Anna Croft - Comments

#iip11 RT @DrVes Only 8% of doctors say online research done by patients is helpful http://www.ama-assn.org/amednew... via @amednews

March 12, 2011 from Twitter - Comment - Like - Share

Steve Koch liked this

surely that's often because the source information is so poor, or behind pay per view walls. - Anna Croft from BuddyFeed

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Indeed, Anna. I tagged that tweet with #iip11 which is the tag for this forthcoming event:- http://www.iip-symposium.info/ - Graham Steel

Wouldn't it be great if 8% of doctors did online research? - Steve Koch

There's a nurse practitioner that I like seeing and she will actually pull up research and read it with me. Amazing. - Steve Koch

A link or two about the online habits of physicians: http://www.ihealthbeat.org/Data-Po...; http://xnet.kp.org/permane...; http://www.ncbi.nlm.nih.gov/pmc... -- there are more, of course! These seem to... more... - Mickey Schafer

@Steve, I'm with ya. @Mickey, thanks for the links. Much appreciated and just the kind of stuff we're looking for ;-) Will alert @ilk21 (Isla Kuhn) who's in charge of the event. Your input fits in nicely with the Background Reading page:- http://www.iip-symposium.info/backgro... - Graham Steel

Anna Croft

Google Global Science Fair 2011 - http://www.google.com/events...

March 12, 2011 from Bookmarklet - Comment - Like - Share

Get involved anyone you know ages 13-18. If you're a teacher/lecturer then you can be a judge! - Anna Croft from Bookmarklet

Anna Croft

First impressions of .@colwiz (http://www.colwiz.com/). Nice idea if I were just starting out, but I already have my endnote and papers libraries set up; google calendar working fine (for me and my group), academia.edu page and a webpage. I also don't have time to spend reimporting all this information and fixing the bugs :/

March 11, 2011 - Comment - Like - Share

suelibrarian liked this

Could have potential with a critical mass of users though. - Anna Croft

Noel O'Boyle

Computational Organic Chemistry » News from Science Online 2011 - http://comporgchem.com/blog...

March 4, 2011 from Google Reader - Comment - Like - Share

Marie, Ruchira S. Datta, Pawel Szczesny and Cameron Neylon liked this

"I was greatly taken by the lack of risk-taking being expressed by so many people in the crowd. Academics young and old were advising to be careful with your blogging, tenure and promotion is solely driven by publications and grants, worry about a comment leading to some sort of retribution. People were advocating for the anonymous comment, the pseudonym-using blogger as a way of protecting oneself from the unnamed backlash that would destroy a career." - Noel O'Boyle

10 more comments

amazing. NIH blocks Steves Bachrachs blog :( - Rajarshi Guha

What, how, why?? - Egon Willighagen

how, by filtering. And why, who knows? - Rajarshi Guha

Rajarshi, more details please! - Bill Hooker

Not much more details than "You have attempted to access an Internet site that NIH has identified as a security threat or inappropriate for government use* - I had no idea comp ochem or Steve was so subversive :) - Rajarshi Guha

Rajarshi, please let us know how they respond when you ask them to fix the glitch... - Egon Willighagen

I often get those at work due to lack of proper file endings or something. It can be due to something about the validation of the page rather than the content itself. - Cameron Neylon

@Rajarshi: Sounds like you are "risk-taking" by reading about comp ochem! Steve would be happy. :-) - Noel O'Boyle

@Noel: it didn't seem to destroy Bruno Rossion's career despite the comment here on some poor student's blog: http://phineasgage.wordpress.com/2007... [and the student probably got waaaay more traffic] - Anna Croft

it turns out to unblock Steves blog, I need to fill out a 4 page form! I think I'll skip it. Aah, the joys of government .... - Rajarshi Guha

Blog, blog, blog, blog! Oh, and please pass around the forms...we'll fill it out for you... so curious what the next hurdle will be :) I mean four forms... that can only be just the start... will you need CIA clearance? An oval office stamp... who knows... but I want to know :) - Egon Willighagen

Cameron Neylon

Parallels my wondering whether I should get out of academia...so I can do more and better science... from @kubke: http://buildingblogsofscience....

February 20, 2011 from Twitter - Comment - Like - Share

Daniel Mietchen, Meryn Stol, John Dupuis and 7 other people liked this

but isn't it frustrating to think that the solution is to 'leave' academia? what is it about academia that hinders 'good science' and why cannot that be changed from within? I wish I had an answer. - Kubke from BuddyFeed

36 more comments

I'm not sure that academia doesn't lead to good science. Rather, the environment is not always to ones liking. And for some it can be difficult to do good science in that environment. For others, it's not a problem - Rajarshi Guha

I agree with Rajarshi, up to a point. I think the systems we had in place are no longer valid and have resulted in either a sense of complacency, false entitlement or sheer lack of understanding of what it takes to get science done. If academia is essentially limiting your need to explore and discover (which the system ensures it does) then we have a problem - Deepak Singh

I've seen a lot of this "Science sans academia" meme recently (http://www.nas.org/polArti... http://blog.devicerandom.org/2011...) but I'm still puzzled by how it might be made to work sustainably and independently of academia. Is there anyone who's actually proposing something workable, or better still a way of hooking up these like-minded individuals? - Dan Hagon

Dan, I don't have your answers but I have been thinking about the same questions (and I left academia 18 mo ago). Kubke says "it is not business that I am not into: it is the traditional business models I don’t like and I don’t fit in" -- and I think there is at least part of the answer. Imagine if a biotech type business answered not to a thousand faceless shareholder factions, all... more... - Bill Hooker

@Bill Hooker hits the point I think. What/who are we compromising 'for'. Big pharma? That is not for me. Big journal publishers? that is not for me. Scientific secrecy? That is not for me. But I don't seem to be given a choice, given the current assessment measures. So I wondered whether we could learn a thing or two from companies like Catalyst IT whose products are open source... more... - Kubke

It has to be a mix. There is no one way. Making money is a good thing. It encourages innovation, and it's good in the long run. The reason there has been so much innovation in internet technologies and sequencing instrument technology is that there was a profit to be made (the same goes for semiconductors, etc. On the other hand, there is a need for scientific discovery with no profit... more... - Deepak Singh

@Deepak innovation is also driven by giving away for free - as I think you can see from our discussions here, what do we imagine we will be able to discover when taking any capitalist glasses down - for some change? - Claudia Koltzenburg

@kubke: thank you for your blog post! "are the academic systems open enough to embrace that change?" I think this is an interesting question vis-a-vis your (defensive?) statement "I don’t have an intrinsic problem with science being commercialized. It is the ‘for money’s sake’ that does not engage me." seems to me that one generation of flashback might bring up a few points here: I have... more... - Claudia Koltzenburg

[disclaimer: pushing again over the edge] I see this "no apetitite for risk" that Deepak mentioned in majority of _discussions_ like this one since 2008. Is anybody here willing to actually step out and try anything in practice? Anything, maybe only on a side, such as forming non-profit, starting open consulting, starting co-working space for science nerds, or whatever else (OK, maybe... more... - Pawel Szczesny

@Claudia Not sure I understand you well. Just like business models, there are different ways to commercialise. For example, should a medical school do research to try to find a cure for cancer? I think yes. Should those findings be commercialised? I think yes, it should be available. Should the University be doing that commercialisation? I think no. I think Nat Torkington says it best:... more... - Kubke

Having said that, I am all for the universities 'giving away for free'. I started Uni under dictatorship and as we were shifting to democracy there were massive discussions/movements about the 'roles' of universities and their research for society. We fought hard to keep unis free, autonomous, and for them to be a 'community asset'. I still hold those values. If a University patenting a... more... - Kubke

@Kubke, thanks, re "But I dont see a problem with providing the basic research for it to be possible" my question is if funding that is driven by profit interests should go into Universities, be this for "basic" or any other research. In my opinion, generally speaking, as soon as the for-profit rationale enters the University, many academic concerns as expressed in Mertonian Ethics (or... more... - Claudia Koltzenburg

I was actually thinking along a different slant to be honest. Mostly that the amount of time I spend trying to get (or argue for) money would be better spent working in a place with some clear resource level and a clear strategy to achieve goals I'm interested in. Absolutely take Pawel's point about taking risks tho, the follow up tweet in response to @new299 I said that security and... more... - Cameron Neylon

And in response to @kubke's original comment: What is it about academic that hinders "good science" (or at least lets me get on with what I want to do and am good at)? The business model. - Cameron Neylon

@Cameron do you think that academia has spinned off to a point of no return though? Or could the 'business model' be changed to optimise the use of your (our) time? - Kubke

Some of you might be interested in Open Source Drug Discovery http://www.osdd.net/ - Ruchira S. Datta

I think there might well be shifts backwards and forwards over the next decade. Things are so up in the air here in the UK its hard to tell where things will land. But at the moment there is more interesting and focussed innovation happening in the commercial sector here. I think I'm a little different to you in that its the hard focus that business (including perhaps big business)... more... - Cameron Neylon

@Cameron It was exactly that 'hard focus' that came through in the talks at webstock that got my head spinning. - Kubke

Cameron is exactly right - the more I look around me, the more I see exciting innovation coming out of industry rather than academia. In academia, you need to have already done most of the rearch that you are applying for a grant for. Reason? Metrics and perceived usefulness. To beat the old Oscar Wilde adage to death - we currently know the price of everything and the value of nothing.... more... - Nico Adams

I was about to link to some of the same blog posts as Dan, as this seems to be a recurrent theme (at least within my networks) at the moment. Pawel mentions why don't we take a few more risks? My personal response is that I'm worn out already running the treadmill - I have no energy (or time when I have energy) to start anything creative (or even write job applications) any more beyond... more... - Anna Croft

interesting discussion! one question: how about assessment measures, e.g., @Bill Hooker: do you think those outside academia sound a nicer tune for your creativity than those you heard when still in academia? e.g., @kubke, can you imagine any assessment measures that would not throw obstacles on your road and maybe even power you not only to create but also to follow your best ideas? @anyone else? - Claudia Koltzenburg

@Claudia, there are wins and losses -- the need to fulfil investor expectations does limit what you can do, but I've found business to be rather more receptive to new ideas than academia. That's just my experience though, which is more years than I like to think about in academia but only 18 mo in industry. I am still at the stage of looking around and trying to get as thorough an understanding of the business world as I (like to think I) have of academia. - Bill Hooker

I've definitely found business to be more receptive of new ideas, but I'd like to reiterate that the correct answer is a mix. You need to change funding and expectation models in funding agencies, the VC community, etc. We need to keep the option of monetization open while welcoming and encouraging true commons (not the "academic" only concept which assumes that only academics do science, and kills the ability for one or two smart people to do something cool). - Deepak Singh

@Deepak, re "not the "academic" only concept which assumes that only academics do science" - interesting reservation about the commons concept you see as dominant, could you point me to any proof thereof, should be highly interesting to look into this issue; I also liked your term "expectation model" (new to me) - so what is yours re true commons more specifically, maybe? - Claudia Koltzenburg

A commons in my mind is data and/or software with permissive licensing CC0/PDL/Apache, that allows people to leverage data and code for building new, more useful stuff. Anything low level (raw data, precompetitive data, core algorithms and code) are ideal for this. Expectation model is equivalent to a long term outlook, something I have really learned to appreciate in my current job.... more... - Deepak Singh

@Claudia I am trying to incorporate alternative measures in my academic performance reviews - force the system to evaluate me for what I consider more valuable. For example, I dont report on my H-index or citation rates alone, but also on changes on H-index and citation rates over time. Is a paper cited in a pattern that is different from expected? I am asked to report on IF of... more... - Kubke

Really nice discussion. I've worked on both sides, at a startup and academia. The short answer is that there is no panacea and both have trade offs. The key is to put yourself in a position that minimizes the amount of off-target work necessary to do the things you are good at. My approach has been to try and surround myself with collaborators with complementary skill sets. This can be... more... - Brad Chapman

@kubke: sei grandiosa :) "and try to force the change of focus from within" <-- my applause! this strategy of yours is certainly worth its own extended blog entry plus discussion "force the system to evaluate me for what I consider more valuable" +1 - @all: has anyone seen a personal strategy explained this well? if yes, please point me to it - Claudia Koltzenburg

if there are upsides for leaving academia, what do people perceive to be the downsides? @Rajarshi, while I like the relaxedness of your individualist approach, I fear there is more to say about @kubke's initial questions in political terms, do people feel this is one of the keystones: "a long term outlook, something I have really learned to appreciate in my current job" (@Deepak) - does this chime in with "security"? - Claudia Koltzenburg

btw, which countries and fields are we talking about? countries with English as (one of the) official language(s)? STM fields only? - Claudia Koltzenburg

@Brad, sounds sensible to me :-) has this been easier to achieve in academia or without any "academic rationale" behind daily work? - Claudia Koltzenburg

Tenure or startup aren't the only choices and even within the academia one can find quite a lot of flexibility (if you're... flexible enough). The real reason for my question above wasn't to convince anybody to quit job or something like that - it was to encourage exploration of possibilities/models/approaches Deepak mentioned. Such exploration doesn't happen on a large scale yet, so we don't have many success stories. - Pawel Szczesny

@Claudia well, of course it is still possible I am not given 'tenure' as a consequence :) - Kubke

@Kubke if tenure is what you are aiming at, maybe let us prepare some nice and effective grassroots open science action to support you publicly in case of need :-) has anyone seen this done before? would certainly be a test of the flexibility of "the system" - @Pawel, yes, "encourage exploration of possibilities/models/approaches" and test the flexibility on all sides [nice neoliberal speak, eh?] and care look at the potential losses, too - Claudia Koltzenburg

@Claudia When I was applying for jobs I 'followed the rules' and nothing happened. Ready to leave science I said what the hell and did a CV that "i" liked and valued- got the job. Questions during interview were interesting. So sticking with it. One of the talks at webstock was about 'blogging rules' and how one may be surprised what happens when one breaks them in order to be more authentic. - Kubke

"what is it about academia that hinders 'good science' and why cannot that be changed from within?" -- given this discussion, including of course Pawel's [pushing over the edge] -- why be so sure it cannot? ;-) - Claudia Koltzenburg

This (or at least the abstract :)) looks useful wrt this discussion: http://www.sciencemag.org/content... - Dan Hagon from Android

Anna Croft

Lower Costs and Better Care for Neediest Patients : The New Yorker - http://www.newyorker.com/reporti...

February 21, 2011 from Bookmarklet - Comment - Like - Share

Or how data and data sharing can make a(nother) real difference - Anna Croft from Bookmarklet

Anna Croft

Memolane: a time-line generating feed aggregator; beta available using 'netted' invite code ... - http://beta.memolane.com/login

February 21, 2011 from Bookmarklet - Comment - Like - Share

Cameron Neylon liked this

Seems to be quite interesting. Here is my timeline: http://beta.memolane.com/annakcr... - Anna Croft

Egon Willighagen

oi... 45 minutes between email sent remote, and it entering my #ki inbox :/

February 21, 2011 from identi.ca - Comment - Like - Share

ours can be up to two days (including internally). bring on outsourcing. - Anna Croft

Matthew Todd to Matthew's feed, Orgnet Australia

Postdoc in my lab available from April 1st. Aiming to demonstrate open source drug discovery, in collaboration with Medicines for Malaria Venture. Really exciting and unusual project. Need someone skilled at synthetic organic chemistry, and who speaks and writes well. Details: https://docs.google.com/documen...

January 14, 2011 - Comment - Like - Share

Steve Koch, Mr. Gunn, Anna Croft and 4 other people liked this

Wow, this is moving fast... - Cameron Neylon

Saw this on orgnet. - Anna Croft

Mike Sullivan

Off to Pacifichem in Hawaii. See you in 20 hours. (@ Terminal 2 w/ 2 others) http://foursquare.com/venue...

December 13, 2010 from Twitter - Comment - Like - Share

I'm on a poster (although not there) - it'd be cool if you stopped by and said Hi! to my colleagues :) (Becky Bjork and Catherine Drennan ...) - Anna Croft

Ok. If you know where and when it is, let me know. If not, I’ll try to find it. - Mike Sullivan from email

Jean-Claude Bradley

Mirza PhD defense on the Ugi reaction for anti-malarial screening - http://www.slideshare.net/jcbradl...

December 13, 2010 from SlideShare - Comment - Like - Share

Congratulate him from me! - Anna Croft

Thanks Anna. - Khalid Mirza

Anna Croft

A short note on traceability - http://akcscience.wordpress.com/2010...

December 12, 2010 from A Current Opinion » A short... - Comment - Like - Share

Heather Piwowar, Bill Anderson and Cameron Neylon liked this

I think there is an option within the ORCID framework to include contact information? Or conversely one could infer it from a publication track. Find the most recent paper with that person on it and grab associated email address? Actually a rather interesting set of issues here... - Cameron Neylon

True that you can do traces through previous publication track if necessary, but where the information is limited, this can be an issue - for example forward tracking of unlisted/untracked data (where the researcher themselves has failed to curate - currently an issue). There are a couple of advantages to a deinstitutionalised email address though that I was thinking up after making the... more... - Anna Croft

Egon Willighagen

to all US scientists who are tired of the US political system, you could opt to move to one of EUs top universities... just to make a point

December 11, 2010 from identi.ca - Comment - Like - Share

len hat and Pawel Szczesny liked this

Before or after we shut them down...? - Cameron Neylon

3 more comments

If only someone could fix the US political system... perhaps we could start by stop calling them a democracy, but a lobbiocracy... someone coined that term recently... I like it. - Egon Willighagen

I was thinking of moving out of the UK for the same reason - any suggestions for positions for a mid-career bioorganic chemist and early career cognitive neuroscientist? - Anna Croft

@Anna: well, I did say EU... as they say in the UK, "UK and Europe"... :) - Egon Willighagen

Let's summarize academic position job sites. I know of this one: http://academicpositions.eu/ - Egon Willighagen

Egon Willighagen

open access organic chemistry journal: http://www.mdpi.com/journal...

November 16, 2010 from identi.ca - Comment - Like - Share

Jean-Claude Bradley liked this

Pay to publish though. Better is BJOC: http://www.beilstein-institut.de/en... - Anna Croft

3 more comments

Indeed! And they are doing cool semantic web stuff too... IIRC - Egon Willighagen

Following Anna, only 2 free to publish organic OA journals BJOC and Arkivoc http://www.arkat-usa.org/ - Jean-Claude Bradley

OK, we're going to use this BJOC paper: http://dx.doi.org/10... for unit testing #oscar - Egon Willighagen

Thanx got the pointers! - Egon Willighagen

AJCann to AJCann's feed, Future of Education

Times Higher Education - Research reputation not priority for potential students - http://www.timeshighereducation.co.uk/story...

November 16, 2010 from Bookmarklet - Comment - Like - Share

"Students choose their university on the quality of its teaching and social life, not its research standing. That is the conclusion of new research by the Institute for Employment Studies, which claims that new universities could threaten the position enjoyed by members of the Russell Group of large research-intensive institutions by becoming more attractive to students." - AJCann from Bookmarklet

2 more comments

Not true for parents though. Parents make the choice based on research standing (because this is equivalent to brand) - we have had several pointed questions on open days to this effect, and we see it through the pattern of applications that parents still have a strong influence. - Anna Croft

Not in my experience. Parents are concerned about employability, many are concerned whether emphasis on research will reduce the emphasis on education. - AJCann

Maybe we get different types of parents matched with different types of students :) - Anna Croft

Mackenzie Cowell

SNP PCR + sequencing workshop at BU- $16 per SNP. Just set up my first sequencing order (yay @Genewiz)! http://twitpic.com/3774tr

November 15, 2010 from Twitter - Comment - Like - Share

Anna Croft liked this

Great to hear you got it sorted out! Look forward to hearing more on the results. Keep up the good work :) - Anna Croft

Anna Croft

anyone have experience extracting >1000 starred items from google reader? I read the online helps but obviously the wrong ones as can't find the continuation XML that is discussed. Also wanted to see if could import these links (mostly papers) to Mendeley.

November 15, 2010 from BuddyFeed - Comment - Like - Share

Cameron Neylon liked this

I don't have any particular experience but someone around here ought to. - Cameron Neylon

Thanks Neil - this was much better/more helpful than the other things google turned up for me. Now have my xml, and am ready to parse. Now to see how I can feed the info back to Mendeley ... (no experience [yet] with apis). - Anna Croft

Chris Miller to Chris's feed, The Life Scientists

With the current state of affairs, is it even possible to go straight from grad school to a tenure-track professorial position without doing a postdoc first? Am I wasting my time by applying?

November 10, 2010 - Comment - Like - Share

Mickey Kosloff, Mickey Schafer, Scoble, Alex Scoble and Khader Shameer liked this

Especially interested to hear from anyone who's been part of a search committee. Is my app just going to get tossed to the bottom of the stack, behind all those with postdoc experience? - Chris Miller

11 more comments

Apparently, if you in fields like CS or Statistics you don't need a post doc to get a TT position. I've always wondered why life sciences insist on post-doc'ing. Is it simply due to a crowded market? - Rajarshi Guha

That's the feeling I get, Rajarshi. The NIH boom created way more applicants than positions. They've gotta go somewhere, so we end up with a glut of postdocs (it doesn't hurt that they're cheap). - Chris Miller

The odds are against you, as you clearly know, but I don't see that it would be a waste of time. What's the worst that can happen: you never hear back, but in the meantime you've practiced your application skills (there's no such thing as too much practice for this), spruced up your CV and thought hard about what you want from a TT position and what you want to do once you get there. I say go for it. - Bill Hooker

Be advised, though, that if you do go straight from grad school to a TT slot, there will be a lot of postdocs who want to punch you in the junk. I mean, a LOT. :-) - Bill Hooker

A different thing to consider is that if you get a TT position, the clock starts ticking. You need to get funding and start publishing pretty quickly and you get a lot more (time-guzzling) responsibilities than a postdoc or graduate student. A postdoc has a lot of negatives, no argument there. But there are positives for the future of an academic career - if you do a (hopefully) short... more... - Mickey Kosloff

You make some good points, Mickey. I'm really just discouraged by the state of affairs and think postdocs are a bum gig for anyone. We somehow think it's okay to pay highly trained experts considerably less than the research techs working under them. The insanity of it all is one of the reasons I'm looking around in industry as well. That all said, if you can't beat 'em... - Chris Miller

You can do industry postdocs -- e.g. I know Genentech offers 'em, and they pay OK. - Bill Hooker

Genentech postdoc positions are highly regarded and I hear it's a great place to do science. However, I think it's still too early to tell if the Roche take-over will eventually change the culture there for the worse. - Mickey Kosloff

Or you can just work in industry ... Which is what I did with zero regrets. - Deepak Singh from iPhone

If you can't beat 'em... forget 'em! ..... :) - Shirley Wu

As someone who had an extremely short postdoc before getting a TT (equivalent) postition, I would strongly recommend postdocing before getting an academic job. The experience is invaluable, the pay is (at least in the UK/AU) not much different, and it is one last chance to devote time to research and not all the administrative crap that surrounds it. If it weren't such a short-term... more... - Anna Croft

Decided difference there between US and Aus/UK -- in the US, as best I can tell, typical postdoc salaries are roughly 50-60% of the starting salary for a TT position. - Bill Hooker

Matthew Todd

SciFoo (and how about some more Science Unconferences) - http://intermolecular.wordpress.com/2010...

October 25, 2010 from Intermolecular » SciFoo (and... - Comment - Like - Share

Marcin Wojnarski, Pawel Szczesny, Alex Holcombe and 7 other people liked this

"So many talks at the ACS would have been more interesting if the speaker had simply given out paper copies of their latest paper and given us 10 minutes to read it in silence then 10 minutes to talk about it." - Alex Holcombe

2 more comments

Hey Matt - why not come to the Blue Obelisk meet up next time at the ACS? Keep an eye on the BO mailing list just before conference time. - Noel O'Boyle

Alex++ (a preprint would do fine too...) - Egon Willighagen

I'd certainly be up for a chemistry-themed/populated unconference. Let me know about any plans (and help required). - Anna Croft

Björn Brembs

Have you paid the rent to your university this month? - http://bjoern.brembs.net/news...

October 28, 2010 from bjoern.brembs.blog : a... - Comment - Like - Share

Egon Willighagen liked this

This has been the case for a while in the more cutthroat british institutions. Ours have done the same thing and it is reasonably damaging - I still need to confirm whether the rents charged by the university are above market rate (although I suspect so). It starts to make one think of going independent, since we are headed also towards the style of having to cover our salaries with grant funds. - Anna Croft

I think is the normal practice at Uppsala University too... - Egon Willighagen

Steve Koch

Exp 181-same flasks (ONS Solubility Challenge) -- Google Docs is telling me this page is in Welsh and asking me if I want it translated :) - https://spreadsheets5.google.com/ccc...

October 26, 2010 from Bookmarklet - Comment - Like - Share

Andrew Lang, Pierre Lindenbaum, Jean-Claude Bradley and Cameron Neylon liked this

That's nuffin. GReader keeps telling me it can't translate Bjoern's blog from English to English :-) - Cameron Neylon

4 more comments

Ha! - Steve Koch

well, for a start it should be Fflasc - Anna Croft

Steve I noticed that too - weird - BTW thanks for the detailed feedback for this month's ONS challenge deliberations - Jean-Claude Bradley

You're welcome, Jean-Claude -- I think the ONS challenge is such a great idea and it was fun to look over the notebooks - Steve Koch

lol @cameron! - Björn Brembs

Cameron Neylon

I should point out that shutting up is something I am terrible at (ideally before someone else does)

October 25, 2010 from Twitter - Comment - Like - Share

Kubke liked this

problem is, keeping quiet doesn't get you noticed ... - Anna Croft from BuddyFeed

(O wad some Power the giftie gie us...) In my experience you listen more than you talk, and don't speak up without having something to say. - Bill Hooker

+1 Bill. - Andrew Lang

Cameron Neylon

Some notes on Open Access Week - http://cameronneylon.net/blog...

October 17, 2010 from Science in the Open - Comment - Like - Share

Sandeep Gautam, Christina Pikas, Björn Brembs and 7 other people liked this

Open Access Week kicks off for the fourth time tomorrow with events across the globe. I was honoured to be asked to contribute to the SPARC video that will be released tomorrow. The following are a transcription of my notes - not quite what I said but similar. - Cameron Neylon

7 more comments

You're welcome. Wondering now whether I should lock down my site prior to 9am eastern... - Cameron Neylon

Still think that ADNI is not a flagship example for Open collaboration in general, though it is amongst the best available in the area of psychiatry, neuroimaging and related fields. Exact terms at https://ida.loni.ucla.edu/collabo... . - Daniel Mietchen

It's nice to focus on the many hardly measurable small improvements. - Daniel Mietchen

"The last ten years of the Open Access movement has been about how to make it possible for people to touch, read, and interact with the outputs of research. Perhaps the challenge for the next ten years is to ask how we can create access opportunities to the research itself. This won’t be easy, but then nothing that is worthwhile ever is." - Amen. - Daniel Mietchen

Agree that ADNI is not in itself reaching as far as we would like but it is an example of how what is possible changes when the underlying assumptions about how much to share change. I tried to be careful about how I worded it - can't remember exactly what came out in the video and there will be a few mis-steps. I think I used "public domain" in an unclear way in the video as well... - Cameron Neylon

And the video is now available here: http://www.vimeo.com/15881200 - Cameron Neylon

you made my morning ... - Anna Croft

Well that's a good start. Does that count as impact? - Cameron Neylon

Björn Brembs to Björn's feed, The Life Scientists, Science Online

Dear Lazyweb, how do I get a list of genes, ranked according to degree of conservation between two species? Or, how do I get a list of the most conserved genes in sequence-space of any sequenced species?

October 6, 2010 - Comment - Like - Share

Carl Boettiger, Christopher Fields, Anna Croft and 5 other people liked this

We're trying to find out if our gene (family) of interest is more or less conserved than any other genes with deep homology. - Björn Brembs

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Ideally gene sequences, but proteins would do if need be. It also finds our gene of interest as #3753 when I compare flies and humans. Interestingly, the human gene it finds is a different gene in the same family compared to a genetic comparison. Is there a way to constrain the search to non-housekeeping genes or transcription factors? - Björn Brembs

You think someone might be interested? We're in the process of assembling the data for a paper right now and if the sequence data allow us to make the claim that our gene in question is particularly conserved compared to any run-of-the-mill (non-housekeeping-, or transcriptionfactor-)gene, there may be an authorship in there :-) First author is the graduate student who does our PCRs.... more... - Björn Brembs

http://biostar.stackexchange.com might help you - pn

You can constrain the sequence searches to non-housekeeping genes or TFs from sequenced species using gene descriptions or GO annotations. But significant number of genes from most of the sequenced genome still remains unannotated and that will make the annotation based search limited in scope. If you have couple of protein domains of interest, best way is to run a HMMER search using your domains of interest against 'nr' database from NCBI. - Khader Shameer

Neil, fun graph. Less similarity at high CAIs makes good sense; these are genes that are very well tuned to Drosophila codon usage so will likely either be fly specific or at least have different codon usage in humans. The lower CAI results are less clear. I wonder if this is a sampling bias due to lower numbers of proteins or if there is something interesting about the codon usage at... more... - Brad Chapman

Could this be a statistical distribution? I mean, there seem to be more genes in the medium CAI range and thus the probability that highly conserved genes are among them is higher (similar argument as Brad's). - Björn Brembs

Would it be possible to highlight certain, known genes of interest in this graph? - Björn Brembs

Awesome! Would you do that for me? I'd be interested in transcription factors in general (if possible) and this one in particular: http://flybase.org/reports... - Björn Brembs

There was some recent cool work on something I think is similar by Eric Alm at MIT. - Anna Croft

@Neil: Hmm, interesting! So it doesn't seem to be particularly conserved when compared to all of the genes. So it would be interesting to carve the genome up along annotations. I agree with forgetting CAI, that doesn't look very helpful, for now. - Björn Brembs

I know that InParanoid does nice two-way comparisons, but there are a few other databases and methods out there that do multi-way comparisons and list both orthologs, in-paralogs, and co-orthologs. The OrthoMCL database comes to mind, for instance, but I'm not sure how others view it. - Christopher Fields

Fascinating! Does our gene of interest rank anywhere in particular in the TF group? Are TFs significantly less conserved than the other genes? - Björn Brembs

nan braun

Anyone.bought and love or.hate the new ipod touch??

October 8, 2010 from Twitter - Comment - Like - Share

we like ours. just like an iphone; only no phone. - Anna Croft

yes I have one and I love it to bits!! it is indeed very much like the iPhone without the annoying feature of haivng to receive phone calls on it ;-) The cameras are very low quality (less than 1 M Pixel) but good enough for quick snaps. However, the video is great. Using friendfeed on it is really easy, there is a lovely interface for it from a web page: http://friendfeed.com/iphone... more... - Dr Jo Badge

thanks for the ipod touch feedback. would you consider the camera and new display sufficient for an upgrade to the current ipod touch? consideration especially for a/r application exploration. Agreed- i really love the touch/mifi combination. debating on just holding out a little bit longer for an android tablet... - nan braun from email

Pawel Szczesny to Pawel's feed, The Life Scientists, Science 2.0

Tricky question: if you could secure funding, would you still work in academia, write grants and papers etc? In other words, if money didn't matter, how big your involvement in academia would be?

May 12, 2010 - Comment - Like - Share

Mike Chelen, george, Piotr Byzia and 15 other people liked this

Started out of the question: if your funding didn't depend on papers, would you consider going totally open (in the sense of open notebook science) - which is not that tricky. - Pawel Szczesny

21 more comments

Yes, definitely. I'm certainly not in academia for the money. (Who is?!) - Ruchira S. Datta

Well, I might not write grants--what would be the point if I already had funding? - Ruchira S. Datta

I probably wouldn't bother trying to obtain tenure at a university or research institute or writing grants, but yes I would still write papers. I know this because I am out of work due to illness, but still writing papers, albeit extremely slowly. - Matt Leifer

I'd work in academia because it makes sense to share the core facilities and to be in a community, but yeah, open notebook would be the way to go. - Mr. Gunn

If I had money I wouldn't write grants, probably write some papers, but would aim to get on and _do_ more, or at least make more happen. - Cameron Neylon

If you could take money out of the equation, academia would be what it was *supposed* to be. So if I had secure independent funding, I'd look for an academic environment for exactly the reasons Mr Gunn gives: core facilities and community. I'd still write papers, but mainly as a sort of periodic roundup of data and ideas; my main communication would of course be an open notebook. I... more... - Bill Hooker

I wouldn't. Just prefer the pace of industry - Deepak Singh

for me "being in academia" could be _defined_ as "have insecure funding, write grants, papers etc" or do you define academia as "gradu-stud/post-doc/tenure track position/prof at a research university" ? - marcin

At the moment I am in academia _despite_ having to secure funding. With a fully-funded, tenured post I might be able to actually get something meaningful done. - Anna Croft from BuddyFeed

I'd still write papers - that's the whole point, isn't it? - Björn Brembs

Yes, and write papers, and go open. - Endre Sebestyen

I would perform the science the same way as now, just won't have to bother so much writing grants (= save time to do science !). One thing that would be different is that I would be able to do more risky projects and I would also invest more energy trying to link my work to the world (take philosophical question into account, try to speak more to the general public,...). I mean, all these things I would love to do, but have no time since I need to gather data if I want to be funded another year... - Julien Colomb

The same - I am not doing this for money - I am in academia because it is where I can make a difference that is meaningful. - Dan owns Comicsforge.com

I would go open as far as technically possible - contribute to wikis and databases instead of writing stand-alone papers, and contribute to grant propoals that others (in less stable positions) write in the open, all this on the basis of an open notebook in which much would be recorded that is not fundable nowadays. - Daniel Mietchen

Related thread: http://ff.im/l2HWm . - Daniel Mietchen

I was in a situation like that before I switched careers - I worked in a lab that was funded by proceeds from the horse racing industry. They (the state racing commission) were required by law to devote a % of profits to research. The research was pretty tightly controlled, but we did regularly publish peer reviewed articles. - Elizabeth Brown

To address the ONS question - it might be difficult to have ONS from independent funding, as it can be heavily based on personal connections. If your connections don't want to be public, or the group that controls the money doesn't want the attention, ONS support might be difficult. - Elizabeth Brown

Elizabeth - I haven't come across a funder yet who doesn't want attention to what they are funding :) - Jean-Claude Bradley

Well, horse racing is unusual in lots of ways. My recollection was the commission board didn't want results disseminated before they were "briefed" or any potential negative attention surface. I should add the board was mostly composed of political appointees and wealthy race horse owners, not scientists. - Elizabeth Brown

Jean-Claude, what about VCs funding startups in stealth mode? - Ruchira S. Datta

I love teaching, it's the other parts of academia I don't like. - Piaw Na

I definitely wouldnt work in academia if I had unlilmited independent funding. - Joonas Jämsén

AJCann

UK science braces for impact - but REF sidelined? - http://www.nature.com/news...

May 12, 2010 from Bookmarklet - Comment - Like - Share

"The second key change is the apparent sidelining of the Research Excellence Framework (REF), a complicated formula to distribute millions in research funding throughout the university network that was due to be implemented in 2014. Many researchers have criticized the planned REF for its increased emphasis on scientists having to prove the economic and societal benefits of their work. During the campaign, both the Conservatives and the Liberal Democrats said that they would suspend the REF, pending a review." - AJCann from Bookmarklet

hurrah! - Anna Croft from BuddyFeed

Jean-Claude Bradley

Just received the First Edition of the Reaction Attempts Book http://onsbooks.wikispaces.com/Reactio...

May 7, 2010 - Comment - Like - Share

Bill Hooker and Andrew Lang liked this

It stands up by itself! Also, where is the cat? - Andrew Lang

yay - Anna Croft from BuddyFeed

the cats would not stand still this time :) - Jean-Claude Bradley

AJCann to AJCann's feed, Future of Education

South Australia to 'poach' British students - http://www.telegraph.co.uk/educati...

April 7, 2010 from Bookmarklet - Comment - Like - Share

"The Government of South Australia will focus on the poor job prospects of graduates in Britain – combined with the gloomy weather – as part of a marketing drive to tempt students to universities Down Under. It will take a roadshow around five cities in England in a bid to increase the number of students taking up degree courses at four universities in the state." - AJCann from Bookmarklet

so how come I'm over in the uk then ... - Anna Croft from BuddyFeed

AJCann

Science, Nature Team Up on New Journal - ScienceNOW - http://news.sciencemag.org/science...

April 1, 2010 from Bookmarklet - Comment - Like - Share

Yet another one I'm going to file away under "It would be funny if it wasn't so sad". - AJCann from Bookmarklet

isn't it supposed to be called plos? ;) - Anna Croft from BuddyFeed

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