nodalpoint.org - News - Comments

Looks great

Neil — Thu, 05 Jun 2008 23:07:34 -0400

It looks very nice indeed. I'll be interested to see how the categoriser handles "bioinformatics" :)

clustering news as microarrays

dalloliogm — Thu, 05 Jun 2008 04:57:29 -0400

I'm a microarray analyst, so I used the same techniques I use to cluster genes, but this time to cluster news!

So cool!! :)
Congratulations. What kind of approach have you used to cluster those news?

The Broken Double Helix

Duncan — Mon, 29 Oct 2007 14:02:32 -0400

There is a good overview of the media-furore surrounding Jim's recent trip to the UK over at the molecular systems biology blog...

Another boo-boo

chris — Tue, 23 Oct 2007 11:09:35 -0400

Yes - he's rather famous for these. When the Jimome was announced at the Biology of Genomes at CSHL in May, he gave an impromptu little homily before the keynote speeches. In his usual rambling style, he trotted out a number of comments which made his audience (or at least me) very uncomfortable - not least in reference to his son Rufus, who has a rather rare form of depressive (?) schizophrenia.
I wonder if his suspension by the CSHL Board is a prelude to his stepping down, or a slap on the wrist?
I will point out though that CSHL was a backwater when Watson took over; he attracted funding and donations and turned the place around. He still has enormous pull with private donors (eg the construction currently under way at a cost of ~$100 million).

out of his depth

seidel — Mon, 22 Oct 2007 12:45:56 -0400

I saw him speak in Berkeley where he made some of the remarks listed above, including an admonition not to hire fat people or accept them as graduate students because "...they are lazy, and too happy to work hard." The article in the independent gets it right when it describes him as out of his depth on the issue. Scientists can point to data that might be socially uncomfortable or non-PC and that's one thing, but he gets it wrong and throws in personal anecdotes as evidence - which throws all objectivity out the window, and simply paints him as a bigot. Aside from the content, the fact that he can't tell the trajectory of his own remarks disturbs me. I feel bad for Cold Spring Harbor. I hope they don't suffer any fallout (i.e. funding backlash).

blog comments

Neil — Wed, 02 Aug 2006 21:37:28 -0400

Your comment is posted now. The blog requires that people have one previously approved comment before they appear automatically. Anyways, I won't be there much longer. My new blog home is here.

Neat-oh Neil: your blog

Coalescent — Wed, 02 Aug 2006 09:26:38 -0400

Very cool.

Neil: your blog appears to have a penchant for eating comments :P I was going to mention on your post about getting amateurs involved that the main problem is indeed a lack of awareness of what constitutes an interesting bioinformatics question. One very useful resource would be if someone would provide a list of questions that interest them but that they don't have time to research, or something like that.

Par for the course?

Stewb — Thu, 29 Jun 2006 19:31:08 -0400

I think that it's par for the course - I hosted Tangled Bank a while back and the submissions only started coming in late the night before the edition was supposed to go up. Was a bit stressful.

Er, which is why I've left it to the last moment to submit anything myself... sorry. :)

Have you considered emailing

Coalescent — Thu, 29 Jun 2006 16:54:00 -0400

Have you considered emailing people like Razib at GNXP? I bet they'd be willing to give some free publicity for a good cause like this one.

bio::blogs links needed

PedroBeltrao — Thu, 29 Jun 2006 05:57:14 -0400

Yes, like Neil mentioned the deadline for the the first issue of Bio::Blogs is almost up (2 days) and there was only one blog entry submitted so far. So please, open a mail window type in bioblogs(at)gmail(dot)com and paste a link to a blog entry that you like :).

Thank you Neil, and well

Greg — Mon, 29 May 2006 07:48:13 -0400

Thank you Neil, and well said by the way. I'm not sure if it is the promise of lucrative jobs or lack of jobs (IT jobs are becoming a commodity ?) in IT that is driving people to search for information on computational biology. My current take on the lucrative jobs aspect is that from the outside looking in computational biology superficially has all the attributes of the next big ICT boom: large amounts of data, the need for people with IT/CS skills, novel method development, application of statistics, potential to lead to new drug development and medical breakthroughs etc. This leads people to believe that it will be the a ticket to fame fortune and glory.

Of we on the inside know that one point of failure in this little fantasy is lack of standards for biological data. My argument is that the incentives are just not there for biologists to work together on formal standards for the life sciences (it is all about discovery). Industry is also not that focused because the market is just not big enough. While microarrays are good business, mobile phones eclipse them by many orders of magnitudes. I don't doubt that the situation will get better, just not as quickly as you would imagine. What it boils down to is that lack of standards makes it hard to commoditize the knowledge necessary to working computational biology. Hence producing humans with standard compbio knowledge to fit into standard jobs is not possible.

But it goes both ways.

People on the inside looking out haven't yet appreciated the need to *pay* good money for people with IT/CS skills to make their computational pipelines more robust/extensible. It is publish or perish all the way, not re-factor and thrive.

IT market

Neil — Sat, 20 May 2006 06:39:53 -0400

My naive assumption would be that you're seeing IT graduates in search of employment. India and SE Asia have seen a huge increase in IT investment and education in recent years and many graduates are under the impression that biology is a source of lucrative jobs. Recall when the human genome project neared completion - there was much hype about disease gene discovery, cross-fertilisation of the IT and pharmaceutical sectors, even dire predictions that the amount of data would be too great for current hardware.

As it turns out, identifying genes is just the first tiny step in any kind of biomedical advance and whilst we can certainly handle the raw data, extracting what we want from it is immensely painful due to inadequate data standards and integration. And now I hand over to Greg :)

If you look at google

maximilianh — Sat, 20 May 2006 05:47:51 -0400

If you look at google trends, almost all queries for "bioinformatics" come from India! The list is INDIA (5 times more than number two), Singapore, Korea, Malaysia, then, heck, Ireland! United States are ranked 8th on this list!
"Football" immeditely gives United Kingdom, Biology quickly UK/US, but "molecular biology" again gives India, Korea etc. Any ideas? Is India so much stronger in "molecular biology" and "bioinformatics" than these other countries or why do people type in these keywords into google, if not?

GTrends

PedroBeltrao — Fri, 12 May 2006 05:01:54 -0400

The time we can waste on Google trends :). I gave it a go as well but it is a pity that they don't have an option to restrict to the search volume of Google Scholar. Maybe there are not enough searches there to make these trends. This way the trends don't really represent the scientific view of these terms. We don't really see in GTrends the buzzword chasing phenomena when you try to compare the different keywords (like genomics, proteomics, systems biology, synthetic biology).
Go give Co-Op a try, it is a bit obscure but there might be something there of use. You can tag online content and make your meta-data available for subscription to anyone (social search). I am not sure that you can access the meta-data trough the normal Google web API but if it is possible than there might be some interesting uses for it. If we can't use the API then it will be again like Google Base (only potentially useful)

More avian flu resources, and a note on the Connotea resources

Declan Butler — Sat, 05 Nov 2005 05:12:05 -0500

Hi, I'm the keeper of the avian flu firehose on Connotea -- its meant to be used via its RSS feed as a sort of daily newswire. At Nature we also have an updated focus section on avian flu. I've also made some rough Google Earth maps of avian flu outbreaks, that will be refined when I get a moment.

Declan