Sign in or Create an account
Andrew Perry's Comments and Likes - View full feed
del.icio.us
Ntino bookmarked a page on del.icio.us
3 hours ago - Link
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
Blog
June 20 at 10:20 am - Link
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
Don't forget that NCBI has quite a reasonable API: eutils (http://www.ncbi.nlm.nih.gov/en...). It gets a lot of use in programming libraries (e.g. Bioperl) but for some reason, doesn't get much publicity or usage in web applications, mashups etc. - Neil Saunders
@Duncan I wondered if there is a recent paper using Biodas ? On my side, I've been trying to use the one from UCSC/Genome-Browser but the results where unuseable (not enough verbose, information missing, etc...) and I then went back to their anonymous mysql server. - Pierre
@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
Blog
yesterday at 6:53 pm - Link
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
Twitter
Neil Saunders posted a message on Twitter
Blog
yesterday at 5:19 pm - Link
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
Flickr
Neil Saunders published photos on Flickr
Sunset I
Sunset II
Sunset III
22 hours ago - Link
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
Twitter
Brian Daniel Eisenberg posted a message on Twitter
Google Reader
Neil Saunders shared an item on Google Reader
yesterday at 6:24 pm - Link
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
Twitter
Neil Saunders posted a message on Twitter
Google Reader
Heather Piwowar shared an item on Google Reader
yesterday at 7:55 am - Link
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
Google Reader
Cameron Neylon shared an item on Google Reader
June 25 at 5:29 am - Link
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
The business model is sort of unclear as it's largely an academic project with industrial partners. Taverna is there for workflow enactment really, as well as workflow creation, although we're waiting on Taverna 2 for all the features we need. The web services layer is actually handled by something called DynaSOAR for dynamic webservice deployment. Currently we're in the process of trying to educate our neuro community who are happy writing Matlab/C++/R to produce webservices from their code. Fun! - Daniel Swan
URLS : http://www.neresc.ac.uk/projec... and http://www.carmen.org.uk/ Try and spot Frank and myself in the awful photo.. - Daniel Swan
It was cool how popular the talk was, esp in the QA and post talk discussion - Deepak
we will give you a clue - Dan and I are both standing beside each other - Frank
Is one of you the fellow who is sticking his neck out at the back? - 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
FriendFeed
CARMEN: A Scalable Science Cloud
June 25 at 2:31 am - Link
see also http://friendfeed.com/e/3ad1d6... for where the comment stream seemed to end up :) - Cameron Neylon
Twitter
Neil Saunders posted a message on Twitter
Twitter
Deepak posted a message on Twitter
YouTube
Mr. Gunn favorited a video on YouTube
MUTO a wall-painted animation by BLU
July 3 at 1:41 pm - Link
This one of the coolest things I've seen in a while. - Ricardo Vidal
Google Reader
Deepak shared an item on Google Reader
July 3 at 11:03 am - Link
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
Wasn't Nvidia the company that bought the remains of 3dfx after the voodoo5 debacle ? - Daniel Jurczak
I believe you're right. - Mr. Gunn
I really hope they survive, in the interests of competition and because ati linux drivers generally suck. - Andrew Perry via fftogo
and then some, despite getting them in a room and making them listen to complaints and dire threats for a couple of hours - Deepak
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
FriendFeed
July 3 at 11:34 am - Link
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
it is crawling flash already? - PauloNuin
Looks like it is (e.g. http://google.com/search?q=fil...) though I don't think this can explain the mysterious YouTube videos. - Eric Jain
it might, if part of the movie coding has segments of the sequence in it. - PauloNuin
Maybe it assumes that if someone just mashed the keyboard randomly and typed some very long strings, they are bored, so why not give them some videos to watch ? - Andrew Perry
I checked, any sequence of random chars, 130+ renders that list of videos. The same videos :) - Ricardo Vidal
Hidden DNA sequences in a Snoop Dogg video? We may be on to something BIG here :-) But note that any term that is too long appears to result in the same list of videos. Also, while Google may now be extracting text from Flash content, I don't think they process Flash video. - 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
FriendFeed
Stefan Hayden posted a link
July 2 at 5:46 pm - Link
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
85%...and the funny thing is that I waffled on 2 of the 3 that I got wrong. Darn! - Dawn M. Armfield
100%, so I definitely hit "Like" - RAPatton
70% for me...jeez I suck...granted I moved to the States when I was 11; but still I am American....it's how I identify myself and believe it - Snay Trivedi
95%. I misread one of the questions. *sigh* - Mark Trapp
80% and I'm not a citizen of the US. - Morton Fox
0%. I misread all of the questions - Dan Kaplan
Q: What did Susan B. Anthony do? A: Hid John Wilkes Booth, the assassin of Abraham Lincoln. LOL oh *that's* why they put her on a coin! - Karim
At least I can say I was good in math and science. This was embarassing! - kbourke
50% for me. I'm from Portugal :P - Ricardo Vidal
80% I second-guessed myself out of two of them. I hate it when I do that. - NIcholas Sanders
Yes, I just did it for real :) - Jonathon
55%. Spanish here. - PauloNuin
60%. i am not Spanish, I am not Portuguese; i was born in NJ - edythe
95%. I missed the one about the number of amendments. - Chris Johnson
95% Missed first line of the Constitution... D'oh! - Sprague D
Did better than I though I would:70% - Grant Bierman
@Jonathon, BTW, congrats! - Sprague D
Only 50%. I'm a legal alien - Les
@ Sprague - Thanks - Jonathon
Missed year Constitution was written. Hey, at least I would get in! - Candace Holly
Nailed it: 100% - Glen Campbell
@edythe I'm from NJ too! I'm in hackensack now - Stefan Hayden
75%... but I only missed the hard ones ;) - Russell Holliman
my wife just got 85% - Stefan Hayden
70% and I'm not even American! Damn that western influence! - Rahul Das
35% .. seemed more like a high school history test than anything to do with citizenship .. and since I didn't take the class, (in the US, at least) I failed ... - Andrew Perry
80% I always think the constitution was written in 1776, I should know better by now. - xero
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
Tumblr
Ricardo Vidal posted an item on Tumblr
July 2 at 6:41 pm - Link
Like ... but I haven't become jaded or nuffin', I promise. - Andrew Perry
FriendFeed
July 2 at 10:13 am - Link
"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
Google Reader
Neil Saunders shared an item on Google Reader
July 2 at 7:14 pm - Link
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
del.icio.us
Rebecca Holz bookmarked a page on del.icio.us
July 2 at 7:56 pm - Link
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
FriendFeed
Mr. Gunn posted a link
Anyone know details on Church's Polonator Next-Gen Sequencer? - SEQanswers
July 2 at 12:15 pm - via Bookmarklet - Link
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
1 2 3 4 5 6 7 8 9 Older »
Other ways to read this feed: Feed Facebook