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Rob Syme › Comments
Didn't know there was a movie of Slaughterhouse-Five. On ABC2 tonight. Any good I wonder?
Mike Chelen liked this
one of the better, more faithful movie adaptations of a book
- Mike Chelen
Double bill with Fahrenheit 451. I foresee a night on the sofa :-)
- Neil Saunders
Fantastic! Thanks for the heads-up.
- Rob Syme
I know "agility" favours working code over documentation, but you need enough documentation to at least run it...
slidedown?
- Rob Syme
:-) They are far from the worst offender. That said: the github page fails to mention (1) that output goes to STDOUT and (2) that libopen4-ruby is required.
- Neil Saunders
Rubber and EC2 presentation - http://zapnap.github.com/present...
Rob Syme, simone brunozzi and Neil Saunders liked this
Like the clever use of github - how is that done?
- Neil Saunders
Slidedown, I think: http://nakajima.github.com/slidedo... or http://github.com/nakajim...
- Rob Syme
Because the slides are on github, you can peek behind the curtain. http://github.com/zapnap...
- Rob Syme
BRAGOMAP – a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations - http://dx.doi.org/10...
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doi not found. This might work instead: http://precedings.nature.com/documen...
- Rob Syme
Watch this ratio (my estimate); 1:2 fungal sequencing projects in labs vs sequencing centers. #EMBO-CGME
Rob Syme liked this
By "in lab" sequencing projects, do you also mean labs doing the assembly/annotation in house using reads sequenced elswhere?
- Rob Syme
Sure - if that is fee for sequencing at commercial entity as well as university sequencing cores (or just illumina machine in someone's lab I guess). Really just a gut feeling estimate. Something it would be interesting to quantify as time goes on. We need both streams of data I think - my concern is the place that will check quality and aggregation of that data when it comes from so many sources becomes GenBank/EMBL?
- Jason Stajich
Okay, so maybe I'm just a little slow. I finally figured out how to tell what the 'new unread' replys in Wave are - green bars down the side
Press space to scroll through all unread blips
- Rob Syme
I think I missed some of the key "getting started" videos. Going hunt them down, as it's clear there are a few feature I'm not going to discover easily by just playing ...
- Andrew Perry
Rave: a Google Wave robot client framework for Ruby
http://github.com/diminis...
"super-alpha" and incomplete, but looks like fun. Jason also looks to have taken a break from developing until the protocol is more settled. http://jasonrush.com/blog...
- Rob Syme
Yet another high-throughput sequencing start-up: http://www.halcyonmolecular.com/
Khader Shameer, Sung W. Lim, Jason Chin and 6 other people liked this
Examples of others?
- Hope Leman
@Hope - Pacific Biosciences and Helicos maybe? Not sure on 454 and Illumina's origins.
- Paul J. Davis
Complete Genomics
- Eric Jain
NABsys
- Eric Jain
Hi, guys--thanks for the info!
- Hope Leman
Illumina has been around for a while and acquired Solexa, which was a next gen startup. 454 also been around a while and now part of Roche Applied Science. Pac Bio, Complete, there's one with nano in the name that I can't remember. Does Helicos still qualify as a startup (they are a public company)
- Deepak Singh
@Deepak, perhaps you're thinking of Oxford Nanopore Technologies? http://en.wikipedia.org/wiki...
- Rob Syme
Rob, I think that's it. Thanks
- Deepak Singh
Latex editor spell checkers *really* shouldn't ask me whether usepackage and documentclass are spelt correctly.
Egon Willighagen and Neil Saunders liked this
Try 'aspell -t' which does the best job I have seen...
- Egon Willighagen
Thanks Egon :)
- Rob Syme
+1 to aspell - magic!
- Allyson Lister
Hey Egon, I've got a spare wave invite if you're not already in.
- Rob Syme
@Rob, we have a wave collecting invites for Scientists in FriendFeed... let me know your wave account, and I'll add you...
- Egon Willighagen
Data Analysis Using R Functions As Objects - http://www.bioinformaticszen.com/r_progr...
Heikki Lehvaslaiho, Brad Chapman, Tom Walsh and 5 other people liked this
I want to like but is the URL broken?
- Neil Saunders
I wish there was a more emphatic 'like' option. Thanks Michael
- Rob Syme
I think the URL works? I did temporarily revert to a previous version of the site because pygmentize wasn't formatting the R syntax.
- Michael Barton
from iPod
@Rob Cheers!
- Michael Barton
works for me now, thanks
- Neil Saunders
New blog post: Abstracts wordle http://stajichlab.fungalgenomes.org/home...
Neil Saunders liked this
I look forward to seeing the signs
- Rob Syme
First challenge for the day: in *.sh, distinguishing $1 (the command line arg) from $1 (the awk field).
Try using $$1 in the awk part
- Rob Syme
If that doesn't work, you can always try passing it in via -v: awk -varg1="$1" 'script goes here'
- Rob Syme
Thanks, gave -v a go but something else not quite right - will try the $$.
- Neil Saunders
All fixed using -v. Onwards!
- Neil Saunders
Bookends for physics geeks: Bra-ket bookends http://www.evilmadscientist.com/article...
Deepak Singh liked this
I like the suggestion /* and */ for CS books. May I suggest 5' and 3' for the biologists?
- Rob Syme
Invite codes for Infochimps.org - http://mndoci.com/2009...
Mr. Gunn, Daniel Swan, Bill Anderson and 8 other people liked this
First 50 people to use the invite code in the blog post can sign up for an Infochimps account
- Deepak Singh
Done, thanx.
- Egon Willighagen
Me too, thanks Deepak
- Pierre Lindenbaum
Thanks.
- Jan Aerts
Thanks!
- Endre Sebestyen
and me, thanks
- Neil Saunders
Cool, many thanks!
- Konrad Förstner
Thanks Deepak!
- Rob Syme
thank you, deepak, :)
- chaz2b
Anytime ... thank Flip Kromer actually. I am just the conduit :)
- Deepak Singh
Thanks Deepak, having a look around right now... I never knew there was that much data about major league baseball available. It puts our obsession with cricket to shame ;)
- Daniel Swan
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum - http://www.biomedcentral.com/1471-21...
It seems that most methods for gene model validation complement each other nicely, so the more the merrier. That said, ms/ms is a cheap and easy first port of call.
- Rob Syme
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. - http://www.citeulike.org/user...
Rob Syme liked this
I don't have access to the library today, but surely this isn't the first filamentous fungi to be sequenced using a variety of technologies?
- Rob Syme
N.crassa has been sequenced many times over with many technologies. JGI with us has done N.tetrasperma, Mycosphaerella by several groups, Sordaria, and I am sure lots of others. But looks like this is 1st published...
- Jason Stajich
Ramaze - http://ramaze.net/
Web framework for Rubyists.
- Neil Saunders
The first time following the link, I get "RuntimeError at /" followed by a traceback. Works fine now, but it doesn't inspire confidence. At least the traceback had nice javascript folding sections...
- Rob Syme
:-) unlucky I guess, I didn't see that one
- Neil Saunders
ah, I see it now but only in chromium - firefox is fine.
- Neil Saunders
I saw it in ff (only once), I think it may just be intermittent.
- Rob Syme
You're right, chromium fine now :-) Well, don't be put off, it looks like a fun and useful framework.
- Neil Saunders
I'm just not yet convinced that I need an ORM that isn't either DataMapper or ActiveRecord. Same goes for templating and DB adapters.
- Rob Syme
I'm not convinced that I'm as productive as I could be using Rails. I like DM, don't mind AR, erb is fine, but just don't seem able to bring a Rails app to completion. So I'm investigating "more coding but less magic" options in the hope of increased agility.
- Neil Saunders
Getting closer to what I've been trying to achieve. aka, it's not as crappy as I expected :) http://twitpic.com/gxga9
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Marco Garcês, Mike Chelen, Pierre Lindenbaum and 4 other people liked this
So many bugs and so much still to code...
- Ricardo Vidal
If I understand correctly, this is a helper application for designing primers for creating BioBricks-based constructs ?
- Andrew Perry
Andrew, yes. A very shabby and beta-proof-of-concept-ish type of application. Packed with unafold, local blast, and various biobrick standard lookups and the obligatory sequence information. Web based, one search form, one page of results. Many many bugs :-)
- Ricardo Vidal
Starting to look pretty good!
- Mr. Gunn
Sounds cool. If the source is somewhere, I wouldn't mind having a play (might even be able to fix some of those bugs in the process - no promises :) )
- Andrew Perry
I'll do my best to put the source up at github or something. As soon as I have a chance to fully comprehend how ;-)
- Ricardo Vidal
I have some brief, terse "getting started" notes for git/github - http://neilfws.wikidot.com/categor...
- Neil Saunders
Thanks Neil! The notes are great! The other day I did download a video tutorial, watched it and quickly forgot it all :) So the notes will come in handy
- Ricardo Vidal
Just found the ShortRead package in R. Interesting...
Deepak Singh and Rob Syme liked this
You've prompted me to go back and look through the bioC packages. Great stuff there. It's like Christmas :)
- Rob Syme
@ericsuh Always an issue :-) It's near-impossible to get some people to try OpenOffice or Google Docs, never mind LaTeX
I was able to write my honours thesis in LaTeX by getting most of it done before the prof realised that it wasn't in word :)
- Rob Syme
daughter's uni is requiring LaTeX (Physics major)
- suelibrarian
All of my physics and engineering friends are quite comfortable with LaTeX, as are many structural biologists (who are often physicists by training or at heart). Most biologists are either unaware of it, or aware and terrified, for some reason.
- Neil Saunders
I'm sure this has come up before -- but I think a big part of the (rational, e.g. not the "but it looks weird" complaint) resistance to LaTeX is lack of a WYSIWYG "track changes" feature -- has anyone seen anything like that? A graphical front-end to a VCS for the TeX source maybe?
- Benjamin Tseng
I think LyX does version control.
- Neil Saunders
You're right! Amazing! http://www.lyx.org/news... -- alas, it won't be out until a future version :(
- Benjamin Tseng
Truffle hunting in Australia via @latimeshttp://travel.latimes.com/article...
Rob Syme liked this
Local truffles are super-hot at the moment. Went to a meal recently where every dish contained the stuff.
- Rob Syme
Lucky you!
- Jason Stajich
Wow. Just left my mouse pointer over an audio file icon in nautilus (ubuntu) and it started to play! When did they introduce that?
Egon Willighagen and Abhishek Tiwari liked this
Before 8.04, at least :)
- Rob Syme
Actually, at least 6.10, Edgy Eft
- Rob Syme
How about that :) Just one of those actions I've never done or read about.
- Neil Saunders
It's the little things like the autoplay preview make Ubuntu great (IMHO).
- Rob Syme
Never noticed that either... #ubuntu++ for audio 'preview'
- Egon Willighagen
bowline : Ruby/JS GUI and Binding framework for Titanium (GitHub) - http://github.com/maccman...
Neil Saunders and Rob Syme liked this
Looks like Adobe Air in spirit, with code written in Ruby/JS/HTML to generate desktop apps.
- Andrew Perry
Anyone able to get the Titanium SDK installed on linux?
- Rob Syme
I was running version 0.5.2 on Ubuntu 9.04 two weeks ago. I seemed to work, although I didn't test it heavily. No special trick - I selected the option in the GUI to install in my home directory.
- Andrew Perry
... and just now I gave it another run. On startup it asked if I wanted to install the new mobile SDK (which I do !). It did that, but now it crashes on the on the "Community" view. Looks like I'll be reinstalling a fresh copy from scratch new time I want to play with it.
- Andrew Perry
Well you're one step ahead of me, my SDK install can't find modules that exist in the locations that it is looking for them. Not looking hard enough, I say. Something for tomorrow.
- Rob Syme
Yandell Lab - Software - MAKER - http://www.yandell-lab.org/softwar...
Have you had a chance to kick the tyres at all? We've just got 7 fresh fungal genomes (38-50Mbp) that need to be annotated. Looks promising...
- Rob Syme
Kicking as we speak. Need to be able to upload parameter files for different ab initio progs and it expects ESTs, but you can definitely give it a try. The results I've seen in other spp are quite promising. Be curious which 7 fungal genomes you've got going on when it can be public knowledge...
- Jason Stajich
All plant pathogens. Two Stagonospora nodorum strains (not the sn15 strain already published) with different toxin profiles and some others that I have to check with the prof before talking about publicly.
- Rob Syme
My prof (you probably met him at Asilomar - Richard Oliver ) is being coy and will only let me say that we're doing the assembly/annotation of various Dothideomycetes. I think this sort of secrecy is a bit over the top, but I have to live with the rules.
- Rob Syme
no worries. good luck and all!
- Jason Stajich
Maker is taught as part of the GMOD class. let me know how it goes
- Ian Holmes
The Pushbutton Web Now In Google Reader - http://www.lifehacker.com.au/2009...
PubSubHubbub. Great tech, great name.
- Rob Syme
RT @leahdemilio RT @jasonstaples http://twitpic.com/cwnol - with due respect to @leahdemilio, this is the best essay ever written.
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Andrew Spong, Shirley Wu and Neil Saunders liked this
What it lacks in accuracy, it makes up in melodrama. Love it. When will those "scientists" learn.
- Rob Syme
ScienceDirect - Vaccine : Composition of the ANTIGENome of Helicobacter pylori defined by human serum antibodies - http://www.sciencedirect.com/science...
Thanks Rob .. not exactly sure why that link got mangled by Diigo ...
- Andrew Perry
The Trouble with the Segway - http://paulgraham.com/segway...
Michael Kuhn and Ola liked this
Well written, as always
- Deepak Singh
Time and a place. I work in a science museum for fun on the weekends, and they provide a great conversational... what's the word.. link... to talking about gyroscopes, coriolis effect etc...
- Rob Syme
Shared Twitter Updates Done Right: The Case of NPRTechTeam - http://dltj.org/article...
[caption id="attachment_1198" align="alignright" width="437" caption="Image capture of NPR Tech Team Twitter account."][/caption]All day today, the staff at NPR's Digital Media team have been preparing to launch a new version of their website, and we've be
- Peter Murray
that URL is a gzip file?
- Neil Saunders
Looks to me like an incomplete download file from Firefox. <edit> fixed now
- Rob Syme
OK, looks like the blog author has fixed it now. All post title hyperlinks were behaving as file downloads, for some reason.
- Neil Saunders
Yeah, I had turned on an option in the WordPress caching plugin to gzip the files. The setting came with a warning that said "this option may not work for some web hosting settings". I unset the option, so things should be back to normal now. Sorry 'bout that.
- Peter Murray
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