nodalpoint.org - Information management - Comments

great tip

Neil — Mon, 24 Jul 2006 08:00:19 -0400

That's a great tip. Are there any neat web tricks that alf doesn't know ;)

mozex

alf — Mon, 24 Jul 2006 05:25:24 -0400

Mozex (Firefox extension) is worth a mention here too.

Marking nar tests

Neil — Sat, 22 Jul 2006 21:42:38 -0400

I thought about that (a column with a tick or something). I think it's easier if people just look for the "none yet" in the comments column. Also, there's no reason not to have >1 comment per service. Wiki editing is a freeform process - I think this troubles people who prefer a clean forms interface to a database, but I'd encourage people to give it a try. You need to get into the "wiki mindset" :)

wiki format is tricky

Neil — Sat, 22 Jul 2006 21:01:46 -0400

I just knew that someone would have this criticism :). You're quite right though - the people in my group have the same complaint about the lab wiki. I know that Twiki has a table editor plugin which provides a form interface for table editing - does dokuwiki have similar?

I did consider a forms/database solution, but wasn't sure if it was worth the time. If people are keen to contribute to this, leave comments and I'll cook something up. The good think about the wiki though, is that it's already setup for Nodal users.

In the meantime, you can always copy the wiki-formatted text to an editor and search for what you want, then paste back, I guess.

[s, |s and URLs

Stewb — Sat, 22 Jul 2006 18:42:29 -0400

You probably don't want to hear this after all that copy n' paste but the format on the wiki is a bit tricky: it's hard to find the program that you want to add a note to. :)

The wiki is a good starting

Greg — Sat, 22 Jul 2006 14:43:43 -0400

The wiki is a good starting point, but some kind of database listing these services would be better. Amazingly these resources now have a term: Resourseome. This comes from a recent perspective in PLOS compbio, Time to Organize the Bioinformatics Resourceome.

The article mentions the Bioinformatics Links Directory, which in fact has all the NAR web server issue links with categories. Of course there is no machine readable representation of the data to help avoid the copy-and-paste problem. Sigh.

Some more detail on the reasoning behind using a 'links directory' is available here. There is only one other effort I know of that catalogues biological resources: BiowareDB. I have previously toyed with using this kind of thing as a starting point for RDF descriptions of biological resources. Read more about that here.

As an aside, I find the use of "web server" annoying, it should be "web services". Maybe I'm just pedantic.

suggestion for NAR test

PedroBeltrao — Sat, 22 Jul 2006 11:13:03 -0400

Maybe we could mark the ones that we are testing so that we don't re-test stuff.

What need is there?

Duncan — Tue, 30 May 2006 03:14:37 -0400

The word GRID reminds me of the word GENE. It is either used in a vague and ambiguous way or it has multiple but precise definitions that are completely different. Despite this I think both words are useful and will continue to play an important role in the life sciences :)

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.

If you consider any kind of

ejain — Sat, 27 May 2006 09:08:26 -0400

If you consider any kind of distributed computing or clustering to be grid computing, then I guess you can indeed say that grid computing "plays an important role in the life sciences". Of course, if that's all it is, what need is there for the term "grid"? Wasn't the original idea of the grid concept to create a standard mechanism (not tied to any specific application) for consuming (or even sharing) resources such as processing power and disk space, similar to the way the power grid works?

Grids, Google etc.

Neil — Sat, 27 May 2006 01:52:49 -0400

It's been interesting to watch the minor 'Google backlash' of recent months. This seems to happen to all companies that start small, promote themselves as more ethical than others then achieve success. I remember a similar media reaction to the Body Shop back in the 80s. Google's foray into the Chinese market seems to have caused a lot of this reaction.

I've always had my doubts about grid computing and bioinformatics. As the original post points out, there's always been a lot of esoteric debate about "what is a grid" rather than "what can I do with one". In their cluster computing presentations, Bioteam, for whom I have a lot of time, have been quite dismissive of the grid concept in the past, simply because noone can quite define what it is.

Keeping it simple, let's say a cluster is a pile of machines in one physical location, tightly-coupled through a network switch and dedicated to a few specific tasks. A grid is a bunch of machines in numerous locations (perhaps scattered worldwide) that in theory can cooperate on any task with appropriate tools and services to couple them together. In the former case your tool is very clearly defined, in the second it is not. Which is why currently, local HPC resources for typical applications such as BLAST have the advantage. I simply can't imagine posting off my sequences to a Google-like service and getting back results in any reasonable time with the current state of grids.

Google @ help

Animesh — Fri, 26 May 2006 09:12:50 -0400

Guys I read about GDisk thing [ http://blogs.zdnet.com/Google/?p=121 ] sometime back and then I also heard about google providing the ssh access to their supercomputer[ http://www.vmunix.com/mark/blog/archives/2004/07/27/what-is-google-build... ]. It may all be rumor but if it is going to be true, then I feel this will really be like a Venter to NIH thing looking at the above post!

______________________"The Answer Lies in Genome"______________________
http://fuzzylife.org/

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)