Bio::Blogs is a monthly bioinformatic-related blog journal. This issue, number 19, is hosted here at O’Really? and focuses on the the fascinating relationship between Biology and Engineering. Below, for your reading pleasure, is a brief roundup of blog posts during February-ish 2008, and a few other related Bioengineering resources.
March 7, 2008
BioBlogs 19: Bioengineering
March 5, 2008
Science 2.0
I’ve often wondered how all the ridiculous fluffy Web 2.0 marketing hype (see Tim O’Reilly’s principles of Web 2.0) maps into the world of Science. In a talk yesterday, Dave DeRoure argued there is a massive gap between scientists and infrastructure on the Web of Science, most people would agree with this. He points out that there is nothing in the middle to bridge between the two disparate worlds of people and technology. He also claims that Web 2.0 can bridge the gap, and also explains how Web 2.0 “design patterns” maps onto Science. You can see the original slides for yourself, here is my summary. (more…)
Cheminformatics 2.0
February 29, 2008
Lablogs
Some notes from a workshop on blog-based laboratory notebooks “LaBlogs” (Laboratory Logs / Weblogs) held at the Cosener’s House in Abingdon, Oxfordshire, hosted by Cameron Neylon, a protein biochemist based at the Rutherford Appleton Laboratory (RAL) and the University of Southampton. (more…)
February 26, 2008
So, no-one told you life was going to be this way
So, no-one told you life was going to be this way
Your job is a joke, you are broke, your love life is DOA.
It is like you are always stuck in second gear
Well, it has not been your day, your week, your month, or even your year…
OWL be there for you, when the rain starts to pour. Software engineer Leigh Dodds explains how: (more…)
February 21, 2008
Biological Complexity
Details 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
February 8, 2008
Video Killed The Webbio Star
We can’t rewind we’ve gone too far.
January 18, 2008
One Thousand Databases High (and rising)
Well it’s that time of year again. The 15th annual stamp collecting edition of the journal Nucleic Acids Research (NAR), also known as the 2008 Database issue [1], was published earlier this week. This year there are 1078 databases listed in the collection, 110 more than the previous one (see Figure 1). As we pass the one thousand databases mark (1kDB) I wonder, what proportion of the data in these databases will never be used?
R.I.P. Biological Data?
It seems highly likely that lots of this data is stored in what Usama Fayyad at Yahoo! Research! Laboratories! calls data tombs [2], because as he puts it:
“Our ability to capture and store data has far outpaced our ability to process and utilise it. This growing challenge has produced a phenomenon we call the data tombs, or data stores that are effectively write-only; data is deposited to merely rest in peace, since in all likelihood it will never be accessed again.”
Like last year, lets illustrate the growth with an obligatory graph, see Figure 1.
Figure 1: Data growth: the ability to capture and store biological data has far outpaced our ability to understand it. Vertical axis is number of databases listed in Nucleic Acids Research [1], Horizontal axis is the year. (Picture drawn with Google Charts API which is OK but as Alf points out, doesn’t do error bars yet).
Another day, another dollar database
Does it matter that large quantities of this data will probably never be used? How could you find out, how much and which data was “write-only”? Will Biologists ever catch up with the physicists when it comes to Very Large stamp collections Databases? Biological databases are pretty big, but can you imagine handling up to 1,500 megabytes of data per second for ten years as the Physicists will soon be doing? You can already hear the (arrogant?) Physicists taunting the Biologists, “my database is bigger than yours”. So there.
Whichever of these databases you are using, happy data mining in 2008. If you are lucky, the data tombs you are working will contain hidden treasure that will make you famous and/or rich. Maybe. Any stamp collector will tell you, some stamps can become very valuable. There’s Gold in them there hills databases you know…
- Galperin, M. Y. (2007). The molecular biology database collection: 2008 update. Nucleic Acids Research, Vol. 36, Database issue, pages D2-D4. DOI:10.1093/nar/gkm1037
- Fayyad, U. and Uthurusamy, R. (2002). Evolving data into mining solutions for insights. Communications of the ACM, 45(8):28-31. DOI:10.1145/545151.545174
- This post originally published on nodalpoint (with comments)
- Stamp collectors picture, top right, thanks to daxiang stef / stef yau
January 15, 2008
Who’s the Daddy? PCR…
♫ PCR, When you need to know who the Daddy is ♫ …
♫ There was a time when to amplify DNA,
You had to grow tons and tons of tiny cells.
Then along came a guy named Dr. Kary Mullis,
Said you can amplify in vitro just as well.
Just mix your template with a buffer and some primers,
Nucleotides and polymerases, too.
Denaturing, annealing, and extending.
Well it’s amazing what heating and cooling and heating will do.
PCR, when you need to detect mutations.
PCR, when you need to recombine.
PCR, when you need to find out who the daddy is.
PCR, when you need to solve a crime. ♫
(repeat chorus)
When you’ve finished chuckling at that ridiculous viral marketing video, go and Dance Naked in the Mind Field with Kary Mullis. Found via Respectful Insolence: Scientists for better PCR.
December 21, 2007
Blogging: Speakers’ Corner of the Internet
There is a famous place in London town, inside Hyde Park, known as Speakers’ Corner. It is a space where free speech and self-expression prevail. At Speakers’ Corner, anyone can say anything they like about anything they want to anyone who cares to listen. There are some obvious parallels between blogging and Speakers’ Corner as well as one rather striking difference.
If you’ve ever been there, you’ll know Speakers’ Corner is full of circus acts. A quick wander around and you are almost guaranteed to encounter: conspiracy theorists, anarchists, bible salesmen, drunks, religious fundamentalists, pimps, tramps, radicals, punks, politicians, self-promoting exhibitionists, drug addicts, prophets and philosophers. Curiously you don’t often see professional scientists there. Some speakers will talk sense, others will talk nonsense. Either way, a stroll around Speakers’ Corner never fails to entertain, Sunday morning is usually best. Your personal beliefs will probably be challenged and you will almost certainly find someone to strongly dis/agree with. The digital equivalent of Speakers’ Corner is the blogosphere, the bloggers’ corner of the Internet.
Bloggers’ Corner?
There are some obvious similarities between Speakers’ Corner and Bloggers’ Corner. They both involve free speech, entertainment and cheap technology:
- Zero cost free speech
- At Speakers’ Corner you need is something to stand on, a soapbox or stepladder, anything will do. Speakers also need time, an opinion and plenty of air in their lungs. This is “free” speech in two ways. Firstly, it doesn’t cost anything, so you don’t need money or powerful friends to be a speaker. Secondly, speakers are free to discuss anything they want. The same is true of blogging, all you need is some kind of blogging software and off you go. The hecklers will post their comments if they choose.
- Shout, shout, let it all out!
- At Speakers’ Corner anyone is free to shout. Speakers, like bloggers, have to entertain, and shout loud, to build an audience and get their voice heard, whichever corner they find themselves in. No sh*t Sherlock!
- Not about technology
- Speakers’ Corner is not about technology, and neither is blogging. The digital technology that makes blogging possible (news feeds, software, servers etc) is no more interesting than their analogue counterparts: soapboxes and stepladders. Yes, digital soapbox technology is cheap and readily available but to my mind, blogging is not about technology. Well, duh!
One striking difference
As well as all these similarities, there is one striking difference between Speakers’ Corner and the Blogosphere. When you have had enough of the speakers ranting and raving, you can walk away, returning to the relative peace of Hyde Park.
However, on the Internet, bloggers are everywhere not just in the corner of the Internet park. This is partly due to the fact that there are lots more of them, more than 70 million bloggers on the internet by some counts. Consequently, the collective noise bloggers make can be deafening, but it is the unmistakable sound of free speech all over the Internet.
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Since this is my last post for 2007, happy holidays to all readers at nodalpoint. If you’ve read any of my posts here thanks for reading, you’ve been a wonderful audience and thanks again Greg for running the nodalpoint server. While I’m packing up my digital soapbox for the year, may I wish your speech in 2008, wether digital or verbal, to be of the free variety wherever possible. And, if you’ve ever seen a professional scientist talk at Speakers’ Corner, I’d love to hear about it.
[Speakers’ Corner Pictures above by Jim Callender and Cory Doctorow, part of the excellent pictures of Speakrs’ Cornr on Flickr].
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