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.

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.

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!

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

Tracking Grant Writing with Gaming Stats #2

Exactly one year ago, I posted about Tracking Grant Writing with Gaming Stats. Since I primarily game on an Xbox 360 these days, I can track my progress with gaming achievements via Trueachievements.com. Coincidentally, one of my colleagues at MQ (Hi Louise) asked me today if my gaming had been impacted by grant writing. This graph shows my cumulative true achievement score (MS Gamer Scores adjusted by difficulty of achievement) over the last month. Basically there's been close to zero gaming for the last week or two. I have an NIH grant due to be submitted in 5 days, and then the pace picks up with 4 NHMRC grants, an ARC Laureate Fellowship and an ARC Discovery Project due in the next month.

Gaming time has flatlined since grant writing started in earnest a couple of weeks ago

Growing up with Doctor Who

I've always been a big sci-fi fan, and my interest in sci-fi probably significantly influenced my choice to pursue a career in science. It's clearly genetic, as my older brother Steve in his spare time is a published sci-fi/fantasy/horror author.
 
As a kid I grew up watching classic BBC sci-fi programs like Doctor Who and Blakes 7. Though there was the giant spider incident that Steve still hasn't forgiven me for. I was about four years old, and Steve was a teenager. It was Sunday afternoon and time for Doctor Who on the TV, which happened to be Doctor Who and the Planet of the Spiders, with Jon Pertwee as the Doctor. The giant spiders were very terrifying for a four year, and in order to stop my screaming, my mother made Steve turn the TV off to his great displeasure. Although he loves to tell that story these days.

 My reason for bringing up the topic of Doctor Who is that I recently came across Adventures with the Wife in Space, where a guy blogs about watching every classic Doctor Who episode that exists with his wife, and records his wife's opinions of each episode. For a Doctor Who nerd like myself, it is an enjoyable and nostalgic read, though I am surprised that his wife didn't kill him during the process. Now when I want to procrastinate about grant writing, I can just browse an episode or two of Doctor Who on this blog. As an added bonus, they have now started blogging about watching all of Blakes 7 (I'm a huge Avon fan), now they have finished Doctor Who.

To a 4 year old a cardboard cutout spider was very scary

Grand Theft Auto 5 and Southern California Nostalgia

My first job after my PhD was working as a postdoctoral research fellow at UC San Diego. It was the first time I had ever traveled overseas from Australia, and I was pretty young and naive in retrospect. When I first arrived I thought I was living somewhere called "la jolla" (hint to Australian's it's pronounced "la hoya"). Anyway I worked at UCSD in Milton Saier's laboratory for several years, where I developed my love for transporter proteins, bioinformatics and the San Diego Padres baseball team.

I've been playing alot of Grant Theft Auto 5 on my Xbox since Christmas, and in addition to the fun of driving fast cars like a complete maniac, I must admit they have done a great job with the virtual imitation of Southern Californian scenery in the game, playing it has made me feel very nostalgic for my postdoc days. I'm almost at 100% completion on the game, I just need to win a medal in the stupid 26 minute triathalon and then it will be time to move on to the next of my Christmas presents- Assasin's Creed 4: Black Flag (please give your pity to my poor partner, she will have to put up with me talking in stupid pirate accents while I play Black Flag). Of course multiple looming grant deadlines will probably interfere with those gaming plans.

Southern Californian scene from GTA 5

La Jolla cove