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Ruby for Bioinformatics: PauloNuin posted a message

“Looking to setup RoR in our server. What configuration, modules, plugins recommended?”

Friday at 5:17 pm - Link

Deepak liked this

A common setup would be Apache 2.2 with Mongrel. Passenger (mod_rails) is an attractive alternative, especially for lower traffic low maintenance web sites. Capistrano for deployment is highly recommended. - Martin Fenner

Thanks, I will try that. Always good to start with the ideal configuration ... - PauloNuin

Nginx with Mongrel is also a good alternative. Definitely one of the more popular ones in the RoR userbase on EC2. But I've heard good things about Passenger too. - Deepak

The "classic" setup with Apache 2.2 and Mongrel is described here: http://blog.codahale.com/2006/... - Martin Fenner

Definitely give mod_rails a go if you're starting up: works effortlessly, and is ready for production use. - Matt Wood

The Life Scientists: Martin Fenner posted a message

“Would there be interest in developing a set of ubiquity science commands, hosted on Github or Google Code? There are a few commands out already, but it would be nice to have them coordinated.”

8 hours ago - Link

Jason Winget, hubfeed, Matt Wood, Pierre and 5 other people liked this

Thomas Lemberger started a Google Code project here: http://code.google.com/p/tl-ub... and I've just joined since I had the same feeling that we could coordinate our efforts. - Pawel Szczesny

Such a distribution would benefit from using a single license... did you have one particular license in mind? - Egon Willighagen

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Shouldn't something like this just use a BSD or MIT license? - Deepak

I'd be fine with that... - Egon Willighagen

I also joined the Google Code project by Thomas Lemberger. The project uses GPLv3. - Martin Fenner

Can you add me there Pawel? - PauloNuin

Me too, please. - Egon Willighagen

Paulo, Egon, you're in. - Pawel Szczesny

let us know what license would be the most appropriate... I picked GPLv3 close to randomly! - Thomas Lemberger

Should I include my 'add-doi' too? It works for blogger.com, but reported not the work on NN, because they do not use <a@href>... rich text type detection could be hacked in later... or should I set up a blogger/ folder? - Egon Willighagen

I modified Egon's add-doi to use textile formatting (e.g. for Nature Network). Saved as textilize-doi in a separate textile folder. - Martin Fenner

Martin, now if we only could integrate both scripts and make it aware of the target platform... btw, you did not modify my script, but payed close attention to what I did :) otherwise, you would have to list me as author for your script too... - Egon Willighagen

PauloNuin posted a message on Twitter

“2nd try:nuin Looking to setup RoR in our server. What configuration, modules, plugins recommended?”

22 hours ago - Link

What web server are you planning to use? - Deepak

No expert here, but some essentials would include rubygems, capistrano and mysql. You should also decide what http server you're using. NGinx seems to be pretty popular these days. - Deepak

I am setting up for an internal server of ours, running Solaris. I have gems and mysql but don't know if I should install mongrel or any other stuff. - PauloNuin

Using Apache or Nginx to run a Mongrel cluster is a fairly typical RoR setup from my experiece. Post the question to the Ruby for Bioinformatics page. Matt might pick it up there - Deepak

Check this out. It's for a mac, but fairly typical install (except he uses Postgres http://www.sysadminschronicles... - Deepak

Daniel Jurczak posted a message on Twitter

“I don't know what the hell happened, but Austria just won against France 3:1. Strange things are happening today..”

yesterday at 1:48 pm - Link

strange, but good things - PauloNuin

The Life Scientists: Maxine posted a link

Evolutionists Flock To Darwin-Shaped Wall Stain | The Onion - America's Finest News Source

yesterday at 2:03 pm - via Bookmarklet - Link

Onion article, flagged by OWL (Dave Lull). - Maxine via Bookmarklet

Posted twice yesterday and today http://friendfeed.com/search?q... - PauloNuin

Thanks Paulo...once things drop off the first page of FF, it is too easy to miss them. I expect they are working on it. - Maxine

PauloNuin posted a message on Twitter

“One year wedding anniversary came and is going, calm, relaxing ...”

Friday at 7:06 pm - Link

Cameron Neylon, Pawel Szczesny and Sally Church liked this

wait till you get to 10. Congrats - Deepak

Thanks! In fact is very close to 10, this is just the date of the official ceremony, not less important whatsoever. - PauloNuin

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nope .. never - Deepak

Congratulations to you and your spouse! - Chris Lasher

Congrats! - Sally Church

Thanks a lot! I hope I have 100 more of these anniversaries. - PauloNuin

Congrats! My one week anniversary is tomorrow! Any required protocol? :P - Todd Harris

Congrats! - Matt Wood

congratz :) - Jason Tsai

Michael Nielsen posted a message

“At Inbox Zero for the first time in several months!”

Friday at 2:00 pm - Link

Andrew Perry, Christopher Granade and Sally Church liked this

Nice. Me: 1037. - Dave Bacon

I'm at 916 for gmail and <gulp> 4219 for apple mail... is it time for an intervention? one could argue, though, do we really need folders and archiving when we have search? - Shirley Wu

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I hate you - Deepak

who do you hate? the 0 or the 4000? - PauloNuin

Go you! I haven't managed that in months. - Evangeline

the 0. The 4000 I can relate to quite well - Deepak

What's the emoticon for poking your tongue out at someone? - Michael Nielsen

Shirley - Sounds like you need to declare email bankruptcy: http://en.wikipedia.org/wiki/E... - Michael Nielsen

It's :P , Michael. - Dorothea Salo

Well, :P Deepak! :-) Thankyou Dorothea. - Michael Nielsen

I have a stubborn 4 that have sat there for months. Really need to rethink my GMail; huge number of filters and labels which I'm sure are unnecessary. Read some GTD article telling me I only need 3. - Neil Saunders

You mean to tell me there are people who actually delete email? I don't even know where the delete button is in gmail. I'm sure there's 10K+ in there. Search hasn't failed me yet. - Mr. Gunn

Feels good doesn't it :) - Daniel Swan

Mr Gunn - I don't delete it, I simply archive it. But there's nothing left which is actionable :-) - Michael Nielsen

Daniel - You bet! - Michael Nielsen

Cool. Wish I was you. - Andrew Perry

:p to you too Dr. Nielsen. - Deepak

Sally Church posted a message

“You know, McCain has been in Washington some 25 years... if he was gonna reform the place wouldn't he have done it by now? Just wondering.”

Friday at 12:14 pm - Link

Lindsey Smith, Steve Isaacs, Yolanda and AlexScoble(Robert'sBro) liked this

It just crossed my mind he's just as much the Establishment as Biden, Lieberman and all the others. - Sally Church

He is going to get the DC's elitists!! I am counting on it!! - PauloNuin

He seems pretty elitist himself with his wife's $300K outfit, that's more than many pay for a house! - Sally Church

$300K for an outfit? I would not spend $300 for an outfit. Guess that puts me in my place! - Maxine

Pierre posted a message on Twitter

“There's a paper about biojava in the latest issue of bioinformatics. I've never tried to use it.”

Friday at 10:17 am - Link

strangely I subscribe to BioJava mailing list even though I haven't used and Java gives me allergy - PauloNuin

Pierre posted a message on Twitter

“my Murphy's law: good ideas always come on Friday at 18H00”

Friday at 9:41 am - Link

just write down and start working on them on Monday! - PauloNuin

Paulo, tha's what I'm doing. And when I'm lucky, there is a pen near my bed.:-) - Pierre

Personally, I love late Friday experimenting. You don't have to be super rigorous and you can try crazy stuff you couldn't justify actually scheduling during the week - Mr. Gunn

Bora Zivkovic posted an entry on A Blog Around The Clock

Advice To Young Bloggers

Friday at 7:36 am - Link

Jason Tsai, laura, Björn Brembs and Berci Mesko liked this

do I fall in the young blogger category? - PauloNuin

Matt Pfefferle posted a message on Twitter

“Crap, can't get into my bank account because I can't rember my favorite fruit”

Friday at 5:20 am - Link

Neil Saunders liked this

Bananas? - Neil Saunders

Apples? - Michael Barton

wolfberries? - Frank

guava? - PauloNuin

Quentin Crisp? - Bill Hooker

Sally Church posted a message on Twitter

“This war stuff is how many years ago now? How is this gonna fix the economy now?”

Thursday at 7:59 pm - Link

We made the mistake here of playing a drinking game where anything me mentions being a POW, we drink... - Chris Reed

or it could be 9/11 if it was Giuliani. - PauloNuin

Neil Saunders posted a message on Twitter

“stand-off at UQ lakes; 3 crows versus cane toad; not looking good for toad”

Thursday at 5:42 pm - Link

would you mind helping the toad? - PauloNuin

do you really want him to help the toad? - Jonathan Eisen

from Wikipedia: The Cane Toad (Bufo marinus), also known as the Giant Neotropical Toad or Marine Toad, is a large, terrestrial true toad native to Central and South America .... The Cane Toad is now considered a pest in many of its introduced regions, because its toxic skin kills many native predators when ingested. It has many negative effects on farmers because of pets and animals eating the creatures. - Jonathan Eisen

FYI, the crows in question (Torresian crows) are one of the few native predators that have learned how to eat cane toads; http://en.wikipedia.org/wiki/T... - Neil Saunders

For a moment the amphibian phylogeneticist in me overcome the against-introduced-species-ist - PauloNuin

The Life Scientists: Andrew Perry posted a message

“Job Ad: Grimwade Research Fellow (5 year term), Department of Biochemistry and Molecular Biology, University of Melbourne.”

Thursday at 5:05 pm - Link

Neil Saunders, PauloNuin and Pedro Beltrao liked this

This position has just been advertised in the Department I work in. It's a pretty good deal for any senior Postdoc ready to make the transition to PI. - Andrew Perry

Andrew, how do you think your dept would view Open Science? - Bill Hooker

My feeling is that the Department wouldn't have any problem with Open Science per se, however the usual currency of high impact peer reviewed publications and acquiring grants still would apply, like most places. Those who are publishing well and bringing in grants to fund their research tend to be more highly regarded and do less teaching ... I can't imagine the Department really cares either way about the 'details' of how this type of success is achieved (Open vs. the status quo). - Andrew Perry

Thinking of applying Bill? - Neil Saunders

Sorta... it's a bit out of my league I think, plus I did just spend 6 years and tens upon tens of thousands of dollars to get the US to allow me to stay here... I dunno. - Bill Hooker

Michael Nielsen bookmarked a page on delicious

Nature Network Toronto pub night with discussion panel on Science 2.0

September 2 at 10:04 am - Link

Jean-Claude Bradley, Eva and John Dupuis liked this

Pub night is on this coming Sunday, September 7, at 7:30pm. Venue is Fionn MacCool’s (181 University Avenue, near corner with Adelaide). Panelists are Timo Hannay (Nature.com) and yours truly. Hope to see you there! - Michael Nielsen

I'll be there! - John Dupuis

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Cameron Neylon is now on the panel! Excellent! - Michael Nielsen

correction michael. Cameron Neylon is on the panel after a 7 hour flight. I make no promises about my level of coherence :-) - Cameron Neylon via fftogo

Unfortunately I cannot be there. My wife flies on the same day and almost identical time. - PauloNuin

Paulo - that's a shame - will you be at Science21? - Cameron Neylon

Cameron - We may have to deny you beer until after the panel, then :-) - Michael Nielsen

Paulo - Too bad :-( - Michael Nielsen

I won't be going to the Science 21 too. Shame. - PauloNuin

Ooh, I will leave Toronto at about 8 PM.... - Berci Mesko

Michael, you know I don't drink beer. Now withholding coffee might be more of an issue... - Cameron Neylon

Anyone who is not going has to either reschedule their plans and flights OR find 3 other people to attend. IT'S THE RULES! - Eva

I think I might be able to attend, let's see. - PauloNuin

Sally Church posted a message

“Yay, the football season finally starts tonight! Who's watching the Giants vs. Skins?”

Thursday at 2:23 pm - Link

Dom, Jesse Stay, Eric @ CS Techcast, jeff and 5 other people liked this

I'll put it on although I don't like either team. However, any day that the Redskins lose is a good day in my book. - Akiva Moskovitz

Umm...Football season started 3 weeks ago. Oh! You mean that game the Americans call "Football" that has very little to do with feet! - Stephen Pierzchala

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Come on Man Utd!! - Zee at WeDoCreative

Zee... Man U till I die! - John Worthington

Forget that. GUNNERS GUNNERS GUNNERS. - Akiva Moskovitz

I'll watch but I'll be flipping between it and the RNC and Obama on O'Reilly Factor - Aaron Brazell

Victory! I managed to completely change the topic in a FriendFeed comment stream. - Stephen Pierzchala

Stephen: yup realised I had finally become an American instead of a Brit when I referred to throwing not kicking the ball, lol - Sally Church

S'alright. I'm Canadian. I came to Football late, and will never go back. Notice I state no team allegiance...though I am thinking of supporting Hull, if only to prevent their relegation in their first year! - Stephen Pierzchala

Too bad the first game is two teams I'm not really interested in. - Rochelle

I can't wait! The hubs and I will curl up on the couch and watch and roar. He feels like an NFL game on his birthday is an extra gift. - Abby Martin

Redskins FTW tonight. - PauloNuin

I'm not looking forward to the 1st MNF - 2 of my least favourite teams :( - Sally Church

can't, have a playoff baseball game :( - Shey

Redskins? Are they in the 2nd division? - Zee at WeDoCreative

Playing Scunthorpe United tonight are they? - Zee at WeDoCreative

go GMEN! although it doesn't really matter what they do this season. (which is good 'cause it ain't gonna be much). - Morgan

I am so ready to beat Drew Olanoff in fantasy football. - Louis Gray

Go Santana Moss! [Fantasy Team] - AJ Kohn

Plaxico on my fantasy team, baby. - Eric @ CS Techcast

Navy v. Ball State is on my agenda tonight. - Andrew Leyden

Me! - Jesse Stay

The game is starting right now? That's 4 my time. I'm still at work! And I have to go to Costco after work. And there are awesome hotdogs at Costco and... what's that about a game again? - Tad - just Tad

Tad, get a TiVo, man! - Akiva Moskovitz

Ummmm.... I've had a Tivo since 99. :P I'll just watch the end of the game and be about as happy as if I'd watched the whole thing. :) - Tad - just Tad

Go Giants! And my fantasy players :-) - Dom

One of these days I should try the whole Fantasy Football thing. It's just I prefer my fantasy to include swords, magic and chics with huge freakin' knockers. - Tad - just Tad

1UP Tad. I like sports, and I play games like Worldwide Soccer Manager and Out of the Park Baseball, but every time my friends have tried to convince me to get in on a fantasy league, I just make my save and run away. - Akiva Moskovitz

Shey, baseball is for wussies. :) - Aaron Brazell

Finally! FOOTBALL, baby!!! - Steven Perez

Funny, the Redskins played as drearily as McCain's anti-Washington speech last night - Sally Church

Adam Kraut posted a message on Twitter

“skimming through Erlang and OpenMP books recently; thus far OpenMP is much more attractive to me”

Thursday at 11:48 am - Link

which OpenMP book? - PauloNuin

The Life Scientists: Chris Lasher posted a message

“What's an effective way to share a poster on FF?”

Thursday at 11:30 am - Link

I think you should upload it to Flickr in great resolution and then use the Share on Friendfeed feature with which you can share both the link and the image with us. - Berci Mesko

Upload it anywhere, and post the link on FF? - Eric Jain

Flickr, website, you name it - PauloNuin

Post to Nature Precedings and provide link? - Maxine

Didn't we just have a conversation about having conversations again...? Some more ideas at http://friendfeed.com/e/4e0946... - Cameron Neylon

The Life Scientists: Chris Lasher posted a message

“Should I bold important descriptive statistics (e.g., total number of genes, percent of total with one condition) in the results section of my poster that are not included in a table? Is this distracting or helpful?”

Thursday at 9:13 am - Link

$0.02 from me: distracting. I'd prefer the section be structured so as to emphasize whatever you want me to take away from reading it, rather than be confronted with RANDOM SHOUTING in the middle of the text. :-) - Bill Hooker

I second Bill's opinion - Lars Juhl Jensen

Thanks guys. This was my intuition. KISS, right? - Chris Lasher

I am with Bill in this. Less text, less tables, more graphics. KISS - PauloNuin

I think you should bold them. The usability/readability of a poster is a lot like a website -- the vast majority of people quickly browse for something that catches their eye. See useit.com for more details. - Donnie Berkholz

supplementary data as handout? published on the web? ;) - dekay

PauloNuin shared an item on Google Reader

The Daily Photoist: September 4, 2008

Thursday at 9:40 am - Link

This is for Eva. - PauloNuin

Yay! I saw it when it was done, although it was still only half of the intersection (the three crossings you see here, not the three that would be on the other side) - Eva

The Life Scientists: Neil Saunders posted a link

Big data: The future of biocuration : Article : Nature

Wednesday at 9:46 pm - via Bookmarklet - Link

laura, Alexey, Bill Hooker, John Dupuis and 9 other people liked this

"Third, curators, researchers, academic institutions and funding agencies should, in the next ten years, increase the visibility and support of scientific curation as a professional career" - Neil Saunders via Bookmarklet

This article by far the best in the special Nature issue this week. - Neil Saunders

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It's not a free access issue is it? - Deepak

Not sure Deepak - it sure should be, if it isn't. - Neil Saunders

I think the articles are freely-available; follow the links from http://www.nature.com/news/spe..., they are not marked as pay/subscribe - Neil Saunders

The entire issue is free online, but for two weeks only. Download them now while you can... - Andrew Su

exactly Andrew - Graham Steel

Downloading furiously - Deepak

/me is safe in the knowledge the dead tree copy will be waiting for him when he gets home :) - Daniel Swan

Yes it is free access for 2 weeks. I've posted twice about that on this FF group, see here: http://friendfeed.com/e/1489a2... (at time of writing, about 3 or 4 entries below this one). - Maxine

"The exponential growth in the amount of biological data means that revolutionary measures are needed for data management, analysis and accessibility." -- Is the revolutionary measure free access for 2 weeks......? - Frank

I can't wait to read Cory's article!!!! I am thrilled!!! - PauloNuin

Francine Hardaway posted an entry on Francine Hardaway's Blog

The World According to Sarah Palin

Thursday at 6:44 am - Link

Charles LePage, Jon Price, Andrew Terry, Neil Bernhart and 10 other people liked this

Francine you always have a calm voice in the storm. When you moving to Half Moon Bay permanently? - Robert Scoble

Very thoughtful post, I too am concerned. It seemed like last night Gov Palin's speech was trying to accomplish two things: rally the Republican base, and completely muddy the waters and confuse independent and swing voters. - Michael Kowalchik

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Very astute analysis. Easier to see this is true if one is living in the South or 'flyover country' than on the coasts. - Bora Zivkovic

Bless you, Francine. You are reasonable. - Jay Tannenbaum

Brilliant...thank you for this... - JA Castillo

Gay marriage is not a "minor" issue. - Out Wrong

Wait, I'm confused. When were the democrats not the elitist party? - Ben Jackson via twhirl

Great column, Francine. I agree with your conclusion, and regardless of ideology (which, as you point out, has become an empty word), I must wonder if we can move that direction if we elect someone(s) who promote and pride themselves on being a maverick :-(. - asiriusgeek

In all honesty, both parties are showing the need for viable third parties. Sadly, they don't currently exist... - Ben Jackson via twhirl

Your blog was well written but I'd like to point out that your comment about "little issues" being solved in our own family rooms is exactly what Republicans want to dictate. I want choice, I don't believe Republicans (or at least the majority) share that rational. Which is why I find their commentary over the past few days hypocritical. - Steve Sebestyen via twhirl

All politicians are the same, be it republicans, democrats or independent. What really changes is the people that follow them. They really believe what the guys are selling(btw, that's a good thing, cause people have hope). The real objective in this election should be to root for your candidate and support the winner, that way, no matter what happens the objective is to unify the nation with a new bearing. And always remember, that there are several roads to the same destination. Good article! - Jonathan T

Well said, Jonathan T. And regardless of who is in the White House, YOU have more influence over your future than they do. YOU can directly impact, for good or ill, your future if you choose to take on that responsibility. - Craig Eddy

Deepak posted a message on Twitter

“@nuin doesn't that require all links to be on the same page?”

Thursday at 7:04 am - Link

It might. Or you can use something that mirrors the site locally. - PauloNuin

Matt Wood posted a message on Twitter

“Introducing the first code to come out of our work with Ruby in science: http://github.com/mza/denormal...”

Thursday at 5:11 am - Link

Deepak, Sally Church, Neil Saunders and Michael Barton liked this

that's the "release" you were waiting to announce? - PauloNuin

Not quite! Just a small snippet that was ready to go before our main release: should be with us shortly. - Matt Wood

Yay!!! Can't wait to see the whole thing. Trust me folks, you'll love it - Deepak

Do you have any inside information on this? - PauloNuin

If it's the app I think it is, then I've had a chance to see it - Deepak

The Life Scientists: Thomas Lemberger posted a link

PubMed search in Ubiquity

September 2 at 12:18 am - Link

laura, Rajarshi Guha, PauloNuin, Deepak and 12 other people liked this

I am not a programmer and have zero idea about Javascript, so had many problems. Improvements most welcome! Couldn't use properly the xml from ncbi's E-utilities (wrong mime-type???) :-( Anyway, to use the command, copy-paste the code into Ubiquity's command-editor (read more: <http://is.gd/1Wns>). Try a PubMed search by selecting something on the screen, call Ubiquity (option-space) and type 'pubmed', wait and see... - Thomas Lemberger

nice examples on the Ubiquity homepage - Pedro Beltrao

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Brilliant, I love it.. Didn't seem to save the command when I restarted the browser though - Jason Winget

added a little feature to select number of records displayed (eg include #3 somewhere in the query to limit to 3 records) and moved the code to http://code.google.com/p/tl-ub... - Thomas Lemberger

For parsing XML, jQuery is very nice and it's included in Ubiquity. No need to do match() :) - Rajarshi Guha

mmh, I tried this but it did not work... unfortunately ncbi's e-utils return text/html but jQuery expects text/xml (<http://is.gd/bu6>). Is there a workaround? - Thomas Lemberger

if retmode is xml, I can work with it in jQuery. Also in jQuery.ajax() you should set the type as xml. Also, namespaces need to be separated from the element by ':\\'. See http://groups.google.com/group... - Rajarshi Guha

I have a PubMed/JSON proxy in Scintilla if you need it - would make this much easier. - hubfeed

var parser = new window.DOMParser() - Thomas Lemberger

Added the possibility to directly insert citations (eg Smith et al, 2008), citations linked to the respective pubmed record or include the full reference. Should be useful when writing blog posts. - Thomas Lemberger

Deepak posted a message on Twitter

“Wish the Nature special issue had a "download all" button somewhere”

Thursday at 6:53 am - Link

can't you use DownThemAll? - PauloNuin

PauloNuin shared an item on Google Reader

In A World…Without Don LaFontaine

Thursday at 5:37 am - Link

The voice of the movies has passed away. - PauloNuin

PauloNuin bookmarked a page on delicious

XDot - jrfonseca - Google Code - Interactive viewer for Graphviz dot files

Wednesday at 5:53 pm - Link

Another cool viewer is zgrviewer - http://zvtm.sourceforge.net/zg... - Rajarshi Guha