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Deepak posted a message on Twitter
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Berci Mesko posted an entry on ScienceRoll
15 hours ago - Link
Ah, (medical) technology evangelism... it's an attractive idea. PS Thanks for the pointer to the Med 2.0 Congress, looks interesting. - Richard Akerman
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Deepak posted a message on Twitter
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Ginger Makela posted a link
If You’re Open to Growth, You Tend to Grow - NYTimes.com
7 hours ago - via Bookmarklet - Link
From the article: “People who believe in the power of talent tend not to fulfill their potential because they’re so concerned with looking smart and not making mistakes... too many companies believe that hiring the best and the brightest from top-flight schools guarantees corporate success...the problem is that, having been identified as geniuses, the anointed become fearful of falling from grace." - Ginger Makela via Bookmarklet
Hire people who can get things done. Not Geniuses. - Muthu Ramadoss
"Society is obsessed with the idea of talent and genius and people who are ‘naturals’ with innate ability,” says Ms. Dweck, who is known for research that crosses the boundaries of personal, social and developmental psychology." - Hutch Carpenter
Piece is so true. Doubtful that most recruiters do it. Sad - Charlie Anzman
reminds me of this Po Bronson article about praising kids for intelligence versus effort. “When we praise children for their intelligence, we tell them that this is the name of the game: Look smart, don’t risk making mistakes.” http://nymag.com/news/features... - David Vasileff
GE, Xerox, and IBM are unconvincing examples. The iPhone example is about selecting for people excited by risk and opportunity, which doesn't confirm anything about "believing in the power of talent". We've all met prima donnas who think they're superstars and mostly spend their time avoiding challenges (look at all those people pissed off by technical interviews which ignore their years of experience) but does it take "three decades of painstaking research" to figure out those people are bogus? - ⓞnor
It's never too late to grow and learn new things. - Bjorn Tipling
I think there is natural ability, but one should try to grow and improve on themselves anyway and become the best that *they* can be, which may or may not be better than others. I feel like I want to fullfill my potential, whatever it may be. I am not discouraged by smarter or stronger people, because it is about me, and not about how I compare to others. - Bjorn Tipling
I feel like in my industry I'd much rather have an army of people who give 100% instead of just a few geniuses aiming low with a sense of entitlement about what intelligence owes them. - Jason Lowe
Yes, I too would prefer cake to death. - ⓞnor
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Matt Wood posted a message on Twitter
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Thursday at 12:55 pm - Link
very good! thank you for sharing - Alexey
Yeah, nice article. - Ricardo Vidal
Blog
15 hours ago - Link
I'm sure that promiscuous, non-functional phosphorylation occurs to a degree. Not sure that I buy the evolutionary argument. Phosphorylation may consume a tiny fraction of cellular ATP, but it's like the "what use is half an eye" question. Over time, would we expect selection for efficient use of ATP and against wastage, no matter how small the differences? - Neil Saunders
that depends on the selection pressure (effect on fitness plus population size). I don't think that there is enough selection pressure to purify most wasteful phosphorylation for the energy it costs. There is also a high turn-over of phospho sites so at any given moment (i.e. present time) there must also be a large number of sites that are under transition. - Pedro Beltrao
del.icio.us
Duncan Hull bookmarked a page on del.icio.us
13 hours ago - Link
John Sulston and Joseph Stiglitz, Times Online - Duncan Hull
How much does Intellectual Property stifle (rather than just protect) innovation? - Duncan Hull
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Ricardo Vidal posted a message on Twitter
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10 hours ago - Link
According to their website “The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain”. This week they are having a workshop in Cambridge, to bring myself up to speed, here is a quick name check of some of the people involved. * Michael Ashburner, University of Cambridge * Erick Antezana, University of Ghent * Colin Batchelor, Royal Society of Chemistry - Duncan Hull
Blog
July 1 at 9:14 am - Link
Thanks for all your help with this so far guys. I tired to make it very explicit that the answers to this will be released into the public domain for analysis. I wasn't sure but the laws here in the UK are some what strict about releasing information people have given so I thought I should try to be as safe a possible about this. - Michael Barton
Any feedback on the legal implications would be welcome. - Michael Barton
I also deleted any previous answers that had been entered so far, because I wasn't clear about how the data would be used. So if you've filled out the survey once, and are happy about your data being released, you'll need to do it again. - Michael Barton
re-posted the form on my blog. - Pierre
http://en.wikipedia.org/wiki/D... should be enough to figure if you're covered. Data is anonymous and if everyone who takes place understands the data is to be released, not sure what the problem would be - Daniel Swan via twhirl
Cheers Dan. :) - Michael Barton
Michael, for Nationality, should I put "American" or "United States"? "American" is geographically (though not practically) ambiguous. Too bad those fields aren't drop-down boxes so the input is standardized and idiot proof. :-( - Chris Lasher
re-posted the survey as well. - Pedro Beltrao
I've only studied bioinformatics briefly but should be eligible to fill out the survey and I may be able to forward this to some researchers I know - Julian Baldwin
Reposted. [this is good] - Bill Hooker
Big thank you to everyone who has reposted the survey. - Michael Barton
@Chris Yes, I agree. I had planned to standaradise nationality with a set regular expressions but a drop down list would have been better. Also if I had used stardard ISO country codes I could have displayed the data on a map using the Google chart API. - Michael Barton
Blog
June 29 at 10:11 pm - Link
That's what I was saying regarding new citation metrics and evaluating the importance of online contributions. Let the feed-forward loop work a little while and the solution will become clearer, but don't stop doing something because there's no obvious benefit in the present. Do what moves you(within time constraints), and the application will come. - Mr. Gunn
Different tools have different advantages. Blogs are great for "real-time" discussions but are horrible at solidification of content (Wikis are best here). Still, a lot of the hits I get for things that are not on the front page of the blog are for people searching for something in particular so blogs + links + search engine work ok at ranking scientific content on blogs. - Pedro Beltrao
Scientific blogging is great networking also, good tool to make connections if you have not enough data/money to go to conference. - Alexey
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Deepak shared an item on Google Reader
Wednesday at 4:00 pm - Link
formal research streaming? - Deepak
Blog
June 29 at 11:59 am - Link
Deepak, I think you're right... there are so many alternatives, more and more every day, that one has to make choices... NatureNetwork has a negative score (for me; that's personal, not general, and up to now): more investment than return. Chemical blogspace/Postgenomic.com: little investment, much in return. Not just data, also ideas. But I agree, it needs to have a positive balance. - Egon Willighagen
Like I keep saying, the data should be social, not the people (or at least, the people later). Absolutely agree with Egon: it's site design that determines the cost/benefit of participation and NN falls down on that point. - Neil Saunders
I, too, have very little time for all these networks, but it is horses for courses. For me personally, Facebook and MySpace do nothing, nor does Twitter. Friendfeed and Nature Network on the other hand are both great for what I do. I'm not a life scientist on the cutting edge of data sharing technology like you guys. Nature Network is an experimental site, and like all these community building enterprises, it is good for some things, not so good for others. It is not, and was never intended to be, a data-sharing site, for example. But, to take an example of its usefulness, many scientists are not very familar with the "social web" (the vast majority of Nature authors for example). Two ways in which they have used NN is (1) online discussion of Commentary material -- they feel a bit safer, I think (guess), commenting in our "News and Opinion" forum there, rather than on the open Internet -- and we've had some interesting views expressed, some of which have been published in the journal as a result; and (2) pre - Maxine
It's also depends on what you get out of a service. Facebook, for me at least, has little to do with science. I am miles away from home, my friends are spread out around the world (people I went to school and college with, as well as family and colleagues). That's the role Facebook fills. But in the scientific sense, the key is how can I get the most with the least effort. In the end, the internal marketplace in the head sorts it all out. - Deepak
It's true, services serve different roles. Facebook serves the role that Deepak described and does it well. I think too that we can learn from the design and code of social websites and apply that elsewhere, even if we're not interested in what the site offers. Facebook's usability is due in large part to Ajax, for example. We're all waiting for the science networking site with the right combination of features, usability and discovery via data. Imagine a FriendFeed-type interface to NCBI, or PDB. - Neil Saunders
Hmm... PubMedFriend? Has anyone invented that yet? - Richard Akerman
... -asebook? for enzymes? - Shirley Wu
This is where something like Pierre's SciFOAF would come in really handy - who do I know that's working on X? - Mr. Gunn
Blog
Wednesday at 10:04 pm - Link
Couldn't agree more. Love it. Should we wait for someone, or just start pushing the boundaries? - Matt Wood
I was just about to get around to that blog post about SNP profiling being a disruptive technology. Was even going to use that phrase, too. We must be reading the same people, Deepak! - Mr. Gunn
Neil and I have made a habit of telepathic blog posts. I should add that for a moment I was tempted to put a picture of a Klingon disruptor there :) - Deepak
I'll add that the technological disruptions are there (I was pretty much focused on SNP profiling in the clinic for the past six months), but how people use those technologies. Also, even with SNPs, the actual clinical utility is still limited (see Eric Schadt's work on needing network analysis etc to supplement GWAS) - Deepak
I've got into a habit of no blog posts; hopefully that will change on return from ISMB. So other than "just go for it", how would someone (practically) begin to drive a disruptive process? Let's say my goal is "revolutionise drug development". Academia is out - such a grant will never fly. So I need to think startup. Write a business plan, win over a wealthy philanthropist? - Neil Saunders
If I knew, I'd be on a beach somewhere :) - Deepak
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Deepak posted a link
Friday at 6:15 pm - via Bookmarklet - Link
I've read a decent chunk, but need to play some catchup - Deepak via Bookmarklet
Interesting list. I'd definitely add my favourite Sci-Fi author, Vernor Vinge. - Michael Nielsen
I think I was happy just seeing my favorite book right on top of the list (I am a big fan of the Foundation) - Deepak
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Deepak shared an item on Google Reader
20 hours ago - Link
Pedro, as usual, is the voice of sanity in all this madness. I also wonder if people would pay some kind of donor fees (like the NPR model) to PLoS? - Deepak
thanks :). They look set to break even in two years (probably sooner if ONE grows faster). What they could do is create a group to handle the research part to develop the tools (hubs, social filtering , recommendation engine) and apply directly for research grants or collaborate with academia research groups. - Pedro Beltrao
The 4 July New York Times piece on the death of the newspaper industry, and "proper" journalism, rejected the NPR model, but that's newspapers. One of the reasons was lack of local expertise if there is a central decision-making/donor system. I don't quite see how that follows. Does this have any analogies in scientific research publishing? - Maxine
We don't need local expertise in research publishing do we :). As far as I can tell there are three models here. A donor model (micropayments essentially), an ad supported model, or upsell services on top of the content. Not sure a "public library" of science could do upsell. Any others? - Deepak
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Pawel Szczesny posted a message on Twitter
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NatBlair posted an entry on The Junction Potential
June 26 at 6:18 am - Link
Amen, brother. - Bill Hooker
While I don't necessarily agree with all your points, I really like your attitude. - Pawel Szczesny
Feel free to lay your perspective out Pawel! I'm all ears. There's nothing like discussion to sharpen one's understanding of one's position. - NatBlair
I like it too, and I think you can mostly ignore the "tellin' it like it is" bluster physioprof adopts. - Mr. Gunn
FriendFeed
June 25 at 9:56 am - Link
I don't know...does slideshare not meet your needs? - Mr. Gunn
Papers is fantastic, great app. Free alternative is: http://ipapers.sourceforge.net... - Daniel Swan
I loved Papers, but I didn't renew my trial account. It made a lot of mistakes when I used the matching wizard, even when I used DOI to identify a PDF. But to answer your questions, I do not know of a similar app. - Kambiz Kamrani
The matching has got much *much* better in recent versions of Papers and I don't have mismatches anymore. Some DOI's don't always resolve, but that's rare. To stay on topic, just how much metadata do you want to associate with a powerpoint presentation? Maybe suck out all the text for searching? Does slideshare do this or is it just tagged? - Daniel Swan
It's a very useful software, but why only on that unusable system? - Pawel Szczesny
@Kambriz, I also tried an earlier version of Papers and didn't like it. The new version is better. - Maureen
Re Daniel's comment, thanks for free link. I give many talks and lectures and would like to sort through a library of slides to select versions of the same slide when composing a new presentation. Had a look at slideshare but it seems more for, well, sharing. - Maureen
@Maureen, ever look at Leap (Ironic Software)? from the makers of my preferred scientific .PDF organizer Yep... @Pawel, unusable? - dsbreak
@dsbreak, Call me frustrated - I don't have mac anymore ;) . But seriously I don't like OSX for many reasons (not enough linux experience - scientific software doesn't work, or installation is painful; unoptimized system and software etc.) and I tried few years to make it work. - Pawel Szczesny
@Pawel, out of curiosity, which types of scientific software have been difficult? wondering if it's one particular field (large scale sequence analysis, structural calculations, statistical packages, etc.) or in general - dsbreak
I love OSX as my desktop system, and ever since I switched my productivity is way up. That said, I have had some trouble getting a lot of MD/modeling apps to work. The strange thing is almost everyone in those communities that I know uses a mac. - Deepak
@Deepak - likewise, most things I want to run under Linux I just run server side. I have quite a few OSX servers though, and I really question it as a server platform - obfuscated enough to be different from Linux and the *BSDs, lovely GUI tools that only address 50% of the functionality. A fragile authentication system. Continued requirement to reboot for minor system updates. apt for os x would go a long way to easing some of my gripes ;) - Daniel Swan
Daniel .. For a variety of reasons, most of which you list, server side for me will always be Linux. But as my primary desktop, I can't think of a replacement for my MB Pro (esp since I am going to install Ubuntu as a VM) - Deepak
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Cameron Neylon posted a link
June 26 at 2:04 am - Link
Will be trying to liveblog over the day here. Will see how it works out. - Cameron Neylon
BBSRC - can give steer from funder perspective but wanting to see community views and also educate where necessary. Interested in understanding sociological perspectives so bringing together the biologists and sociologists in this meeting. What are the key issues for BBSRC in data sharing? - Cameron Neylon
ESRC genomics network - research into sociology of data sharing in the biosciences. Issues of scale, organisation, technology. Social sciences trying to catch up with what is happening - Cameron Neylon
Been a request for me not to use names so I won't. Just report themes and comments. - Cameron Neylon
Research Information Network is starting up a project on Web2 tools in science - how are they useful? - Cameron Neylon
Mix of funders, scientists, sociologists and information managers - interesting group they've put together certainly - Cameron Neylon
Need both the willingness to share data and the tools to do so. NCRI working on systems for linking cancer resources together. Also interested in facilitating cultural change. Also talking to pharma about releasing data and trying to encourage that. Which company was it that made the recent announcement on pre-competitive data being made available? - Cameron Neylon
Is it possible to solve social issues with a technical solution? How to ensure acknowledgement for tool developers. Understanding the social issues associated with ontologies - move from OWL to SCOS(?) - do the possible technical solutions degrade quality? - Cameron Neylon
Idea of putting data sharing statements from grants in the public domain so people can check. How does BBSRC monitor compliance with data sharing. Issues of not very good data - should it be made public. Again we come back to the issue of sharing data that is not peer reviewed...and administrative load and predictability of that load, possible issues with IP that may arise in retrospect. The issue of 'hostile mining' of data e,g, animal experiments, stem cells etc. - Cameron Neylon
Answer back which is what I would have said - its important its out there and then you need a way to assess the quality. Peer review does not gauruntee data quality - Cameron Neylon
Science ethics course described given by scientists, lawyers, ethicists, economists etc - our (scientist's) perspective is just a perspective, and may not be a very good one. Other disciplines have very different (and possibly valid) perspectives. Potential ethical issues in pursuing sharing policies. - Cameron Neylon
Hit squad at NERC which aimed to provide every possible assistance to labs to get data into a database. Would go out, install computers, provide tools, support, be friendly (not sure about making coffee) etc etc. Sounds wonderful! - Cameron Neylon
Comment that the obsession with access control is less in companies (anyone in the company is perceived to have a 'right to see') than it is in academia. Some experiences that access control is more important to people than the tools. Scientists want control of where, how, and who can access their data. Prior disclosure is a serious issues for people coming to data sharing. - Cameron Neylon
Dataverse project- a loose database that can provide the data in reusable form close to the published papers. Interest from sociologists and cancer researchers (came out of WGS and gene expression data) - Cameron Neylon
JISC project to look at economic benefits of sharing data. Work has been done on costs but relatively little on economic benefits. - Cameron Neylon
Publications can't cope with presenting the data in their current form. If a data set is a terabyte, what goes in the paper? Current data transmission is insufficient. Funders not getting value for money. - Cameron Neylon
This was an introductory session with everyone introducing themselves - hence the collection of fairly scattering points - Cameron Neylon
BBSRC background - Data sharing policy: Policy has been in place for just over a year. Complements existing best practice guide for curation of data. 10 year period in a useable form is the BBSRC standard. *Biology is changing, large datasets, increasing use of datamining, increasing focus on QA and metadata. *Data sharing picked out early on as key area for Tools and Resources Strategy Panel, BBSRC should have leadership role in promoting appropriate research culture - Cameron Neylon
* BBSRC does not own data outputs (rights reside with institutions) but as a funder has interest in value for money. Is also a grant applicant (to government) *Development of data sharing policy to be inclusive and researcher led. Took three years over two stage consultation process - Cameron Neylon
From consultation exercise: Data sharing is a good thing! Critical (and well established) in some areas. Data sharing needs very different across different domains. IP and data sharing are tensioned. Should be no central silo. Decentralised sharing is preferred. Data should be close to the scientists (not sure what that actually means in practice - given how this flows into issues with Institutional repositories) - Cameron Neylon
Policy aim has two roles: Enforcement and aspirational signpost. Recognises the cost issues. Point out that data sharing is different to archival particularly with respect to costs. - Cameron Neylon
Other funders take different approaches - e.g. NERC has much more centralised approach. Potentially different issues in different domains. * BBSRC focusedd on big data and long time series but reserve the right to be more prescriptive in specific cases - Cameron Neylon
Where resources exist for sharing they should be used. If there is a need, create something, and ask for funding to do it! In some cases local ad hoc arrangements may be appropriate. * Will meet data sharing costs through FEC * Will provide resources to develop underpinning tools etc - Cameron Neylon
Issues of funding models - can ask for support in grant but will this work - serious problenmss in repositories charging for deposition. Wellcome trust model for OA where they deal with it and pay for it offline (independent from grant). Also a significant issues in training competent people to manage the curation process, where are these people? - Cameron Neylon
Proposals require a data sharing policy which is refereed by external reviewers against their knowledge of best practice. Expected to report at end of project.Now going into monitoring phase. Onus is on peer review of best practice. - Cameron Neylon
Overall good community buy in so far but big disparity in quality of responses. Some consternation. More mixed outside of established data sharing communities. Not much in the way of resource requests. Early days yet! * Challenges - can you measure value for money? Will it effect a sustained cultural change (or just grantsmanship?). Can understanding of best practice consistently applied by referees and panels? Are there barriers we don't know about yet? What unintended effects? - Cameron Neylon
Moving to new item as that was getting long http://friendfeed.com/e/386543... - Cameron Neylon
SlideShare
Matt Wood posted a slide show on SlideShare
Genomes On Rails
June 25 at 11:44 pm - Link
A repost due to the World's Best Presentation competition, now on over at Slideshare. - Matt Wood
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