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Richard Akerman posted a message on Twitter

“so I'm to support a nonprofit with some web - just bought them a domain - what do you recommend as quick web? ning? googlesites?”

9 hours ago - Link

Ning's nice, but looks a bit barren if nobody posts for a while... - Euan

Thomas Lemberger posted an entry on TL's starred items in Google Reader

Five Thousand Bucks for Your Genome

Monday at 5:00 am - Link

Konrad Förstner, Anders Norgaard, Euan and 2 other people liked this

The price is going down fast - Pedro Beltrao

Cool. Though sequencing companies announcing internal costings like this is still pretty dodgy (didn't Illumina do the same thing?)... what would it actually cost an end-user? :) - Euan

Euan posted a message on Twitter

“No more Dr Pepper in Crinan St. WTF? Rage... too strong... overwhelming anger... HULK WRITE PETITION TO PATRICIA McCULLEY”

Monday at 7:25 am - Link

not even diet? - Paulo Nuin

Nope. Just Coke, Diet Coke and Sprite. - Euan

that's a bad selection there. - Paulo Nuin

Euan bookmarked a page on delicious

Home : Lindau

Friday at 3:53 am - Link

First documentary from the Podcast team. Sponsored by Apple. - Euan

Attila Csordas posted a message on Twitter

“@mekentosj how hard is to write an iPhone (meta)App that collect data from other (game) Apps in order to compare results?”

October 3 at 2:33 am - Link

Mek will know best, but at one point this was have been possible (and was used for cut and paste apps, for example), but I think the OS prevents accessing other application's data now. - Matt Wood

Doesn't each app run in a sandbox? i.e. can't communicate or share files between apps without a third party server or something? - Euan

@Euan: yes, I think so. As background tasks aren't available, such a 'meta' app would be difficult to engineer. - Matt Wood

Good to be able to discuss this stuff at last! - Matt Wood

Euan posted a message on Twitter

“I rent, am a debt free saver and don't own a car. Is the financial 'crisis' actually a good thing for me?”

October 1 at 2:20 pm - Link

Jason Tsai, Yann Abraham, Daniel Swan and 4 other people liked this

Same here, plus I get paid in $$, did you see the $ vs € lately? I guess a short term/sighted answer would be yes. Long term, uhh probably not... - Alexander Griekspoor

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Definite advantages to living "outside of society" :) I also own nothing (no car, property, assets) and it's "crisis, what crisis?" - Neil Saunders

Same here. And apparently, banks are going to give higher interest rates for savings accounts! I don't understand that at all (wouldn't it be cheaper to save on the interest they have to pay out?) but I'm fine with it! - Eva

Same here, the only thing I "own" is a car. And a savings account. - Paulo Nuin

There might be Euan, if the economy doesn't continue to slide. If things go as far as they could (a depression) everyone will be hit. - Alex "Maverick" Scoble

Euan is better set for change though. Easier to adjust his lifestyle as things go down hill. - Christopher Welle

It won't be "good" for you, but you'll be much better off than others. Similar situation here. I have no loans and no credit cards and pay cash for everything. I own a car and a house. The problem is the cost of everything I consume is rising faster than my annual raises. Property taxes have doubled, food has doubled, gas which I no longer use has quadrupled. Salary has only increased about 11% in the last 8 years though. - Adam Turetzky

My grandfather made it through the great depression being in the situation you're in though. No one had cash after 1929 because they all owed on loans which were getting called in. He had cash and was able to get amazing deals on his house, his car, etc. - Adam Turetzky

Also same here (well, I do own a barely driven car but I've value is fast approaching $0). I see no crisis for me directly, but the indirect effects are likely to be annoying. On the positive side, I hear shares are going cheap at the moment ... - Andrew Perry

@Eva: There is a bank here in Australia offering over 8% on deposits. Given that bank deposits in Australia are federally backed, that seems a pretty good deal to me. - Nick Lothian

I rent, am a debt free saver, and I don't own a car. I'm not sure a crisis is good for me except bringing property down in price so can become a heavily indebted homeowner. I am glad thought that my savings are cash savings, and not stocks and shares 'savings' - Daniel Swan

Yeah. My thinking was house prices will fall and interest rates on savings accounts will rise, so that's good, right? As Adam pointed out there is the whole cost of living increase thing to deal with still, sadly. And job security. - Euan

If the crisis is short and you plan to buy a house then it is good for you because the houses will become more affordable. If the crisis is short and you don't plan buy a house then it is pretty much irrelevant to you. If the crisis turns out to be long then it will be bad for everyone, but less so for you than for most others. - Lars Juhl Jensen

Although housing prices might drop, that doesn't necessarily mean that property will be more accessible to those who don't already own. Rising interest rates could place property out of reach of many. And given the woes of the sub-prime market, if you DON'T already have a mortgage, you might want to think about ways to make yourself as credit-worthy as possible. - Todd Harris

Todd, we completely agree. That is why I think that it is only an advantage if you buy a house AND the crisis is short, in which case the interest rates will soon drop again. If the crisis is long, the increase in interest rates will offset the drop in housing prices. - Lars Juhl Jensen

Echoing Adam's observation: "The problem is the cost of everything I consume is rising faster than my annual raises." Inflation is (probably) going to be the biggest problem for anyone with primarily cash assets. Even if interest rates rise, they will have to be higher than the rate of inflation for this to work in your favor, which is unlikely for things like savings accounts. Traditionally, investing in property, the stock market, and/or commodities has been the preferred way to hedge against inflation. - Hilary

Hilary et al. have a point. My portfolio might be down 25% over the past couple weeks, but it's still up long-term. Inflation is the next issue we have to deal with. You won't have a net gain with cash. Now, if you have enough on hand to put down 20%+ on an undervalued piece of property, well, then you're in business. - Mr. Gunn

Just moved to NC for my first "real" job after my masters. We are going through the home-buying process for the 1st time. There are still some tricks up lenders sleaves to get you a good deal. For instance, negotiating the seller to buy down your interest rate. We might need a cosigner though because my school loan debt is too high. The housing market here at least cannot be beat. Unbelievable! - Kevin Z

On the other hand I've noticed I am paying $100-120 more for groceries each trip than several months ago in PA. Inflation is the big issue and it is blatantly obvious and rising quickly. - Kevin Z

Science Online: Maxine posted a link

Brave New World: Richard Charkin Author

October 1 at 1:09 pm - via Bookmarklet - Link

"Today Richard Charkin became an author. It wasn’t a novel, or travel and best restaurant guide, or even a book on 21st dress code, but a print on demand version of his infamous blog." (MC adds: Not about science, but Nature Publishing Group staff will doubtless have fond memories. He's following in Henry Gee's footsteps!) - Maxine via Bookmarklet

For 40 quid?! He should have done it 'pay as much as you'd like' Radiohead style. After covering print costs, of course. - Euan

Ha Ha! I missed the 40 quid. Must send Henry a link. I think RC needs to adjust his publishing model- probably will quite soon I imagine! I bought an excellent book of a blog once, "Grumpy Old Bookman" by Michael Allen, for a fiver (self-published). Having read RC's blog posts while he was writing them, I think that GOB is both better and better value for money! - Maxine

Alexander Griekspoor posted a message on Twitter

“WOOOOOOHOOO! http://developer.apple.com/iph...”

October 1 at 8:17 am - Link

Michael Kuhn, Euan, Cameron Neylon and Martin Fenner liked this

definitely like that one... - Cameron Neylon

Awesome. - Euan

Euan bookmarked a page on delicious

MySQL :: Using the New MySQL Query Profiler

October 1 at 3:27 am - Link

I found this very exciting. I have no life. - Euan

Cameron Neylon posted an entry on Science in the open

A personal view of Open Science - Part I

September 30 at 6:01 am - Link

Garret McMahon, mike seyfang, Michael Nielsen and 13 other people liked this

Are there any "independent" organizations that can support concepts of "Open Science" without being "burdened" by the need to compete and standout for the sake of financial sustainability/continuity? So far, it seems like the journals/publishers dominate "Science 2.0" applications like Nature, BMC, PLoS etc. But they use these concepts to boost their own journals, not necessarily advance "Science 2.0" in general. If we agree that there is room or even a need for specialized apps for scholars, do we not also need a platform specifically for scholars as an end itself and not a means to an end? - Wobbler

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Science Commons are big on platform development but essentially have charity funding (more on this coming in a later part). Are we not our own organisation in essence. As Chad Orzel said 'We are science' so can we not be 'Science 2.0' a loose confederation of like minded and connected people - Cameron Neylon

Well, the issue I have is not so much with centralized versus decentralized, as long as we can be/are connected, as you say. But I am not sure about having journals/publishers "enable" the underlying foundation. Since their primary objective is not about promoting "Open Science" but about increasing readership/citations of their journals. - Wobbler

I am all for loose confederation and that's where having services and APIs come in. However, this cannot be done in a vacuum. You need the journals, CrossRef etc to provide APIs etc that we can build on. If they can figure out how to monetize them, then we will be in pretty good shape, IMO - Deepak

It's also nice to have financial means to support individuals or projects supporting open science concepts (and to have workshops and meetings) but this seems difficult to generate without a formal organization in place... - Shirley Wu

Shirley - I agree and we're working on that from a number of angles - Jean-Claude Bradley

Wobbler, I can see what you're getting at. But why worry about why the applications are being built if they work well (and are sufficiently open, natch)? If open science gets done then everybody wins. Does it matter who enables it and why? Next big thing could be from a start-up, a grad student with some free time on her hands, two guys in a garage... that's the great thing about web development. Being in it at least partly for the money isn't a bad thing! - Euan

What Euan said - Deepak

That is a good point. Maybe I am getting a bit too paranoid. I guess the key is indeed the applications being sufficiently open enough. Still, imagine the scholar working on the next big thing that does not specifically help a specific journal (publisher) get readership but promotes "open science" for everybody from all different research fields. Is there an organization that that person can go to for (financial) support (without "compromising" the "openness" of the concept)? - Wobbler

I also think that while publishers are doing a lot of work in this space (and I think that's a good thing - particularly if they want to survive) that a lot of the interesting things are being done in academic research projects, off the cuff side projects, and those loose confederations. They don't always get the exposure and a lot of it doesn't work out but that's where a lot of the innovation is IMO. - Cameron Neylon

As long as no one works in a vacuum. All of these efforts and fine (and there should be multiple different types), but they also have to talk the same language (http for starters :) ) - Deepak

Well I think talking at all would be a good start - that's what this paper is hopefully about... - Cameron Neylon

I am just wondering if an independent academic organization to support a platform for academics for the sake of improving "science" rather than as a means to an end for journal publishers could encourage more scholars to participate. Example, the PLoS ONE rating model is an interesting initiative, but it is limited to helping PLoS (ONE) improve its feasibility. A better approach would be a system that covers all OA journal publications from all OA journals. That would stimulate OA/Open Science more than... - Wobbler

...just a system that is limited the PLoS ONE environment. On the issue of PLoS ONE's system, Björn Brembs suggests taking it a bit further and use reputation systems. Very potential idea to get things moving, but again, limited if it is only for the PLoS ONE environment/community. I think a global reputation system that is based on all the assessment work of scholars for all OA journals gets far more attention (and likely more support/recognition of those same academic communities). - Wobbler

And that would also stimulate fair "quality" competition between journals, and not have a single journal/publisher hog all the "Science 2.0" scholars because they were the earlier ones to start with the rating/comment thing. And fair quality competition (using volunteers, no less) would give a more accurate view of the distribution of (publication) quality among journals. - Wobbler

Some non-publisher organisations are starting to take an interest and funders in general are looking at providing a range of services. We can obviously set up our own platforms but the funding has to be thought through in the long term. Who is going to pay for e.g. a commenting platform? Or, given that ultimately the funders may for everything where will the cost be charged and how do we make sure it's good value for money? - Cameron Neylon

(cont my own rant for a sec). And whether it is "Science 2.0" or full OA that comes first, it is not going to matter: either of them significantly increases the value of digital scholarly communication. And when that time comes nothing screams (financial) continuity harder than having a big community of capable people doing valuable work for you, free of charge. And on that account, Nature is doing a hell of a job building that community. Others, including PLoS, are trying to do the same. - Wobbler

And the rest are in danger of fighting for "scraps" (e.g. for helpful and capable users and papers). I am not sure if that is truly desirable. Although admittedly, Nature's Connotea is a pretty sweet non competitive service (other than for marketing, but that is more me being nitpicky). Cameron: I think those are indeed important questions to ask. - Wobbler

There is a real danger of getting poor tools because of a powerful incumbent or early mover with good PR. I think this is likely to happen with researcher UIDs for instance. Whoever manages to make the first effective move will probably end up in control - whereas what would be best is probably some form of federated open standard with multiple authorities that the user can choose from. - Cameron Neylon

Euan bookmarked a page on delicious

An ancient evolutionary origin of genes associated with human genetic diseases -- Domazet-Loso and Tautz, 10.1093/molbev/msn214 -- Molecular Biology and Evolution

September 30 at 4:11 pm - Link

Bit wary of 'disease gene' studies that use OMIM... such a messy dataset. - Euan

Ricardo Vidal posted a message on Twitter

“My efforts to learn python sometimes feel like a bad decision given all the hype I read about RoR. Should I backtrack?”

September 30 at 1:43 pm - Link

no it's all good. Python for bioinfo is never a bad idea - Deepak

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python will let you defy gravity :) More seriously, there are many Python web frameworks, so you won't be left wanting for choice - Rajarshi Guha

Do you want to learn RoR? Python won't help (directly). Do you want to learn a great programming language? Keep going! - Chris Lasher

Who said you had to only use one? Keep going with Python and the basic concepts will translate over to Ruby later on. - Euan

Thanks for the feedback guys. I'm already getting into python pretty well. Learning stuff everyday. And django has been doing me well although I'm sure it has it's flaws, I'm still not there. As for ruby, it'll have to wait :) - Ricardo Vidal

Euan bookmarked a page on delicious

Recession blocker

September 30 at 3:54 pm - Link

All this irresponsible talk of recession only makes it more likely. Do your bit for the economy by only reading the news through this web browser, which blacks out unwelcome words. - Euan

Euan posted a message on Twitter

“OpenWetWare 5k registered users. SciLink 47k (self reported, seems high?), BioMedExperts = ?. 12% of PLoS papers are blogged (not by Bora)”

September 29 at 6:58 am - Link

Bora Zivkovic and Duncan Hull liked this

OWW is lower than I thought, but I suspect that some of those "users" are research groups with more than one person - Deepak

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Yeah. Though conversely some users look autogenerated / like bots: http://openwetware.org/index.p... - Euan

You mean bots are not people. And here I thought all along ... *sigh* - Deepak

Wait, Deepak, you hadn't realized I was a bot? *SURPRISE* - Jill O'Neill

A lot of the personal pages on OWW are never modified by the users. I don't have any stats on how many of those users do other edits. - Cameron Neylon

by which I mean an initial user page is generated automatically but the fact that the user doesn't modify it does not necessarily mean they aren't an active user. - Cameron Neylon

Cameron, that's true. The user page that is auto-generated on registration approval is not changed often. OWW users tend to sign up for some specific purpose and tend to keep to editing the pages they asked to register for. Be it a lab notebook, a class or simply to edit protocols that they have something to add to. Although 5k seems low, it's important to look at the content being created, it's at a continuously growing rate. - Ricardo Vidal

I suspect SciLink would have less if they were allowed to leave :) - Neil Saunders

Should have said PLoS One papers, not 'PLoS papers'. - Euan

Euan bookmarked a page on delicious

MoochStand Project « BookMooch Blog

September 30 at 2:32 am - Link

This is a great idea. - Euan

Euan posted a message on Twitter

“10m EndNote seats. 4m RefWorks. 70k each Connotea / Bibsonomy / CiteULike. < 1k Mendeley Web (just starting)”

September 29 at 6:55 am - Link

Chris Keene, Todd Harris, Pedro Beltrao and 7 other people liked this

Additional info - Mendeley Desktop downloads: 2k (just starting) :-) - Victor / Mendeley Team

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Are connotea and citeulike really level on users? What counts as a "user"? Where do these figures come from? - Duncan Hull

out of date pers comm (for the online ref managers stuff). - Euan

Though when I talked about it with Ian he suggested that CiteULike has grown significantly and that you can mine data they've released to show this? Am happy to be corrected. Oh, and user would be a registered non-spammer. - Euan

Yup, you can mine stuff at http://www.citeulike.org/faq/d... I don't know what kind of user information you can find in those public datasets - Duncan Hull

The count of unique bookmarkers, I guess. - Euan

would also be interesting to know how many papers in each, e.g. different apps will have different paper:user ratios... if you catch my drift - Duncan Hull

CiteULike: 19,313 users who have bookmarked something, 1,996,147 papers since May last year. - Euan

That would be in line with Connotea, incidentally (I'm not being biased! ;))... maybe Ian will post stats. - Euan

Hmmmm, thats interesting. The numbers in citeulike aren't *strictly* incremental e.g. not sure if http://www.citeulike.org/artic... suggests nearer to 3,353,106 papers? Where does 1,996,147 papers come from? And 19,313 users? Sorry for my pedantry... - Duncan Hull

How many Zotero users are there? - jokrausdu

parsing script: http://www.ghastlyfop.com/blog... (rename to .php). Actually got it wrong, there are 1,996,147 tag / bookmarks, sorry, not individual papers. There are 616,804 unique bookmarks. IIRC CiteULike autoimports eToCs from popular journals so that could be why the autoincrement ID is so high. Also remember this is only since May '07. - Euan

Many if not all of those EndNote seats would be vacated as soon as people became aware of a useable replacement. It's such a frustrating, clunky, old piece of software. - Mr. Gunn

Euan posted a message on Twitter

“Papers licences sold = ?. Zotero downloads: 400k. Scientists actively using Zotero = ? (20k guesstimate?). 2Collab 5125 total users.”

September 29 at 6:57 am - Link

Duncan Hull, suelibrarian, John Dupuis and 2 other people liked this

That's a lot of Zotero. - Matt Wood

Don't know if updates are included in the download count. - Euan

That's assuming that downloads from zotero.com redirect to mozilla, too. - Euan

Euan posted a message on Twitter

“Nature journal print circulation 60k (New Scientist 170k, Wash Post 650k). Nature.com/nature monthly pageviews 4,600,000.”

September 29 at 6:54 am - Link

Forgot: Nature eTOC subscribers 2.3 million. Don't know bounce rate though. - Euan

Bill Hooker posted a message

“A few FF rooms that may be of interest”

September 29 at 3:51 am - Link

Jill O'Neill, Björn Brembs, Maureen and 3 other people liked this

FriendFeed Hacks (http://friendfeed.com/rooms/fr...), Google Code (http://friendfeed.com/rooms/go...), Ask The Masses (http://friendfeed.com/rooms/at...), Data Mining (http://friendfeed.com/rooms/da...), nptech (http://friendfeed.com/rooms/np...), Invites (http://friendfeed.com/rooms/in...) - Bill Hooker

Is there any way to search for rooms on FF? - Euan

http://ffrd.appspot.com/ - Pierre

Euan: Google [inurl:http://friendfeed.com/rooms/ site:friendfeed.com keyword1 OR keyword2 OR keyword3]; that's how I found the rooms above. - Bill Hooker

Euan posted a message on Twitter

“Humph, it's Nature *Network*, there's no s at the end. NPG people are guilty of this too... http://tinyurl.com/5xxhul”

September 29 at 2:37 am - Link

Wasn't there the idea of the localized networks, like Boston and London? - Egon Willighagen

damn those internets :) - Neil Saunders

Well, multiple hubs, one big social network... - Euan

Yeah - I've been noticing this for months now... - Hilary

Rafael Sidi posted an entry on Really Simple Sidi (RSS)

Thomson Reuters sues Zotero

September 26 at 5:54 pm - Link

Chris Keene, Duncan Hull, carolh and 10 other people liked this

"Reuters claims George Mason is violating its license agreement and destroying the EndNote customer base". Don't know about the first, but there's nothing I'd like to see more than the second. That's it, Thomson are officially "evil" and must be eradicated. - Neil Saunders

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I just don't get it. The case seems to be based on the fact that the new version can convert Endnote Style Files therefore they must have reverse engineered the Endnote software in violation of the licence agreement. But there are style files for Endnote all over the place. You don't need to have gone anywhere near Endnote to get them surely? Are they claiming copyright over a file format?!? - Cameron Neylon

How short sighted. If I were Zotero, I'd just dump the converter and stick with Bibtex - why even try to be cross-compatible with EndNote? You would think that Thomson would appreciate the interoperability developed for them for free. God knows how slow they are to implement anything, and when they do it's usually half-baked. - Todd Harris

I suspect whoever out of citeulike/Mendeley etc who gets a properly functioning word plugin is probably going to wipe Endnote out in very short order - Cameron Neylon

@cameron. Fully agree. Once there's word integration EndNote is over. - Todd Harris

I'm with Zotero but this was only a matter of time, really! Am not looking forward to the first 'we'll store your papers in the cloud for you' court case. - Euan

I've been saying that for years, Cameron, but the integration still isn't here. I do understand to some degree the magnitude of the task, but also I think some effort has been wasted wishing people would just start using LaTeX instead of Word. - Mr. Gunn

@Todd/Cameron/Mr. Gunn: Hope I won't have to eat my words later on, but regarding the Word plugin for Mendeley - it should be available within the next two weeks :-) Closely followed by better LaTeX integration and an OpenOffice plugin. - Victor / Mendeley Team

@Victor, will the Word plugin actually maintain reference ordering and update cites throughout the document when a new references is inserted? - Rajarshi Guha

LaTeX is absolutely a non-starter for non-coding types. As is any type of command line interface. Open office would be better than Word but that's probably a non-starter as well. Integration with a word processor is very very hard, and I understand that, but without it, I just don't see any literature management system going anywhere really. Now if Endnote could just use my citeulike library _as_ its library - Cameron Neylon

Victor - was avoiding saying anything about that but am very much looking forward seeing what you roll out. - Cameron Neylon

Looking forward to it here as well, Victor. - Mr. Gunn

Is it just me or is blogspot running like a pig on stilts? I can't view Rafel Sidi's original entry because "The server at rafaelsidi.blogspot.com is taking too long to respond"... - Duncan Hull

It's just you Duncan - Rafael links to http://stephenslighthouse.sirs... - Cameron Neylon

From the complaint: "Zotero (...) which accesses, uses converts and/or distributes, in whole or in part, Thomson's proprietary EndNote Destop software product (...), without authorization and in direct violation of the express terms and conditions of GMU's license agreement with Thomson, and which, due to the freely distributable, open source nature of Zotero, (...) cause irreparable harm to Thomson." ... some BS - Pedro Beltrao

Here is the full complaint in PDF format (http://www.courthousenews.com/...). They are asking for $10.000 per year until Zotero removes the converter for Endnote files. - Pedro Beltrao

@Rajarshi: Yes, it will! It will also adjust/update the in-text citation format and reference ordering when you change the citation style during editing. - Victor / Mendeley Team

This is indeed not a very smart PR move by Thomson Reuters. I'm looking forward to the Mendeley Word plugin, but Refworks and Sente (for Macintosh) also integrate with Microsoft Word. My Mendeley profile: http://www.mendeley.com/beta/p... - Martin Fenner

I wasn't using zotero, but now I'll give it a try! - Björn Brembs

Strangely reminiscent of this TED talk by Charles Leadbeater: Publishers vs. Innovators... http://www.ted.com/index.php/t... - Duncan Hull

Euan posted a message on Twitter

“You design bastards are cramping my Comic Sans style.”

September 23 at 9:50 am - Link

dekay, Hilary, Andrew Perry and 7 other people liked this

I love to use comic sans in my powerpoints! - Mr. Gunn

11 more comments

http://bancomicsans.com/ - Lars Juhl Jensen

+1 Lars - Richard Akerman

ComicSans? It's all about Chalkboard these days. A little more upright and professional with a suitable degree of whimsy :P - Todd Harris

Perhaps we've been too hard on ComicSans. He did show up at the Font Conference: http://www.youtube.com/watch?v... - Todd Harris

You're allowed to use Comic Sans if you are (a) making a cartoon and your handwriting sucks and you have no other comicky font available for text balloons and for some reason you are incapable of installing new fonts or (b) parodying bad design or (c) it's 1997 and you've never been online before and you just discovered how to make a website (also add animated gifs!) - Eva

but the other MS fonts: times, arial, verdana and... the most beautifuly hinted font in the world tahoma are simply great. - marcin

My small sample size suggests a positive correlation between seniority and comic sans usage. - Neil Saunders

y'all hatin' cause my new font technique is unstoppable. http://staufenberger.typepad.c... - Mr. Gunn

http://www.achewood.com/index.... (nsfw, language) - Andrew Walkingshaw

lol - switch to Giddyup and see how that goes... - Hilary

another +1 Lars. - dekay

I can't believe I never saw Achewood before. Now if only the strips were in the RSS feed... - Euan

Achewood's an acquired taste, but once you're hooked.... - Andrew Walkingshaw

Euan bookmarked a page on delicious

Click to Make - How to Make - Ponoko

September 25 at 3:03 pm - Link

Essentially you're buying time from a laser cutter for $2 a minute. Awesome idea though. - Euan

Euan favorited a video on Vimeo

Firefly Additives

September 23 at 4:41 pm - Link

What is this? Processing script? - Ricardo Vidal

Can't remember (but almost certainly) - I favourited it on Vimeo months ago. Not sure why it suddenly cropped up! - Euan

Euan bookmarked a page on delicious

Music Is Math on Vimeo

September 23 at 8:56 am - Link

Processing rocks. - Euan

Jason Kelly shared an item on Google Reader

Guerilla Open Access

September 20 at 2:16 pm - Link

_alf liked this

I don't disagree with his motivation, but this is not civil disobedience and that phrase should not be used in connection with this effort. I disagree also with the assumption that forward-looking OA will do nothing to "free the archives". In a world of 100% OA, there will likely be more incentive in the new profit models for copyright holders to release those archives than to cling to them. - Bill Hooker

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I think Aaron Swartz is a smart guy but to be frank this is a dumb idea. Scientific publishing isn't like the music or film industry, every scientist is a producer as well as a consumer and has opportunity to effect change by working within the system. That change is already happening, slowly. I'd much rather see Aaron's passion be invested in spreading the OA message or helping to investigate alternative distribution / business models. - Euan

In one sense he may be right - can the STM publishers actually afford to mount the kind of rearguard action that RIAA did? I appreciate the motivation but I don't think this is a good approach at all - we need viable OA publishers and deliberately trying to pull the business model out from under the existing publishers isn't going to help provide that - Cameron Neylon

this seems really naive - 1) some schools in the global south have better access to the literature than some schools in the north due to a)programs like HINARI b)publisher programs c) tiered pricing that goes with GDP 2) librarians DO and always have provided copies --- it's called Inter Library Loan -- and many libraries have reciprocal agreements (we'll lend to you if you lend to us) - state universities tend to be more grinchy (IMHO) and charge for ILL but other institutions do not - Christina Pikas

As always, Peter Suber has the best response: http://www.earlham.edu/~peters... - Bill Hooker

Yup - trust PS to make the comprehensive sensible statement - Cameron Neylon

Hilary posted a message

“Meta-FF-hypothesizing: what do you "like" when you "like" an item/link?”

September 17 at 12:12 pm - Link

Michael Nielsen liked this

I'm wondering why it feels weird to click "like" when I disagree with the content of an article, but I think it's important to read the article... meaning I fundamentally didn't "like" what the article says, but "liked" that it was brought to my attention. - Hilary

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But would we like the system if it was just a 'mark' button. Interesting that they clearly don't want to give us a 'dislike' button but I guess that would actually be more semantically complex. Do I like something because it is important or dislike it because I disagree? And yes I am procrastinating rather than writing a paper.... - Cameron Neylon

Yeah, I use it as a 'thanks for streaming this' action too. - Euan

Same as Euan; I like that it was posted. - Neil Saunders

agree -- it's a tip jar. dislike==hide (c.f. LastFM where you get "Love" or "Ban" -- they are not strict polar opposites, but they do provide positive and negative feedback buttons for the training engine, while having subtly different functions) - Ian Holmes

+1 Euan. I am marking it for my own future reference, and to give it some extra prominence -- doing my bit as part of the "trusted network" filtering. - Bill Hooker

To me it's just like a flag or a star = "of interest" - maybe as a bookmark, maybe because I agree, maybe because I want to bump it up, maybe because I disagree totally. - Richard Akerman

The Life Scientists: Neal posted a message

“how much are things like Nature Networks actually used?”

September 17 at 4:11 am - Link

Alexey liked this

By who? The regular users of a wide variety of services use them a lot, but they are a small minority of all scientists. Probably talking about a few thousand scientists world wide who are using online 'socialt networking' services regularly. - Cameron Neylon

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I agree. There is definitely a community of users around such services (much like the Life Scientists room here on FF), but they are relatively small at present. That's not necessarily a bad thing. - Matt Wood

Some usage stats would be helpful - Cameron, for your survey of services, are you compiling such stats, or indeed able to find them easily? I'm sure Maxine, Euan and others could tell us about # of NN users, weekly activity etc. - Neil Saunders

A comparison of registered users and 'active' users across services would be useful but I think itcould be difficult to do a fair comparison even if people were generally happy to make the stats public - the real thing you want is total number of unique people in some ways and how they are distributed across the different services - Cameron Neylon

Define "used". Jen Dodd and I have been organizing Nature Network pub nights in Toronto, and people that are very interested in those are not necessarily also typing away on the Nature Network website all the time. (Although the reverse is not true: people who participate online seem to _also_ want to go to events) I know from my own experience that I am sometimes quiet on websites where I still like to drop in once in a while and read what's new. (Not on NN, but others might do that there.) - Eva

IMHO it's a safe bet to say that < 100k scientists use all of the science orientated social networks put together. Goes up substantially once you start counting things like Connotea, CiteULike, Zotero and Endnote Web etc. though. You can apply the 1 / 10 / 100 rule to that: 100k users, 10k active, 1k contributors. - Euan

Should say that it's growing quickly, of course. ;p Personally quite optimistic about uptake... - Euan

Thanks for your answers. Realise now it seems pretty 'trollish', but it was a genuine question as to who (out of the people in this room, which is admittedly a fairly self selecting population) uses NN. I'm quite impresses at how it useful it might be for both useful and frivolous interactions, but feel it's not actually used all that much across a broad spectrum of life scientists. - Neal

Following Euan's rough figures it is all a bit nascent, but I see several "useful" types of interactions (and plenty frivolous!), such as the forums set up before meetings to discuss agendas and draw in interested audiences (the British Library talk science group, for example: their upcoming meeting is a sellout), and in my particular case the "good paper journal club" and "ask the editor" forums are spreading the word to everyone whereas previously these questions were answered and advice given in one-off emails, now anyone can share the information. For us editors, it makes us more motivated to provide better and more detailed answers to questions (such as how to get published, career opportunities, details of formatting, how to write, etc) knowing that everyone can benefit not just the recipient. Before NN I posted these Q/As on a blog (Nautlius) but NN fourms are better at capturing and displaying the information in preparation for the time the user wants to know the answer to it. - Maxine

By the way, I have no official connection with N Network other than working for the same company - I like NN and like to help out there when I can, but for official stats and the like, the people to ask are the Editors, Matt Brown and Corie Lok (who are both members of this FF room). Most of my life at work I am having enough "fun" (not) with web 1.0...enough said. - Maxine

The Life Scientists: Euan posted a message

“Where / how could you get, say, 5k SNPs (but more is better) genotyped for a small-medium number of samples (< 92) on the cheap?”

September 15 at 2:54 am - Link

Jason Tsai and Deepak liked this

If they are specific SNPs you could be in trouble with cost. Generally the cost is in making the array/assays/probes. I think ball park for one off assays remains around £1/assay. Given that most of the cost is making the probes doing multiple runs of the same probes should drop cost. But probes will still cost around £5-10k at minimum. I think you'd be luck to get out of it for less than £30-50k but I'm happy to be proved wrong. - Cameron Neylon

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Sorry, I should have said common SNPs - what about a bead chip? What do they use at 23andMe etc.? - Euan

Ah Fair enough - I would guess you would be doing well to get it done cheaper then 23andMe are offering it to be honest. They use a custom Illumina chip I think. - Cameron Neylon

Yes - 23andme use a custom Illumina genotyping chip, as far as I know. I agree with Cameron: even with 100 people, 23andme is probably your best bet: plus you get access to their tools, which are pretty good. - Matt Wood

as others have mentioned the big cost with arrays etc is consumables. 23andme etc are your best bet esp since you can download your data - Deepak

Value for money there is no argument - the combination of price point, tools and number of SNPs I think 23andMe are way ahead. You might find some outdated or old human SNP chips on the market somewhere at a discount and you might find an academic lab that could do the analysis for less but there would probably be a lot of work involved. - Cameron Neylon

I dunno. The context is that I was looking at AssayDepot and wondering how much of 23andMe style stuff you could do yourself (or as a biohacking group). Through AD you can get DNA extracted and amplified for $50 a pop, could you then outsource the genotyping too? Then analyze the resuls in your basement bioinformatics lab? You'd have all the data (more, in fact, if you used a more modern chip). Obviously there's be no nice front end and it ignores all ethical concerns... - Euan

To be clear I don't mean setting up a business along these lines, just wondering if you could do it for a small group of people from your living room. - Euan

The big ongoing cost as Deepak mentioned is the consumables Cy5 costs a fortune - and this can run to more than the chips. For conventional sequencing it is cheaper to pay someone else to do it than to run an instrument in house. To do a small set at home (your original 5K SNPs) would be around 5 slides per set at around £100-200 reagents for the set I would guess. Plus £10k for the oligos, £40k for a cheap slide printer and around £40k for a scanner in upfront costs - definitely a game where volume pays - Cameron Neylon

Cameron hits the mark. This is an economies of scale business, which is why you don't see it in the AD type model right now. Best thing to do is talk to a core facility and find out what their pricing is. - Deepak

The Life Scientists: Attila Csordas posted a link

Academia.edu: A Geni For Researchers

September 17 at 1:08 am - via Bookmarklet - Link

Robert Scoble, Maureen, imabonehead and 10 other people liked this

"Whenever a new member joins the site, they are asked to identify themselves by both their department (for example, Computer Science), and then a more narrow field (example: Search Engine Algorithms). From then on, all activity submitted by this user will be added to the feeds of the fields they participate in. The site also allows users to specify certain members using a Twitter-like “Follow” system. Academia’s success will lie in its ability to build a useful news feed revolving around its professional network" - Attila Csordas via Bookmarklet

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the website has a 500 Internal Server Error for me: http://www.academia.edu/ - Attila Csordas

I think it's pretty cool. Ben Lund who founded Connotea works there now, btw. - Euan

Booh! It's in flash. A no-no in my book. - Ricardo Vidal

I found the enormous CPU-guzzling Flash off-putting too. - Neil Saunders

http://cambridge.academia.edu/... Do these guys upload everybody they find outside in advance to make them sign up? http://cambridge.academia.edu/... - Attila Csordas

Its kind of cool but I don't really see what it adds to the ecosystem really. If they were prepopulating then I can see it becoming useful but if they are expecting people to add their own details I very much doubt they will get much uptake - there's other commentary at http://friendfeed.com/e/668537... and the link in that item - Cameron Neylon

"prepopulating" thx for the perfect term Cameron. That could work actually: are people tempted to edit their own Wikipedia entry if somebody else set it up already? Everybody is at least still an expert in 1 thing: his/her own narrative history and biographical details. - Attila Csordas

Hi Attilla - that's precisely it, I think I got the term from somewhere else, probably a discussion with Michael Nielsen I think. See also: http://blog.openwetware.org/sc... and Richard Akermans most recent blog post http://scilib.typepad.com/scie... - Cameron Neylon

Attila - Wikipedia specifically asks people not to edit their own Wikipedia entries. - Michael Nielsen

Michael, thx, I didn't know that specific policy but obvious enough..for controversial celebrities. What I referred to with 'temptation to edit your own preinstalled profile' is that ordinary scientists probably will contribute to their Academia.edu preprofile if they check it and that's why the 'prepopulating efforts' might be successful. - Attila Csordas

Flash turns the web into television (Glyn Moody). - Bill Hooker

@Attila, not sure prepopulated profiles are good protocol. A scientist may not want to be associated with a specific site or service. - Ricardo Vidal

I think Ricaardo is right about affiliations, the catchword is multiple or the more catchy "interdisciplinary" associations now. But cool project, nomnetheless. - Aarthy

Absolutely - I do not want to be associated with Thomson ISI and want all of my information taken out right away! Seriously though, if it's publically accessible information then I can't see how they can object - worth putting in a 'this profile automatically generated' banner somewhere though - Cameron Neylon

Ricardo, make no mistake: I didn't say that academia.edu's prepopulating concept is 'ethical', on the contrary it seems problematic to me too, but I wanted to say that even if it is 'ethical' or not, it seems like a useful business trick to attract people to the site as it could be a good bait for them. We shall see. I am not tempted at all to sign up. - Attila Csordas

Whether or not it is ethical (prepopulating) it is illegal under terms of data protection legislation, etc. Thankfully. By the way, Noam Chomsky's on there now (academia.edu, that is). And Richard Dawkins - Maxine

Prepopulating reduces the activation energy of contributing. But if a search hits a prepopulated entry, it should display the minimal details to make it recognizable then allow for a user to claim it as their own. That in itself raises interesting questions of identity verification. It's more like, we know you are out there, and we know some things about you, but we're not saying what until you give us approval. - Todd Harris

I still don't see how a site could legally prepopulate with someone's details if that person had not indicated willingness to sign up. Chicken and egg? - Maxine

Sites like this http://www.biomedexperts.com/P... have prepopulated with "my" public details/without my consent and though I used to be annoyed, now I just shrug. It will always be out of date but may suffice as a search result for some. - Heather

It depends on what details they use - I've always been thinking about sites using information from abstracts, which is all I think that BioMedExperts uses, for instance. Technically speaking I guess Medline, Thomson etc are in violation of the UK data protection act. Thinking about it - most journals would be as well for holding email and work addresses. But my view is that if its on a public website it is in the public domain - the question is who allowed it to go on the website in the first place. - Cameron Neylon

A&I services like Thomson et al. are not in violation because what they are publishing are abstracts (content) of journals. Any site that prepopulates with personal data is in breach of not only UK but international data protection and data privacy legislation - legally, a website is "published" anywhere it can be downloaded or accessed, so you can sue a website from anywhere you can see it (not where its servers are based - this is no protection in law apparently). Early days yet for internet law, but any "publisher" that is taking personal details and displaying them without consent is liable to be shot down at some point, so it probably is not worth anyone putting any effort into a site that is doing that (capturing people's information without their consent). Academia.edu is quite properly asking people to sign up befor