Monday, 17 November 2014

Escaped scientists spotted in Tasmania!

It appears that we forgot to lock the lab and office doors again! A few of our researchers escaped and boarded the brand new Australian Marine National Facility research vessel from the CSIRO, The Investigator.

They are taking part in one of the first scientific sea trials which left from Hobart, Tasmania, last Monday. The transect is going northward criss-crossing the continental shelf. These first sets of voyages are used to check, test and optimise all of the equipment onboard, so they can be used to full capacity when the full research voyages start early next year. A few things are still getting sorted on the ship with the usual teething problems, but it seems that a lot of very good science was still being done, so we should have a good crop of seawater samples and other experiments to analyse. Our escapees also had a fantastic time watching various whales jumping around a little way off the ship. I'm sure Martin and Deepa will tell us more about their adventures when we recapture them this week! So stay tuned...
photo of the Investigator from the ship's blog

Thursday, 6 November 2014

Music Videos from iGEM

A number of iGEM teams made parody music videos. A couple of my favourites are here:
Plasmid'outai from the INSA-Lyon team which has a nice Bollywood fell to it.
The St2ool Project from the Valencia Biocampus team- a parody of YMCA.
There was also a Katy Perry parody I liked, but I haven't been able to find the video yet, I'll update this post when/if I find it.




Gold!

Congratulations to the Macquarie IGEM team, who are the first Australian team to ever win a gold medal at an iGEM competition! Congrats to all of the other medal and award winners (full results here), especially the Grand Prize winners, Heidelberg in the undergrad category, and UC Davis in the overgrad category.

The 2014 iGEM contestants-the Macquarie team and myself are in the very front, slightly left of the centre


Sunday, 2 November 2014

Greetings from Boston

I'm in Boston along with the Macquarie iGEM team attending the iGEM Giant Jamboree. iGEM is the International Genetically Engineered Machine competition where teams of undergraduate students from around the world showcase their synthetic biology research achievements. This year there are 245 teams with over 2500 participants attending the iGEM Giant Jamboree. In addition to the Macquarie University team, there are two other Australian teams from Melbourne University and Sydney University.

The Macquarie project was Photophyll: the Green Machine, where our students were looking to express the chlorophyll biosynthetic pathway in the bacterium E. coli, with the idea of trying to make a photosynthetic E. coli that could use light energy to make hydrogen gas as a biofuel by linking photosystem II to a hydrogenase enzyme. We also have a great outreach project- So You Think You Can Synthesize- the worlds first online synthetic biology reality contest, which I have blogged about previously.

Our team gave a great presentation today and did a good job handling the questions from the judging panel, who were excited by So You Think You Can Synthesize. I think our team has a chance at a gold medal, we will have to see how we go. This is the fifth year we have had a Macquarie team competing in the competition, so far we have been the top Australian team each year, and we have won 1 bronze and 3 silver medals.

It has been an interesting experience for me attending iGEM for the first time, quite different from going to a normal scientific conference. There is an enormous range in the quality of the research projects from pretty weak to absolutely amazing. So far the highlights for me were the teams from Imperial College London, Paris Bettencourt, and Stanford-Brown-Spelman. Imperial College would be my pick for the top team overall with their project of making bacterial cellulose that could be used for water filtration, and functionalised with specific binding proteins to remove water contaminants. Paris Bettencourt had a broad ranging project investigating different ways to manipulate the bacteria that live on human bodies in order to change human body odour. Stanford-Brown-Spelman had an ambitious project to make a biosynthetic unmanned aerial vehicle manufactured out of a bacterial cellulose acetate with biologically-programmed waterproofing, programmed timed biodegradation and biosensing capabilities. The imagination and creativity of some of the teams has been very impressive.


The MQ iGEM team in Boston flanking our team banner there in the background

Friday, 10 October 2014

PhD scholarships available



We have a number of PhD scholarships available as part of my ARC Laureate Fellowship- Here's our advertising blurb:

ARC Laureate Fellowship PhD Scholarships- Marine Cyanobacteria

Photosynthetic marine microorganisms are responsible for the production of half of the oxygen in our atmosphere, equal to the contribution of all land-based vegetation. They underpin the entire marine food web and shape the health and sustainability of all ocean resources.  Despite their critical role we know surprisingly little about this crucial group. The Paulsen research group is using a range of cutting edge methodologies (ecogenomics, transcriptomics, single-cell analyses, mass spectrometry, bioinformatics and modelling) to investigate the lifestyle of these key primary producers.

We are looking for motivated candidates with excellent academic records to join our ARC Laureate Award funded research team. Our group is located in a state-of-the-art research facility which is part of the Biomolecular Frontiers Research Centre within Macquarie University, Sydney, Australia.  Our dynamic research team has a wide range of expertise in microbiology, molecular biology, oceanography, bioinformatics, systems and synthetic biology. We currently have a number of scholarships (both Masters and PhD) that span the following research areas:



      1.     Ecogenomics, evolution and interactions in natural environments:
This research project will involve fieldwork at coastal sites and on Australia’s new research vessel RV Investigator, working in blue water from the tropics to the Antarctic ice-edge. Techniques include single cell genomics and Stable-Isotope-Probing to unravel interactions and trace the flow of cyanobacteria-derived compounds and energy through the ecosystem.

2.      How marine cyanobacterial adapt to environmental change
Many variable factors, biotic (microbial competition, infection, predation) and abiotic (seawater chemistry and physical parameters), influence the distribution and survival of marine cyanobacteria. A range of interdisciplinary projects will use a combination of "omics" tools (e.g. comparative genomics, transcriptomics and proteomics) to study the molecular responses of these microbes to relevant environmental factors.

3.      Building virtual cyanobacteria
Developing computational models at both a single cell and ecosystem level.  This project will create and model metabolic processes, and generate working virtual cell/ecosystem units supported by experimental data. This research will deliver the first model of marine phototrophic organism and address fundamental questions such as ‘what defines the minimal set of genes required for a free living photosynthetic organism?’

4.      Cyanobacterial transporter characterisation
Membrane transporters have a central role in determining the success of an individual in any given environment; essential for nutrient import, waste export and maintenance of osmolarity. This project will have an informatic focus, involving developing tools for handling large datasets, algorithms for transporter characterisation and visualisation. Transporter characterisation is a long-term interest and strength of the Paulsen group and this project will integrate closely with the cyanobacterial modelling work.

5. Synthetic Biology, building a molecular tool kit
Novel gene circuits that respond to signals in a predictable way can be built experimentally by modelling metabolic and regulatory networks in silico. This project will identify and optimise vital molecular pathways within cyanobacteria and develop genetic tools to undertake high-throughput mutant screens, validate models and enable us to optimise cyanobacteria for bioengineering.

These PhD positions carry scholarships of AUD$25,392 per annum, tax exempt.

Application process:
Interested individuals are invited to discuss these projects with Laureate Fellow Professor Paulsen (ian.paulsen@mq.edu.au). Initial expression of interest should contain a CV and short statement of your research interests. There is potential for additional projects which connect to the overall research focus of the group to be considered and developed together with prospective candidates.

Application for the PhD positions will be through the Macquarie University HDR website. Please see the website and links within for further information about eligibility and submission procedures. (http://hdr.mq.edu.au/information_about/Scholarships/schol-opportunities/hdr_scholarships_domestic_and_international).

Learn more about Macquarie University's profile, the facilities available and its campus life (http://www.mq.edu.au/about_us/university_profile/ and http://www.mq.edu.au/on_campus.php)

Wednesday, 8 October 2014

I have the grey hairs to prove it

Macquarie University has apparently noticed the grey hairs I'm starting to get, they announced last week that I am one of six new Distinguished Professors. On top of that, on the same day, the Macquarie University Research Excellence Awards were presented, and Karl Hassan and I won the Research Excellence Prize in Science and Engineering. They made 90 second videos summaries for each of the research projects nominated for an award. Here's the video for our project on identification of a new type of bacterial drug efflux pump-

.

Yeast 2.0 on the radio

I was interviewed on 2SER this morning on the topic of yeast 2.0, biofuels and beer.
Transcript and podcast can be found here.
Louise Brown came along for moral support and snapped this action shot of the back of my head:


Thursday, 25 September 2014

So You Think you can Synthesize?

Macquarie University has once again entered a team of undergraduate students to compete in the International Genetically Engineered Machine (iGEM) synthetic biology competition. Over the last four years, our teams have won 3 silver and 1 bronze medals. This year our team is hoping to win a gold medal, though they do have one handicap- I will be coming along with them as a team advisor to the iGEM Giant Jamboree in Boston.

This year as an outreach activity, our iGEM team has created an online reality contest "So You Think You can Synthesize" where you can ask our student team any burning question you have about synthetic biology through a live chat feed and can vote for your favourite scientist. Looks like we are down to the last four scientific contestants now! You can also find videos about each of the eliminated contestants and about our team's experiences in iGEM here.

iGEM team hard at work

Monday, 22 September 2014

There is no I in team, but there is one in Ian

On Friday, I took the labgroup out for a team building exercise, and nothing builds team spirit like shooting each other with lasers! So we went out and played lasertag and ten-pin bowling.
So what did we learn from this outing-
- running around like a maniac with a laser is a good workout, my muscles still ache 3 days later
- being a sneaky sniper does not work as a lasertag strategy- after I was shot by Liam five times in the first 30 seconds or so, I realised running around like a kitten on ritalin is a much more effective strategy
- you definitely want Silas on your team in any sporting activity, he kicked ass in both bowling and lasertag
- it was good to finish up with pool and darts as it gave me the opportunity to win back some respect on the pool table


Lab group bowling


photo of me playing lasertag

Thursday, 18 September 2014

Congrats Deepa!

Deepa Varkey is a PhD student in my group working on how marine cyanobacteria adapt to different temperatures. She has just won a prize for the best poster at the 9th European Workshop on the Molecular Biology of Cyanobacteria in the Netherlands. Great job Deepa!


Deepa and her prize winning poster

Thursday, 11 September 2014

Eureka Awards

Last night, I was at the Eureka Awards Dinner. The Eureka Awards have been described as the Australian Science equivalent of the Oscars. While not quite as glamorous as the Oscars, it was nevertheless a black tie event at the Sydney Town Hall, and we did have some media celebrities present, such as Adam Spencer and Dr Karl Kruszelnicki. It was also the second top hottest topic on Twitter yesterday in Australia.

I was not nominated for an Award, but was there to fly the flag for Macquarie University. I was very excited that MQ's Professor Lesley Hughes won the Eureka Prize in the category of Promoting Understanding of Australian Science Research for her tireless efforts in communicating the science of climate change. Congratulations to Lesley and to all of the award winners of the 2014 Eureka Prizes. The full list of the 2014 Eureka Prize results can be found here.

The dessert was certainly glamorous

Indigo V and Citizen Oceanography

Martin has beaten me to it and already put up a blog post about the Indigo V expedition and our paper in PLoS Biology. I just have a couple of things to add. Martin and Federico were interviewed on ABC radio on Wednesday morning, here is a link for anyone who wants to listen or read the transcript. I like Martin's line- "Every second breath we take the oxygen is being produced by microbes in the ocean.

Also, I wanted to highlight the beautiful photo from the Indigo V expedition, taken by Rachel Lauro, which is the cover image for the current issue of PLoS Biology:

Wednesday, 10 September 2014

Crowdsourcing Microbial Oceanography

For marine microbiologists getting out into the blue ocean is a big deal. Competition for ship time is fierce and we often propose and plan research voyages years in advance. Even with access to dedicated research vessels the ocean is enormous, and vast swaths of the ocean are rarely visited by scientists and therefore poorly sampled.

To attempt to address this problem I set off on a expedition onboard an 18m sailing yacht in April last year to help prove the concept that citizen scientists onboard sailing vessels can fill the gaps in oceanographic data collection. Together with Federico Lauro, Joe Grzymski and Rachelle Lauro we set off from Cape Town into the Indian Ocean on our way to Mauritius.

The first leg of the Indigo V voyage was far from plain sailing. We encountered foul weather, gear failures, lack of sleep, sea sickness and survived the ravages of a fierce gale and cruel waves 1000s of kilometres from land. Fighting to stay on course, stay onboard and remain afloat were our main priorities. However, we also managed to take measurements and preserve samples for microbial oceanography using relatively simple low cost equipment. We survived and proved that CITIZEN SCIENCE IS POSSIBLE.

The lessons we learned form this expedition form the basis of our community page headlining this weeks PLOS Biology.**

Joe Grzymski strapped-in and doing science out in the Southern Indian Ocean.

The timing of this article coincides with the arrival of Australia's new research vessel. These are exciting times for microbiologists in Australia, particularly for biological oceanographers who have been anxiously waiting the RV Investigator which has been delayed for a year. Investigator was built in Singapore and arrived yesterday in her home port of Hobart where she will be fitted out with some impressive scientific kit.

This newspaper article provides some background and interesting numbers. For example, Investigator will be able to accommodate up to 40 scientists and students on voyages from the equator to the Antarctic ice edge for up to 300 days per year. Scientists requested over 800 days of research project time on board for the first year of operation, but the vessel will be funded for only 180 days at the moment.

If you are a student and have an interest in exploring the blue ocean and the organisms that thrive within it then you should get in contact with our research group here at Macquarie University. We have a number of exciting PhD studentships opening early next year for work on metabolic modelling and genomics of marine microorganisms.

**(This is actually the second paper produced from this project, the first was a review of the links between biogeography and traits of marine microbes, that we mostly wrote while prepping the Indigo V for the first leg in Cape Town.)


Ready to set off across the blue Indian Ocean. A picture of our sailing vessel, Indigo V, tied up alongside squid boats in Port Elizabeth, South Africa. 


Wednesday, 27 August 2014

Laureate Fellowship

I received the exciting news last week that I have been awarded a Laureate Research Fellowship from the Australian Research Council. I flew to Adelaide on Friday for the Awards Ceremony, which was held at St Peter's College in Adelaide. This was an impressive venue, looking like it had been teleported through time from the 19th century.  I also learnt that St Peter's has more Nobel Prize winning graduates (3) than any secondary school outside of New York.

I'm now the proud owner of an ARC Laureate Fellow lapel pin, I'm not quite sure when I'm ever going to have cause to actually wear it. My Laureate Fellowship was awarded for my proposal "Building Virtual Cyanobacteria: Moving Beyond the Genomics Era". You can find a description of the project on my my ARC Laureate Fellowship bio page. There's also some further information in the Macquarie Uni press release. Time to go crack open some bottles of champagne!

The cats were very excited and congratulated me on the good news
Receiving congratulations from Christopher Pyne, the Minister for Education (and yes photographic evidence that I actually own a suit)

The successful 2014 ARC Laureate Fellows (we all look very very happy)






Thursday, 14 August 2014

My Kardashian Index is 0

Earlier this year, I blogged about metrics for measuring scientific output such as a H-index, AltMetric, etc. I just came across an entertaining little paper in Genome Biology by Neil Hall about a new metric- The Kardashian Index. Neil was wondering whether there are scientists who are like Kim Kardashian- famous for being famous. Or more specifically, whether there were scientists who are famous for their twitter feeds or blogs, but have not produced much in terms of published research papers of significance. So, he came up with the Kardashian Index- your number of twtitter followers divided by your number of citations from your published scientific papers.

I'm proud to say my Kardashian Index is 0 - since I have no Twitter followers, and 32,000+ citations. Ok, ok, since I am a conscientious objector to twitter, Facebook, etc, and have never tweeted in my life, it's probably not a relevant metric to me.


Fig. 1 from the Kardashian Index paper- identifying scientists who are highly active on social media but don't actually produce much scientific output. 




Monday, 11 August 2014

Minions in Action!

Some of you may recall we received MinION sequencing devices from Oxford Nanopore as beta testers. It's taken a while, but Mike Gillings now has them up and running. Whether they can actually generate useful data is still something we're working out, but in the meantime here are some action photos.

The MinION is the USB device plugged into the laptop


Each dot on the screen represents a protein nanopore through which a DNA molecule is moving and being sequenced. The different colour of the dots indicates how the sequencing is going.

Who doesn't love bar graphs- this one shows the lengths of DNA molecules being sequenced. Some of our read lengths are up to 70,000 bps in size









Best Wishes Daniel

The Paulsen lab went on an outing Friday night to the University bar to farewell Daniel Farrugia. Daniel has just submitted his PhD thesis on genomic analyses of the opportunistic pathogen Acinetobacter baumannii, where he was investigating what is different between strains from hospital-acquired infections, community-acquired infections, and environmental isolates. Daniel has published papers in PLoS One and The Journal of Antimicrobial Chemotherapy; another paper about to be submitted to Nucleic Acids Research this week, and a couple more papers in earlier stages of preparation.

Daniel is moving to Malta with his family, and after a break to recover from his PhD is going to be looking for a postdoctoral position in the EU. We wish Daniel the best of luck for the future!


Paulsen group at the pub; Daniel is in the front of the photo holding a beer

I'm hiding up the back away from the camera

Thursday, 7 August 2014

There's more: Microbiology Faculty position available

In addition to the Synthetic Biology/Bioinformatic Faculty positions we just advertised, we also have a new faculty position available in Microbiology at Macquarie University. This would be a level B appointment (roughly equivalent to a new Assistant Professor in the USA). Again, applications close on Sunday 31 August 2014, 11:55pm.



Tuesday, 5 August 2014

New faculty positions in Synthetic Biology/Bioinformatics

Building off our launch of the Yeast 2.0 Synthetic Biology project at Macquarie University, we have just advertised three new junior faculty positions (level B/C- roughly equivalent to Assistant Professor in the USA). Two of these positions are in Synthetic Biology and the third position is in Bioinformatics. We also have three postdoctoral positions to be filled on the Yeast 2.0 project. The plan with these appointments is to build a critical mass of researchers in Synthetic Biology at Macquarie, and position ourselves as leaders in this field in Australia. 

The Macquarie University web site tell me that applications for these positions closes on 11:55pm Sunday 31 August 2014, Australian Eastern Standard Time. If you are interested in one of these positions, I encourage you to apply or to contact me if you have any further questions.

While searching the internet for a suitable image, I came across this synthetic biology comic from Drew Endy and Chuck Wadey- full version here


Friday, 18 July 2014

What the hell is the Anthropocene anyway?

When I was a kid, I used to drag my parents out gem/mineral/fossil hunting all the time. Possibly in revenge for all these field trips, much later my Dad threw out my mineral collection that had been stored in his garage for a decade or two while I was working overseas (Not that I'm bitter about that or anything).

Anyway, as a 12 year old I was an expert on geological eras, periods and epochs. Apparently, my childhood knowledge is now out of date (and probably mostly lost in forgotten recesses of my mind). Mike Gillings has made me aware that there is a growing scientific opinion that we are now living in a new geological epoch- the Anthropocene. As a 12 year old I would have said we were living in the Holocene Epoch, but humanity is now have such an impact on the earth, that it is likely that we would show a strong signal in the geological record from things like changes to atmospheric CO2, biodiversity loss which would show in the fossil record, changes in trace element distribution due to pollution, etc. Hence we are likely now in a new epoch- the Anthropocene (Age of Man).

When the beginning of the Anthropocene should date from is a controversial topic, but there are probably three distinct phases to the Anthropocene: the ‘paleoanthropocene’, corresponding to the widespread adoption of agriculture some 8 to 10 thousand years ago, when clearing of forests and the consequent release of greenhouse gases potentially started affecting earth systems. The second phase began in the Industrial Revolution, coinciding with significantly increased carbon emissions and the environmental degradation associated with industry. The final phase occurred post World War II, and is called “The Great Acceleration”, because it is associated with very rapid growth in human population, resource consumption, energy use and pollution.

Mike Gillings and I have just published an opinion piece (anyone who knows us knows that we're both pretty opinionated) in the journal "Anthropocene". As can be seen in Mike's beautiful figure below, we argue that the different phases of the Anthropocene has resulted in demonstrable impacts on the microbial population of the globe, including-
1. changes to the human microbiome (the community of microorganisms that live in and on the human body);
2. the evolution of bacterial metal ion and drug resistance genes (from exposure to industrial pollution and widespread clinical and agricultural use of antibiotics)
3. the dispersal of disease-causing bacterial pathogens around the globe, e.g., spread of Old World pathogens to the New World during the Age of Exploration
4. Microbiogeochemical changes on a global scale, microorganisms play a key role in the global nitrogen, carbon, phosphrous, sulfur, etc cycling, and human activities from agriculture to industry have undoubtedly affected composition of microbial communities and rates of microbial activity



Some human affects on the microbiological world




Wednesday, 16 July 2014

We're FORC-ed!

So now we have no end of FORC jokes here, as we have launched our new ARC Industrial Tranformation Training Centre: The Food Omics Research Centre (FORC). The aim of our Centre, led by Professor Paul Haynes is to develop a molecular technology platform enabling the next revolution in the food industry. One of my PhD students, Hasinaka, is working within this Centre to investigate whether a sugar cane fibre-based dietary supplement can improve your digestive health through the changing the microbial composition of your gut. Something, I'll probably talk further about at a later opportunity.

Using omics technologies to improve the process of taking food production from "field to fork"

Monday, 14 July 2014

Yeast 2.0 at Macquarie

I've blogged before on Synthetic Biology, particularly with respect to the success of Macquarie University's iGEM teams- for instance, here and here. Synthetic biology is a new scientific field that combines engineering principles with molecular biological approaches to design and construct biological devices and systems. The rational synthesis of “designer” organisms has the potential to revolutionise biotechnological applications in areas such as bioenergy and biomanufacturing. 

I'm a bit behind in blogging but we've recently-ish (alright more than a month ago) had exciting news that the NSW state government has provided significant funding for Macquarie University to lead Australia in the international Yeast 2.0 project. Yeast 2.0 is an international collaboration between six countries, with the aim of building a completely synthetic yeast by 2017. Each collaborating lab is responsible for the design and synthesis of one or more artificial yeast chromosomes. The project was instigated by Jef Boeke at NYU, whose team has recently published in Science the first synthesis of a functional complete eukaryotic chrosomome (yeast Chromosome 3). Our involvement in this project has been led by our Deputy Vice Chancellor (Research) Sakkie Pretorius, and I'll be supervising the actual research staff working on this project (expect some job postings very soon!). This is a fantastic opportunity for Macquarie University to lead synthetic biology in Australia, and to use Yeast 2.0 as a chassis for developing novel synthetic biology applications useful in an Australian context.

Apparently, we are now doing Chr 16 as well as 14 (India dropped out)


Tuesday, 10 June 2014

Art or Science?

Ooops, looks like its nearly two months without a blog post. Probably my longest dry spell. It's been a little crazy busy here. I've been meaning to post these images for a while. These are the colourful output of my Molecular Biology and Genomics class. In our qRT-PCR prac, we sent the students outside to collect random plant samples, then they got to snap freeze their samples in liquid nitrogen and ground them to a paste with a mortar and pestle, so they could then isolate RNA from the plant cells. As some of you may be aware, I have a history of playing with liquid nitrogen.

Collection of spices? Powdered Dyes? Nope- try plant tissues frozen in liquid nitrogen and ground to a homogenous paste


Tuesday, 15 April 2014

We have Minions!

A couple of years ago, Oxford Nanopore made a big scientific splash when they announced they had developed a new DNA sequencing technology that would revolutionize genomics. Their MinION devices were the size of a USB stick, but were supposedly capable of sequencing long reads from single DNA molecules. After two years of wondering whether these devices were mythical, I can now tell you they actually exist. Together with Mike Gillings, we received five Minions in the mail today as part of a worldwide Oxford Nanopore beta test program. The big question now is- do they actually work?

Not mythical! Of course, we don't know yet whether they actually work

It is the size of a large USB stick. Thanks Mike for providing the skull of one of his students for scale.

I constructed Minionhenge on Mike's desk
Assemble the Minions!

Thursday, 10 April 2014

Racing up the Best Seller's List


Currently #285,426 on Amazon's best seller list (how the hell did it get that high?) is our new book on Molecular Methods in Environmental Microbiology. Andy and I would like to thank all our contributors for their hard work and their patience, as this book took a long time to see the light of day. I now remember why it was over a decade since I last edited a book.




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

Friday, 31 January 2014

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