Ate some last week in the International District. Yummmmmmm - Deepak

Not to be confused with the Dim sim (http://en.wikipedia.org/wiki/D...) ... I really love the South Melbourne Market Dim sims (http://en.wikipedia.org/wiki/S...). - Andrew Perry

Hi Deepak, nice post, when it comes to a more distributed and less centralised annotations of genomic databases, you have to mention DAS / BioDAS http://www.biomedcentral.com/1... - Duncan Hull

Duncan, good point. At some point, I need to compile all the resources and figure out which ones are actually any use. Any other recommendations? - Deepak

@Pierre this is the most recent BioDAS paper I know of http://www.biomedcentral.com/1... - Duncan Hull

I like your comparison with Wikipedia. I guess Wikipedia works because it scales well by distributing curation of information across many users. Would be nice if NCBI/EBI could do this. My impression though is that many scientists would initially look down their nose at this, and would need a good use case to demonstrate the potential. - Michael Barton

@Duncan thanks - Pierre

I have decided I will switch to one of those two when I finish the project I am working on right now, probably python. - Pedro Beltrao

I do envy BioPerls breadth and maturity compared with BioPython .. but not enough to tempt me to switch back to Perl after my early beginnings with that language. I've looked into ways to call Perl functions from Python, but there doesn't seem to be anything that works well and is maintained. - Andrew Perry

BioPerl was essentially my reason for starting out in Perl, about 8 years back. Perl CGI also used to be the way to go for web apps, but the new web frameworks are much more appealing. Increasingly too, I find Perl unwieldy, slow and well...ugly. It's much nicer to write "l = a.length" than to loop through some horrifically complex data structure just to get to a variable. Admittedly, one of my weaknesses is creating horrifically complex data structures :) - Neil Saunders

I suspect it's just a case of English-as-a-second language, but the term "extremely under-wrapped proteins" in the abstract seemed a little strange ... I guess they mean unfolded or disordered ? (I'm basically monolingual myself, so I'm sure I'd do far worse if I ever tried to write a paper in say, French, German or Polish). - Andrew Perry

powerlines is on the desktop :) - Andrew Perry

Cool! That's our local rail line, about 5 m outside the house. You get used to it. - Neil Saunders

While they are at it, just add bike directions too :) - Ricardo Vidal

The article seems to suggest that 'safe areas' may be used to help determine good walking routes ... I wonder if this is a mashup of those 'crime maps' under the hood ? - Andrew Perry

Some very good points in there: "Whilst there are clear benefits to be achieved from providing teachers and students with the opportunity to share ideas in the context of stimulus artefacts, many hold reservations about 'giving away' their intellectual property." [...] "Their main concern is to access reliable, relevant content and information, but the ability to form connections between these resources is one way of adding value to the collection." - Thomas Brox Røst

many people concerned about "giving away their IP" need to have a talk with a VC. Was it Kawasaki that said something like "Nothing is novel anymore, and if someone has never thought of your idea before, it's probably because it's a dumb idea."? - Mr. Gunn

I've also had some contact with people preparing a report on Web2 and science so I need to talk to them and then point them here :) - Cameron Neylon

Paul Watson makes the case for making data available in a useful form - with proper metadata and in proper formats - Cameron Neylon

I saw the talk at the Seattle Scalability conference. Some of the ideas/concepts underlying CARMEN are pretty need, and their use of a workflow engine, Taverna, as the web services layer is cool too. I do think they could do with a more distributed approach and the business model is unclear at this time - Deepak

no we're at the front right... slacker types in jeans ;) - Daniel Swan

I'm hopefully trying to get some Taverna goodness into some data analysis tools we are developing at RAL and the guys at Southampton are planning to build in Taverna via MyExperiment into the LaBLog as the main source of automation over summer - Cameron Neylon

Lots of great ideas here ... hope I get to use it in some form one day. In addition to workflows, I think the fine-grained permissions for data release is a simple but really important feature to encourage adoption. I also like the idea of wrapping up web services as deployable VMs to cater for heavily customized setups (eg more support than just WAR files). - Andrew Perry

see also http://friendfeed.com/e/3ad1d6... for where the comment stream seemed to end up :) - Cameron Neylon

This one of the coolest things I've seen in a while. - Ricardo Vidal

Didn't quite realize that things were bad - Deepak

I've still got an old 3dfx card in my old PC, hope they don't suffer the same fate - Mr. Gunn

I'm always amazed at the level of Linux support for nvidia (everything works) versus ati (very little works). Unfortunately we are stuck with ati at work. They have at least made a lot more effort in the past year, but still very far from nvidia standards. - Neil Saunders

About 4 years ago, I had to make a rather tough decision, at least on the face of it. A decision to formally say that we would not support ATI on Linux (and even on windows their OpenGL support was not as good as NVidia's). In the end, it was an easy one. Better to have a few people grumble, than have them run something substandard - Deepak

hmmm. was this $200 million write-off due to die issues, or $125 million revenue miss? either way some people are thinking "bargain" while other people are drafting obits. - Karim

It seems that 130+ bases/chars and it returns this weird list of videos. Anything less, it doesn't return anything. - Ricardo Vidal

The maximum word length in Google appears to be 128 bytes (looks like they increased it after the llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogoch debacle). But I do wonder why there is this list of 10 videos that is returned for all queries that consist of words that are too long! - Eric Jain

Talk about an easter egg. Question is how did you chance upon this wonderful discovery? What sequence did you put into the GOOG? - Deepak

It's a sequence from a Part from the partsregistry.org and we wanted to see if Google was indexing the sequences. Seems it isn't and what happens is the weird videos :) - Ricardo Vidal

Imagine if Google did index sequences. Proteomics researchers could abandon Mascot and identify their peptides via Google :) - Neil Saunders

75% for me... kinda sad. I was close on most that I missed. :( - Stefan Hayden

70% for me, I second guessed myself on a bunch - Adrienne Van Houten

100%. Okay, so I'm a history nerd. - R. Francis Smith

95%... for some reason, I thought that the President Pro Tempore of the Senate was next in line of succession. - Roger Benningfield

65% which isn't too bad considering I'm not a citizen and didn't do any preparation. - Fraser Smith

Like ... but I haven't become jaded or nuffin', I promise. - Andrew Perry

"incompleteness of evidence is not merely a failure to satisfy a few highly critical readers. It not infrequently makes the data that are presented of little or no value" -- and yet, whenever I say that there is no longer any excuse for "data not shown" in a modern scientific paper, there's sure to be someone around who gets angry or dismissive. - Bill Hooker

I don't like "data not shown" either. There's no need for it on the web as there may have been in print. Personal communications, now, are a different story. - Mr. Gunn

I don't feel that publishers are doing much to encourage (or allow) large amounts of supplementary data to be lodged ... it seems to come from two ends; authors use it as a way of avoiding proper scrutiny and publishers haven't helped by not stepping up to the plate and requiring submission and archiving of more data. Or if they do, they subsequently manage to lose it anyway (sounds like Bill has lots of examples of this). In a hyperlinked world where storage space is cheap, the excuses are dwindling ... - Andrew Perry

Andrew, we do (at Nature journals). We encourage SI, we require deposition of data into public dbase where there is one, and we encourage more details of methods etc to be uploaded into Nature Protocols when the N journal paper is published. Feel free to contact me for more details at Nature (m.clarke@nature.com). - Maxine

We could start by not growing rice and cotton anymore. Doubt that would be popular though. - Neil Saunders

I hear asparagus grows really well under the future conditions we expect to find in that region ... :) - Andrew Perry

Asparagus! Brilliant. Which reminds me of my fun genomics project... - Neil Saunders

Nice find :) - Ricardo Vidal

There is also a more comprehensive list of WSDL files at http://seekda.com/search?q=bio... and also http://www.mygrid.org.uk/wiki/... both of which include the DDBJ ones listed above, and many more in bioinformatics... - Duncan Hull

Kevin McCarthy shares some status updates on der Polonator. Performance data expected ~August. - Mr. Gunn via Bookmarklet

Still getting my head around all these new generation high-throughput sequencing technologies, but reading bits like this are helping me catch up. - Andrew Perry