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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.”

9 hours ago - 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

Francine Hardaway posted an entry on Francine Hardaway's Blog

The World According to Sarah Palin

19 hours ago - 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

The Life Scientists: Thomas Lemberger posted a link

PubMed search in Ubiquity

Tuesday 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

Python for Bioinformatics: an entry from Python: what's new online

fabulatr with Pylons: Multi-user instance starter for EC2.

Wednesday at 12:36 am - Link

PauloNuin and Andrew Perry liked this

Ian Holmes posted an entry on Genome Dynamics

Perl, R, C++ win the bioinformatics language olympics

Monday at 11:46 am - Link

PauloNuin liked this

Python for Bioinformatics: an entry from Python: what's new online

virtualenv 1.2 - Virtual Python Environment builder

August 29 at 1:25 pm - Link

PauloNuin liked this

Cameron Neylon shared an item on Google Reader

Trident: A workflow system for doing data-intensive science with reproducible results

August 29 at 2:04 pm - Link

Jill O'Neill, Bill Anderson, PauloNuin, Deepak and Richard Akerman liked this

Duncan Hull posted an entry on Quote of the Day news feed

Nobel chemist Paul Lauterbur on why people don't always love new ideas (bio-itworld.com)

August 28 at 8:22 am - Link

Aarthy, PauloNuin, Björn Brembs and Michael Nielsen liked this

Quote: "You could write the entire history of science in the last 50 years in terms of papers rejected by Science or Nature." - Duncan Hull

Timothy Driscoll posted an entry on In the Pipeline

PNAS: Read It, or Not?

August 28 at 5:36 am - Link

PauloNuin and Chris Lasher liked this

Jason Kelly shared an item on Google Reader

The failure of open science

August 26 at 12:08 pm - Link

PauloNuin and Pawel Szczesny liked this

Python for Bioinformatics: an entry from Python: what's new online

Aptana Acquires Pydev to add Python Support to Studio

August 26 at 7:26 am - Link

PauloNuin liked this

Mike Fruchter shared an item on Google Reader

A strategy for the cloud

August 25 at 3:19 pm - Link

PauloNuin and John Duff liked this

Python for Bioinformatics: an entry from Python: what's new online

Python-unixtools - A set of Unix utilities implemented in pure Python.

August 24 at 10:00 am - Link

Stuart Woodward and PauloNuin liked this

Python for Bioinformatics: an entry from Python: what's new online

An Epic Introduction to PyObjC and Cocoa

August 22 at 5:39 pm - Link

Stuart Woodward, Andrew Walkingshaw and PauloNuin liked this

Python for Bioinformatics: an entry from Python: what's new online

What does Ruby have that Python doesn't? (A Discussion at HackerNews)

August 22 at 11:10 am - Link

PauloNuin liked this

Björn Brembs posted an entry on bjoern.brembs.blog : a neuroscientist's blog

Yale researcher in Science: "High-Profile Journals Not Worth the Trouble"

August 21 at 11:54 pm - Link

Stephanie•CogSciLibrarian, Berci Mesko, Bora Zivkovic, Thomas Brox Røst and 11 other people liked this

Filing away to share with others. Interesting. - Jill O'Neill

I love the fact that it was printed in Science :) - Jean-Claude Bradley

Are they trying to shoot themselves in the foot? Or go kamakaze? Or do they realise they are already doomed? - Duncan Hull

Not at all - they really don't need it. He is absolutely right. Not that I may not try again personally in the future to publish in one or another, but many other journals can offer a wide audience and therefore lead to your being cited. - Heather

Feed so well into this discussion: http://scienceblogs.com/drugmo... - Bora Zivkovic

Where was my brain when I posted this? I had of course read DM's post. It's now linked! - Björn Brembs

Python for Bioinformatics: an entry from DZone: python

Python: An Introduction to Thread Programming

August 21 at 6:38 am - Link

Jason Tsai and PauloNuin liked this

Bora Zivkovic posted a link

Most Scientists are Perfectly Happy Not Publishing in GlamourMagz

August 20 at 5:26 pm - Link

Pawel Szczesny, Duncan Hull, Michael Kuhn, Björn Brembs and 2 other people liked this

The CNS disease afflicts only the loudest - others have jobs. - Bora Zivkovic

The Life Scientists: Bora Zivkovic posted a link

Most Scientists are Perfectly Happy Not Publishing in GlamourMagz

August 20 at 6:08 pm - via Reshare - Link

Michael Kuhn, Pawel Szczesny, Ricardo Vidal and PauloNuin liked this

Python for Bioinformatics: an entry from DZone: python

A Guide to Debugging in Python

August 20 at 3:16 pm - Link

Mitchell J Stanton-Cook, Jason Tsai, PauloNuin and Matt Wood liked this

Heather Piwowar shared an item on Google Reader

Yet another reason I am not an academic

August 19 at 10:35 am - Link

Dan Gezelter, Deepak, Bill Hooker, AcademiaConnect.org and 3 other people liked this

I had my name taken out of publications because my contribution to the process (aka 4-5 months of fulltime work) was not "intellectual enough" - PauloNuin

Where by "like" I actually mean "that sucks". - Bill Hooker

I've been talking a lot about data citation but I hope I haven't said anywhere that data collection isn't science :( - Cameron Neylon

Python for Bioinformatics: an entry from Python: what's new online

PyUseCase 1.4.1 released! - PyUseCase is a record/replay layer for Python GUIs.

August 18 at 10:19 am - Link

PauloNuin and Pawel Szczesny liked this

Python for Bioinformatics: an entry from DZone: python

van Rossum shows us the way with Django, App Engine

August 17 at 9:54 am - Link

PauloNuin liked this

Python for Bioinformatics: an entry from Planet Python

IronPython-URLs: Calling IronPython Functions from VB.NET

August 16 at 12:39 pm - Link

PauloNuin liked this

RAPatton posted a link

Newsarama.com : KAREN BERGER ON THE VERTIGO CRIME LINE

August 16 at 6:54 am - via Bookmarklet - Link

PauloNuin and Thomas Brox Røst liked this

"Announced during San Diego Comic-Con this year, the new Vertigo Crime imprint will act as a "subimprint" of the long-running Vertigo line and be composed of black and white hardcover graphic novels. The crime genre has been an integral part of Vertigo Comics since it's early days, counting 100 Bullets by Brian Azzarello and Eduardo Risso as well as several works by Criminal writer Ed Brubaker. But this new imprint Vertigo Crime pulls crime into a sharper focus in both genre and format with the black and white graphic novels. The imprint is launching with two titles in Spring 2008: Brian Azzarello's Filthy Rich and Ian Rankin's Dark Entries. Ian Rankin is a new name to comics, but not to crime fiction. The Scottish author" - RAPatton via Bookmarklet

Michael Kuhn posted an entry on bioCS

CiteWeb: Following citations made easy

August 15 at 4:00 am - Link

Bill Hooker, John Dupuis, PauloNuin, Jill O'Neill and 8 other people liked this

Great idea!!! - AcademiaConnect.org

Fantastic job, Michael! - Lars Juhl Jensen

Very cool, Michael! - Michael Nielsen

Tnak you, that is so useful!!! - Aarthy

Michael Nielsen posted a link

Toronto Hot & Spicy Food Festival | Hot Sauce Blog

August 15 at 7:54 am - via Reshare - Link

carolh, PauloNuin and Jamie McQuay liked this

Simon Cockell posted a message on Twitter

“connotea on a go-slow again - definately migrating to citeulike this time...”

August 15 at 2:23 am - Link

PauloNuin and Neil Saunders liked this

Today might not be the day if you want working bibtex import, but the rest seems fine... - Neil Saunders

Is there an API for citetulike ? just like delicious ? - Pierre

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No API, unfortunately - Neil Saunders

bibtex export has not been working for a while now - Frank

They are normally pretty good at responding to bugs in the forums, but it's a bit quiet just now; maybe they're away - Neil Saunders

all went fine using RIS. migration complete - Simon Cockell

Our issues are due to scaling problems. Currently non-trivial to fix, but we are balancing taking on a rewrite vs a hardware fix. - Ian Mulvany

would you ask to community to write a new software ? which language ? - Pierre

I've never seen a project with so many CPAN dependencies; http://www.connotea.org/code; this complexity can't be good - Neil Saunders

Neil, have you tried Gbrowse or even Turnkey? :) - Pawel Szczesny

if we re-write it is likely to be ruby, that's what Nature Network is in and we have resources and internal support for it - Ian Mulvany

@Pierre: yeah, IMHO you could use the Connotea webcite backend and the API to just swap out the user interface part relatively quickly. As long as everything stayed open source... as a company we prefer Ruby and Java. - Euan

But for such a large codebase one has to approach a rewrite with great care and plan a migration strategy that keeps service live - Ian Mulvany

That's personal opinion, btw, Ian is better placed to tell you what the official attitude is. - Euan

personally, I'd like to do it in Python - Ian Mulvany

@Pawel - Gbrowse works for me, but I did try Turnkey a few weeks ago and can't get anywhere with it. The install instructions appear to be mostly hacks to fix broken Perl modules... - Neil Saunders

@Pierre, one of the things that we failed in doing with the perl version was engage the community to create a bunch of developers for the project, I think due to the complexity of the architecture. Would definitely rethink this in a new version. - Ian Mulvany

Duncan Hull posted an entry on O'Really? A Personal Laboratory Notebook

Anyone for a game of Fantasy Science Funding?

August 14 at 7:37 am - Link

Michael Nielsen, Björn Brembs, Pawel Szczesny, John Dupuis and 2 other people liked this

We should set up a funding prediction market :) - Deepak

Fantasy Science Funding is a fun game that anybody can play. You select a Science funding body of your choice, imagine yourself as its all powerful chief executive, and decide which areas of scientific research you would “hire and fire”. What could be easier? Here is how it works… - Duncan Hull

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At last years (2007) SciFoo there was discussion of a prediction market for scientific papers, is this related? I don't know whatever came of it, Hendler and um Carl Bergstrom were discussing it. - Richard Akerman

@Richard Akerman That sounds interesting, can you dig out a link? - Duncan Hull

me likey. i was just checking out the nanotechnology index fund NNZ - Michelle Cadieux

@DuncanHull The idea is at the bottom of Hendler's post from last year http://www.mindswap.org/blog/2... Maybe that will provide you with a starting point - or you could just email him and Carl. - Richard Akerman

Fun game, really. - Aarthy

re: the Scifoo paper prediction market the argument against was that it'd take 2-4 years per round (to get the citation count in) - Euan

@Aarthy Yes a fun game, with a serious message (I hope) - Duncan Hull

@Euan. Could you use page views instead? BMC have "highly accessed" articles. Is page views correlated with citations? - Michael Barton

Eben shared an item on Google Reader

Genentech rejects Roche bid (Reuters)

August 13 at 5:06 pm - Link

Ricardo Vidal, PauloNuin, Andrew Perry and Deepak liked this

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