O'Really?

August 17, 2012

What is the collective noun for a group of Systems Biologists?

From helix to hairball

According to Arthur Lander, “hairball” networks like the one of human proteins above, are the new icon of biology, taking over from the famous double-helix. Image originally published in BMC Biology [1].

What happened was, I was looking for a creatively commons licensed picture of Pedro Mendes to upload to commons.wikimedia.org. Not the footballing Pedro Mendes who played for Rangers, Spurs, Pompey and Porto but the systems biologist Pedro Mendes who plays for Virginia Tech and Manchester. Thankfully, another systems biologist, Michael Hucka kindly pointed to his impressive collection of pictures, taken at various events over the years which include some shots of Pedro. Looking at these pictures made me idly wonder: What is the collective noun for a group of systems biologists?

Systems biology is the study networks of various kinds [2,3] so it’s ripe for a collective noun, and there were several suggested on twitter. Since twitter has recently developed a nasty habit of disappearing tweets, here is a collection gathered and preserved for posterity from the twitterome*:

A jamboree of systems biologists?

Tom Williamson and Mike Hucka initially plumped for a Jamboree of systems biologists:

A loop or an ome of systems biologists?

Mike Hucka and Nathan Pearson voted for a Loop or an Ome of systems biologists:

A cluster of systems biologists?

Then again, maybe it should be a cluster of biologists?

A network of systems biologists?

Douglas Kell reckoned on a network of systems biologists:

A system of systems biologists?

Ewan Birney thought it had be be a system:

So there you have it, according to the twitterome, the collective noun for a group of systems biologists is a system, network, cluster, ome, jamboree or loop (delete as appropriate). No doubt there are many more, that’s what twitter hashtags are for, #SysBiologists.

References

  1. Arthur D. Lander (2010). The edges of understanding, BMC Biology, 8 (1) DOI: 10.1186/1741-7007-8-40
  2. Hiroaki Kitano (2002). Systems Biology: A Brief Overview, Science, 295 (5560) 1664. DOI: 10.1126/science.1069492
  3. Trey Ideker, Timothy Galitski & Leroy Hood (2001). Systems Biology: A new approach to decoding life, Annual Review of Genomics and Human Genetics, 2 (1) 372. DOI: 10.1146/annurev.genom.2.1.343

* That’s another #badomics award for Jonathan Eisen’s growing collection…don’t blame me, blame Leonid Kruglyak

June 19, 2011

Sunday at the Lab with Uri Alon

Ah Sunday, a day of rest, recuperation and roasted food

Unless you’re a scientist, that is, in which case you might be working. If that’s you, this one goes out to all you committed high-calibre, driven scientists [1,2,3] who are spending this Sunday working at the laboratory bench. The amusing little ditty below is written by biologists Michael Elowitz and Uri Alon, and performed here by Uri Alon.

I kissed my wife and kissed farewell
I must go down to run my gel
I’m going to spend another Sunday at the lab

My wife said “Uri, you’ve got to promise,
you love me more than doing Science”
I said “Honey, can we discuss this another day?”
I’m going to spend another Sunday at the lab

My mum said “Son, don’t waste your life,
go home and spend time with the wife
you must have heard this from your father
why can’t you be more like your brother?
No son of mine spends Sundays at the lab.”

My dad said “Son, you need a shrink”
The shrink said son “you need a drink”
Those Rorschach spots reminded me of blots
He said “Oh God, you obviously have an obsessive compulsion
to spend all your Sundays at the lab”

My wife she left me
My mum disowned me
The shrink pretends he doesn’t know me
Because I can’t be myself
Without some buffer on the shelf

So if you need me, you can phone me at the lab
I’m going to spend another Sunday
I’m going to spend another Sunday
I’m going to spend another Sunday at the lab

References

  1. Elowe J (2010). Workaholism: between illusion and addiction. L’Encephale, 36 (4), 285-93 [Boulomanie : entre illusion et addiction] PMID: 20850599 DOI: 10.1016/j.encep.2009.12.002
  2. Overbaugh, J. (2011). 24/7 isn’t the only way: A healthy work–life balance can enhance research Nature, 477 (7362), 27-28 DOI: 10.1038/477027a
  3. Anon (2011). The 24/7 lab: Nature’s readers comment online Nature, 477 (7364), 280-280 DOI: 10.1038/477280c

November 17, 2008

Science blog meme: Why do we blog?

Keep Calm and Carry On via AJC1I have been virally infected by Martin Fenner’s “why do we blog” meme.

1. What is your blog about?

Science and technology, especially bioinformatics, systems biology and the Web. It is a personal laboratory notebook-cum-diary, with a few facts and many opinions that would be difficult to publish conventionally [1].

2. What will you never write about?

Banal personal trivia (“I went shopping today”), confidential work, collaborative projects before they have been published. If in doubt, I try to ask people, “is it OK if I blog this?”

3. Have you ever considered leaving science?

Already did, I left science after my undergraduate degree to work in industry, but came back after six years to do a PhD. I don’t think Science ever really leaves you, once a scientist, always a scientist. Can’t see myself “leaving” again, but you never know.

4. What would you do instead?

Tend olive trees in Greece. Sequence 10,000 + Olive tree genomes, do some olive tree systems biology [2]. Subsidise scientific research with money from olive oil export business.

5. What do you think will science blogging be like in 5 years?

Pretty much the same as it is now I reckon, maybe more senior scientists will start blogging, see big boffins with blogs.

6. What is the most extraordinary thing that happened to you because of blogging?

I’m pretty sure blogging was a significant factor in being invited to Science Foo Camp (scifoo)

7. Did you write a blog post or comment you later regretted?

Non, rien de rien. Non, je ne regrette rien. Some of the posts about semantic web and molecular biology I might come to regret in the future though, but life is too short. There is an ever present temptation to write controversial blog posts (that might be regretted later) to get more visitors to your blog. Sometimes I can’t resist. Also, there is no safety net of peer-review, so you can make mistakes very quickly, even faster than by drinking tequila. I often wonder what prospective employers and/or funding bodies would make of it all – by the time I find out, it might be too late :)

8. When did you first learn about science blogging?

Via nodalpoint which is run by Greg Tyrelle.

9. What do your colleagues at work say about your blogging?

So far, there have been five basic responses to my blog among colleagues.

a) Great idea, carry on (see picture, top right). Can you blog this for me?

b) Bad idea, why do you waste so much time blogging? When are you going to do some “real” work?

c) Teasing: “I’m drinking a coffee, are you blogging this?”

d) Head-in-the-sand, no acknowledgment, denial, look the other way.

e) Ignorance is bliss. What is a blog? Do you have one of those interweb things on your computer?

References

  1. Michael R. Seringhaus and Mark B. Gerstein (2007). Publishing perishing? towards tomorrow’s information architecture. BMC Bioinformatics 8, 17+. DOI:10.1186/1471-2105-8-17, pmid:17239245
  2. Royston Goodacre, Douglas B Kell, Giorgio Bianchi (1992). Neural networks and olive oil. Nature 359 (6396), 594. DOI:10.1038/359594a0

[Keep Calm and Carry On via AJC1]

October 14, 2008

Open Access Day: Why It Matters

Open Access Day 14th October 2008Today, Tuesday the 14th of October 2008, is Open Access Day. Like many others, this blog post is joining in by describing why Open Access matters – from a personal point of view. According to the wikipedia article Open Access (OA) is “free, immediate, permanent, full-text, online access, for any user, web-wide, to digital scientific and scholarly material, primarily research articles published in peer-reviewed journals. OA means that any individual user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article. An OA article usually has limited copyright and licensing restrictions.” What does all this mean and why does it matter? Well, in four question-and-answer points, here goes… (more…)

July 25, 2008

How to spend a £400 million Science budget

A thought experiment with lots of money

The Queens Ahead by canonsnapperThe Biotechnology and Biological Sciences Research Council (BBSRC) is the United Kingdom’s funding agency for academic research and training in the non-clinical life sciences. It supports a total of around 1600 scientists and 2000 research students in universities and institutes in the UK. The head of our laboratory, Douglas Kell, has recently been appointed Chief Executive of the BBSRC [1]. Congratulations Doug, we wish you the very best in your new job. Now, according to bbsrc.ac.uk, their annual budget is a cool £400 million (just short of $800 million or €500 million). This has left me wondering, how would you spend a £400 million Science budget for the life sciences? For the purposes of this article, imagine it was you that had been put in charge of said budget, and Prime Minister Gordon Brown (texture like sun) had given you, yes YOU, a big bag of cash to distribute as you see fit. A mouth-watering prospect, I think you’ll agree. Here, is my personal opinion of how, in my dreams, I would spend the money. (more…)

March 20, 2008

Genomes to Systems 2008: Summary

Filed under: sysbio — Duncan Hull @ 4:23 pm
Tags: , , , , , , , , , , ,

G2S sponsorsGenomes to Systems is a biannual conference held in Manchester covering the latest post-genome developments. The final programme for Genomes to Systems 2008 is available here. To supplement this with a little more information, the following briefly overviews sessions during the three days of the 2008 conference. (more…)

Genomes to Systems 2008: Day Three

Systems biology of the cell cycleGenomes to Systems is a biannual conference held in Manchester covering the latest post-genome developments. Here are some brief and incomplete notes on some of the speakers and topics from the third and final day of the 2008 conference. (more…)

March 19, 2008

Genomes to Systems 2008: Day Two

Space Travel and Genomics in SpaceGenomes to Systems is a biannual conference held in Manchester covering the latest post-genome developments. Here are some brief and incomplete notes on some of the speakers and topics from day two of the 2008 conference. (more…)

March 18, 2008

Genomes to Systems 2008: Day One

Filed under: sysbio — Duncan Hull @ 9:27 am
Tags: , , , , , , , ,

Genomes to Systems is a biannual conference held in Manchester covering the latest post-genome developments. Here are some brief and incomplete notes on some of the speakers and topics from day one of the 2008 conference. (more…)

February 21, 2008

Biological Complexity

Filed under: sysbio — Duncan Hull @ 11:00 pm
Tags: , , ,

From Molecules to Systems @ UCLDetails of two-day conference titled “Biological Complexity: From Molecules to Systems” at University College London (UCL) in June 2008 have recently been announced. Speakers and topics are described in the link above and also by Martyn Amos on his blog.

Speakers from the UK include: Martyn Amos, Cyrus Chothia, Jasmin Fisher, Mike Hoffman / Ewan Birney, Jaroslav Stark, Michael Sternberg and Perdita Stevens.

Speakers from the Weizmann UK include Nir Friedman, David Harel, Shmuel Pietrokovski, Gideon Schreiber, Eran Segal, Ehud Shapiro and Yoav Soen

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