tuesday, 25 March 2014

The Alphabet Soup of Measuring Scientific Output

When I returned to Australian science after twelve years in the USA, one of the first things I encountered was the use of metrics to try to assess a researcher's output. I was used to writing grants in the US system where I would simply list my number of publications. Over drinks with Mark Schembri and Steve Djordjevic at a pub in Adelaide in 2007, I was introduced to the concept of a H-index, which I had never heard of before.

After indoctrination into the mysteries of the H-index, I learn't that this metric tries to measure the impact of a scientist's publications by factoring how often they are cited by other scientific publications. So a H-index of 25 (about typical for a tenured professor) means that you have published 25 papers that have each received at least 25 citations. Depending on how you define citations, your H-index may vary considerably. For instance, according to Thomson ISI Web of Science, my H-index is 83, but according to GoogleScholar, my H-index is 94.

H-indices have a number of limitations, e.g., they are a cumulative measure, so a young scientist will virtually always have much lower H-indices than older scientists; citation rates vary alot between different scientific fields; review articles tend to be much more highly cited than original research papers, so write lots of reviews if you want a better H-index.

I've subsequently encountered a whole alphabet soup of ever more obscure metrics, which i don't really use. There is an M-index, which is your H-index divided by the number of years since you published your first paper. There's an i10-index, which is the number of publications to have at least 10 citations, and many others.

This latest grant round, Karl Hassan in my group introduced me to an entirely new metric for scientific impact- AltMetric. AltMetric tracks mentions of your scientific publications on news media, twitter, blogs, etc, so gives some indication of broader impact. Its pretty cool, though I'm not sure how much direct use I will make of it, but lets do a quick analysis.

IMHO, our two most important papers published in the last year were:

Hassan, K. A., Jackson, S. M., Penesyan, A., Patching, S. G., Tetu, S. G., Eijkelkamp, B. A., Brown, M. H., Henderson, P. J., and Paulsen, I. T. (2013) Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins. Proceedings of the National Academy of Sciences, USA 110: 20254-20259.

Tetu, S. G., Breakwell, K., Elbourne, L. D. H., Holmes, A. J., Gillings, M. R., and Paulsen, I. T. (2013) Life in the Dark: Metagenomic evidence that a microbial slime community is  driven by inorganic nitrogen metabolism. ISME Journal 7: 1227-1236.

What does AltMetric think?
Hassan et al.- 7 news stories, 2 blog posts (curiously does not include my blog), 15 tweets, and recommended on the Faculty of 1000; which puts it in the top 2% of all papers in terms of impact.

Tetu et al.- 1 blog post (also does not include my blog), 6 tweets, 2 facebook posts, 1 mention on reddit; which puts it in the top 6% of all papers in terms of impact (curiously, I know this paper was featured in many news articles, yet none of those are included).

After quickly checking all our other 2013 publications, altmetric and I agree, those are our two highest impact papers for the year. Based on this small sample then, altmetric seems to do any effective job. It also provides a very nice way of summarizing who is blogging or tweeting about your work.

Thursday, 20 March 2014

Life in the Dark video

While we're on the topic of videos. I've been meaning to post this video for sometime, but for some reason, I can't embed this particular video, but here is a link to it instead. A research team led by myself and Sasha Tetu were one of three finalists for a Macquarie University Award for Research Excellence in Science and Technology. As a nominee for these awards, a short 90 second video was made of our research and shown at the awards night. It includes lots of cool footage of cave divers in the Nullarbor Plains caves.

Wednesday, 19 March 2014

Indigo V video

Our ARC and NHMRC grants have now been submitted, with the last one being submitted today. So now I can hopefully squeeze in some time between teaching and research to catch up on my blogging.
Some of you may recall that Martin from my group participated in the Indigo V expedition organized by Federico Lauro, where an 18 metre yacht sailed across the Indian Ocean to collect seawater samples for microbiological investigation. Some previous blog posts about the expedition-
All Aboard
Voyage Preparations- Cape Town
Sailing Log- part 1
Sailing Log- part 2
Lost at Sea- Sailing Log- part 3
The Indigo V expedition- a prototype for citizen oceanography

The Indigo team made a video of their endeavours (see below). And the video has been selected as a finalist in the American Society for Microbiology Global Video Challenge. Yay! In addition prizes for 1st/2nd/3rd, there is also a People's Choice Award, so I encourage you to vote for the Indigo V video at this link.
Good luck Federico and colleagues!

Saturday, 1 March 2014

JAMS turns 3

Wednesday night, we celebrated the third birthday of JAMS (Joint Academic Microbial Seminars)- a monthly microbiology seminar series held at the Australiam Museum in Sydney. The celebration as usual took the form of an annual dinner in the Dinosaur Room at the Australian Museum. This was preceded by talks from special guest speakers. David Bourne from the Australian Institute of Marine Science gave a great talk on the microbial inhabitants of corals. Teresa Zelante gave a fascinating talk, which I half understood, on the interplay between the immune system and your gut bacteria, nd how they cooperate to fight pathogens. And I gave my first ever talk at a JAMS meeting- Building Virtual Cyanobacteria: To Metagenomics and Beyond! As part of my talk and accompanied by the beautiful artwork you see below, I told the story of how JAMS first started, when Federico Lauro gave several Sydney microbiologists a mysterious invitation to a pub in Surrey Hills, and after some beers the plan for JAMS came together.
One of the slides from my talk showing an artists reconstruction of how JAMS started