Heather - Comments

The Life Scientists: Alejandro Montenegro

Which one would you say is the BEST Real-Time PCR thermal cycler?

Depends a lot on your use. We've settled for an Eppendorf Mastercycler for our needs, but the Roche is very good as well, (as are the machines sold by Applied - painful soft, though - and BioRad, and it depends what you want it for. - Heather

The Life Scientists: Ami Iida

eLab Genetics :Gene therapy technique slows brain disease : http://www.scientistlive.com/Europea...

Thursday - Comment - Like - Share

kanagarajadurai, Khader Shameer and Ruchira S. Datta liked this

Also see: http://network.nature.com/people... (if I may put in a plug). - Heather

I'm tired of the same article.however I have impressed upon your web pages and open wet ware, immediately bookmarked it. - Ami Iida from email

Mr. Gunn to Mr.'s feed, The Life Scientists

I need some feedback/career advice.

November 8 - Comment - Like - Share

Bora Zivkovic, TheIndustryStandard, Meryn Stol and 23 other people liked this

Many of you know I've been working with Mendeley as a sort of ambassador/community liaison. I started this because I've always felt a little shut out from contributing to open science/open access/open data because I don't work for a publisher, don't really write code, and wasn't in a job where I could openly share data. This was a way to influence how things develop by promoting the people who "get it". - Mr. Gunn

41 more comments

I had to quit for the "real job" a little while back and found not only that I had more time to work for Mendeley, but that I started getting other offers/opportunities also. - Mr. Gunn

Now I've got a newborn daughter and am liking the time I can spend at home with her, which raises the following conundrum: Can I do more of this community liaison work for companies that support/promote open access and put my research career on hold, or is there not any future in this? - Mr. Gunn

Can I trust the friends and colleagues I've met on here to be able to have a real discussion with me, keep me honest, and tell me if I'm backing the wrong horse as I take on more clients, or would I be considered a sell-out? Would people believe that my opinions still come from me and my experiences, or would people just think "You're only saying/supporting that because they're paying... more... - Mr. Gunn

Do you think there's room to grow in this kind of role or am I just wishfully thinking that I can make my own job in this tough economy and get to spend time with my daughter too? - Mr. Gunn

I really believe this is a way I can contribute to changing how science is being done, opening up the process, disintermediating scientific discovery, and all those noble sounding things, but do you buy it, or do you think I'll not only become corrupted by money but lose my relevance because I'm not really doing science anymore? - Mr. Gunn

Can I help companies that don't quite get it to improve and become better and more responsive to their community of users or will I lose touch? - Mr. Gunn

I will be saying nothing works better than inspiring people by setting examples, I will not go with holding my research career even it is not working well as long as I have passion for discovering something. But there are certain realities and money is one of them. Ambassador/community liaisoning is other way to contribute back to the science, but it will be too early to give up your... more... - Abhishek Tiwari

Mr. Gunn. You can absolutely do so, but as you note, you cannot do this with one client. It will have to be a consulting/pundit role (you should probably have a chat with Paul Miller at some point http://cloudofdata.com). The life science industry will be challenging given the limited opportunities, and in this economy, this will not be a walk in the park. As to whether you have to be... more... - Deepak Singh

And we'll tell you if you're being an idiot. It also depends on what you really want to earn. You're not going to get rich doing this, at least not quickly. - Deepak Singh

Abhishek, I could cite all the times when I've recommended Papers or Zotero instead because it really was better for what the person was looking for as evidence that I don't always have to say what the official line is, but that wouldn't illustrate all the discussions I've had where the company point of view _became_ my point of view. This is exactly the kind of discussion I want to be... more... - Mr. Gunn

Thanks Deepak. I know you will, and I'm not looking to get rich. I'm looking to do work for people I believe it, be a force for good, and at least for the moment, spend more time at home with my daughter. - Mr. Gunn

Mr. Gunn, it will only taint it if you let it, although there will people who'll always be skeptical. As long as you are honest and present your point of view rationally, you'll be fine - Deepak Singh

I'd like to think that being open and transparent online helps illustrate my biases, too. - Mr. Gunn

Way outside my area of expertise, but I would think the "consulting/pundit" thing that Deepak mentions would involve lots of travel, especially to start. Not sure how conducive that is to spending more time at home... - Andrew Su

Andrew, missed that bit. There would be a fair bit of travel - Deepak Singh from iPhone

Tough call MrG. I'm not concerned about you selling out, plus I will call you out if I think you are sliding into that trap (as, I'm sure, will the rest of the FF posse). My larger concern would be whether you can make a living that way. Is there a more regular (but part-time) gig that you could get to buffer the difficulties of forging a new path? For instance, do you write easily and... more... - Bill Hooker

Having a part-time gig would allow you more freedom to take risks and experiment, and could be phased out as and when your liaison/consulting work grew. - Bill Hooker

Bill, that's a really great idea. My current commitments are only part-time, so having something more steady would both help the bottom line and insulate me from selling-out criticism - "I don't need to do this." Please, put me in touch. - Mr. Gunn

the ultimate evidence for or against bias is behavior, would such a position restrict or inhibit assuming a critical perspective? - Mike Chelen

What fun would that be, Mike? I just wanted to do a sanity check against my friends and colleagues here to make sure that at least some of them would promise to call me out if I started to not make any sense or drift away from the principles of openness this community takes as a fundamental principle. - Mr. Gunn

Interesting situation! My take is that people who have no history of interaction with you, will not spend a lot of time looking you up online. As soon as they know you're being paid to do this, you'll be a sales rep - which means there isn't even any need to look you up, they already know who/what you are. Thus, IMHO, no online history will get you out of the sales rep box. - Björn Brembs

I agree with Bill's suggestion, and also his non-worry about bias. Or rather, we're all biased, but you don't come across as a sell-out company mouthpiece to those who know you, so you can let that slide. Bjorn isn't tender, but he's right. Either way, you won't change it by adding on more opportunities to be a facilitator. And forging your own path to be more with your family - having been there, I would say you won't regret it later. One always has career regrets, but that's because we only have one life. - Heather

Mr. Gunn. A full time liaison for a company will effectively make you sort of a sales rep. I have been a sales rep myself - which was a valuable learning experience, but I suspect, like me, not one you would fit comfortable into for a longer period of time (several years). When I left university, my friends and colleagues told me that I had a time-limit of 1-2 years to get back into... more... - Nils Reinton

Thanks, Nils, Heather, Björn. My intent is not to work full-time for a specific company, and I'm not doing that now. My intent is also to talk more about ideas and trends and less about specific products. Although I do spend a fair amount of time recommending Mendeley, I think Zotero shares their mission and I just personally prefer Mendeley. I used Zotero to write my first paper and it came down to me just wanting a desktop, full-screen app instead of their browser add on. - Mr. Gunn

Björn - We all have our various reasons to believe what we do and say what we do. In my role, I'm not being paid to say anything or to have a certain opinion. In fact, I think where I disagree with the Mendeley guys is more valuable to them than where I agree, because what they're basically paying me for is my insights as a scientist who knows the field and keeps current with... more... - Mr. Gunn

I know I can't speak for anyone, and I'm not appointing myself spokesperson, but if I spend a lot of time listening to, talking about, and synthesizing ideas, and I can also effectively market those ideas to people who need to hear them (that is, companies who want to listen and adapt), isn't that a win? Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in? - Mr. Gunn

"Couldn't that be my way to make a positive contribution to open access and linked data and personalized medicine and these causes that I already believe passionately in?" YES, absolutely, you are already doing this very well. If you can make a living out of it, I salute you :-) - Nils Reinton

Perhaps consider not just consultancy for companies, but also undertake work for public sector agencies (major libraries or funders), charities or not-for-profit companies. - Frank Norman

Mr. Gunn - sure I think such a person would definitely be worthwhile to us! I was referring to people who do not know you: if you approach them and tell them you work for company X, my bet is that most of them will think "ah, he's a failed scientist trying to get me to use their products". Of course, this doesn't stop people from using company X's products (or sales reps would die out... more... - Björn Brembs

this is a great thread, Mr. Gunn, cheers for starting it, very interesting points, everyone; I would like to second Nils and Frank, and I think that some journals might also be interested in your advice (and community liaison work) and that this would certainly be a great service for anyone near to being an OA and linked data addict - isn't this a pretty wide range of users? we might create a list of arguments that you might wish to choose from when talking to journal publishers - test them on me ;-) - Claudia Koltzenburg

Mr Gunn...you might know me from the ChemSpider system. For almost 3 years ChemSpider was run as a "for the community" project at my cost. i.e. My wife and kids lost a lot of access to me, despite the fact that I worked from home. It did NOT pay any bills...it just about covered costs. No, I was a consultant for a number of companies and worked hard for them, traveled a lot and used my... more... - Antony Williams

OT b/c it's blog not job related *but* I would cite this FF thread at some stage in this one. http://ff.im/YB4p from Feb '09. - Graham Steel

Nils, thanks! Frank - that's a great idea. Can anyone put me in touch with someone at one of those agencies/companies? Björn - I see what you mean. Online rep doesn't translate offline automatically. Claudia - I've got a series of arguments, gleaned over the years from participation here and elsewhere. Can I send you an email? Antony - yes, I'm familiar with your work, and I have a... more... - Mr. Gunn

Mr. Gunn, one thing I've noticed in recent conversation with doctors (not academic MDs) is that most do not know much at all about OA, aren't sure what to make of a statistics-rich, data-driven science environment (or how to connect that data to actual human patients), and are leery about packages being hawked to them. Many are similar to me in age, meaning they didn't grow up in a... more... - Mickey Schafer

Well, I see myself being able to help in explaining these issues, but I don't think I'd get too far hawking products. I'm just not that kind of person. - Mr. Gunn

Even products you truly believed were worthwhile? - Jack (a.k.a. Jeber)

Yeah, I just don't think I'm the salesman type. I think I'm more effective developing ideas than products. - Mr. Gunn

You don't have to be a salesman to develop products. Product development requires a better understanding of customer needs than anything else out there. Being a product manager was one of the most satisfying jobs of my life - Deepak Singh from IM

Mr. Gunn -- I wasn't suggesting that you represent product -- actually, I was thinking more in terms of a "knowledge broker" -- the slow adoption of some technologies (whatever they may be) is often b/c the persons needing the tools don't know how to evaluate them -- sometimes, they may not know how to evaluate their own needs. Having an expert who can help someone understand the landscape, help them make choices based on needs (as opposed to sales pitches) is a very valuable resource. Just a thought! - Mickey Schafer

Another area that is worth looking at, though probably represents a short term play, is that there are lots of people out there putting out calls for tenders to do small research projects in the Social Media/Publishing/Data/Science space. Again its patchy, and not regular but with some reliable money coming in from e.g. editing and writing this kind of work could do two things, firstly... more... - Cameron Neylon

MrG, did you get my email? I sent it to a gmail address that I have listed for you in my address book. - Bill Hooker

Yes, I got the one you sent and I really appreciate it. I do plan to follow up when I get back into town. - Mr. Gunn

References Wanted: Daniel Mietchen

Brain Behav Evol 1989: Gyrification in the Cerebral Cortex of Primates - http://content.karger.com/Produkt...

November 6 from Bookmarklet - Comment - Like - Share

http://is.gd/fPLI - Thanks! - Daniel Mietchen from Bookmarklet

4 more comments

Sorry, no access. - Björn Brembs

Yes, that really seems buried. Thanks for trying, though! - Daniel Mietchen

not even as hard copy - Kubke

no access here either, sorry - Ian Simpson from twhirl

Likewise none, sorry! Keep looking, folks. - Heather

Heather

Modern technology saves the day - or at least, one's motivation - http://network.nature.com/people...

November 10 from A Developing Passion - Comment - Like - Share

This is the future. There's no way to achieve the sort of reduction in carbon budgets that we are going to be forced into without a severe reduction in energy-intensive travel. Online conferences are here to stay, so the better we become at them, the better it will be for science. - AJCann

And the better that conference organizers get at disseminating them, the better for all - since there are people who would not dream of enrolling otherwise, but it can boost attendance numbers and attract more sponsors thereby (thinking, exhibit hall). - Heather

Miss Elle to Miss's feed, Science in the long run, Science 2.0

Do any of you know anything about science outreach/science educator type positions? I'm a high school science teacher (degree in chemistry, picked the teaching cert. up after college) who thinks she'd be more useful as a science outreach educator. I have no idea how to make this happen, however, so I'm asking anyone I can come across.

November 7 - Comment - Like - Share

Heather, imabonehead, FFing Enigma (aka Tina) and 'Like' robot (frɐnc) liked this

I am sure you could make it happen but am not sure how you would get paid to do so. Start perhaps by talking with your local science museum, or a local college or university, who could have you coordinate a community outreach day to start? you'd have to build up some credibility in that role, so starting small is likely to be a good idea. - Heather

I'd get a list of Science Museums. The one here in St. Paul does a lot of education programs in house and outreach to the schools civic etc - WarLord

Heather to Heather's feed, The Life Scientists, Science 2.0

Liked: Shining a light on dark data - http://dmm.biologists.org/content... by Chris Patil (http://friendfeed.com/mycopha...) and Vivian Siegal (editor of Disease Models and Mechanisms).

November 5 - Comment - Like - Share

Paul Bacchus, Mr. Gunn, Greg Tyrelle and 5 other people liked this

"We are increasingly keeping scientific records in electronic form; it would be straightforward to wrap our notebook pages describing an orphan result with a bit of searchable text, generate a web page, and submit the whole thing to a database. The act of conducting research would thus become practically synonymous with the act of disseminating the resulting knowledge. Along the way, we would have to spend some energy improving the records that we keep in order to ensure that our notebooks were more accessible to outside readers and less like the quirky private diaries they often become." Heh. - Heather

.. and if this could result in a proper citable reference on the other end, that'd sweeten the deal :) See e.g. Jean-Claude Bradleys comment near the top of this thread, about 'dumping' data to Nature Preceding to get a reference + DOI in return: http://friendfeed.com/the-lif... - 'Mummi' Thorisson

References Wanted: Björn Brembs

http://www.mitpressjournals.org/doi... to bjoern@brembs.net - thanks a lot!

October 28 - Comment - Like - Share

on the way - Neil Saunders

Thanks so much! I'd be so screwed without this room! That alone is worth keeping FF alive as far as I'm concerned. On the other hand, a 'references wanted' mailinglist could also do it, if need be. - Björn Brembs

Anyone wonder if, should FF finally disappear, the new Lists function on Twitter might be helpful as a backup for Refs Wanted? We could make it a "public" list. Not sure the turnaround would be as fast, because no alternative notification as far as I know. Maybe one day one can follow parallel lists or something, in real time. - Heather

Noah Gray to Noah's feed, The Life Scientists, Science 2.0, Science Online, Science News

A site dedicated to non-OA article sharing leads to an est. saving (loss) of $1.4M. Nature articles=most-requested - http://www.ispub.com/journal...

October 28 from Bookmarklet - Comment - Like - Share

'Mummi' Thorisson, Wobbler, Dan Freeman and 11 other people liked this

"This method of accessing data is highly effective, but issues are raised. Ethical issues and financial implications are the most important. N-OA journal publishers should recognise the problem, research its size and implications, but the discussions must occur in the open access area." - Noah Gray from Bookmarklet

10 more comments

Thanks to Gavin Baker from Open Access News for posting this. - Noah Gray

"Other users who have access to those journals then download the requested articles from those journals, and make them available to the requester by posting the articles either into the forum or to a publicly-accessible web site." IMHO this sort of redistribution is problematic, unlike e-mailing them directly to the requester. The latter's fair use, the former's republishing (for the ex-website). However, the study itself is thoughtful and interesting. - Heather

I would be very interested to know which website is being referred to in this Manuscript, and whether or not, it is still functional. - Graham Steel

me too... - Noah Gray

Me three... anyone got a connection to the author? - Bill Hooker

One pq "One might argue that, while $1.4M is a sizable amount, this is spread across 2,867 journals and conference proceedings, so the loss to each journal is not substantial. In addition, there is, ironically, a benefit to the journals: their articles would possibly otherwise go unseen and uncited". On average, that = $488 @ Journal... - Graham Steel

@Bill - Nope, but "IT Health Ed can be contacted via e-mail: kmasters@ithealthed.com" - Graham Steel

$488/journal is considerably less than the page and colour charges that most of 'em levy, on average, against a single article... [edited for clarity] - Bill Hooker

I like how it's handled in the references wanted room here, one step removed from posting the file itself, but it is unwieldy and lacks searchability. - Mr. Gunn

John Timmer's story in ars technica about this: http://is.gd/4Hk9a - Noah Gray

Thanks, Noah. Interesting comments thread too:- http://arstechnica.com/science... - Graham Steel

References Wanted: Heather

Fwd: A site dedicated to non-OA article sharing leads to an est. saving (loss) of $1.4M. Nature articles=most-requested - http://www.ispub.com/journal... (via...

Fwd: A site dedicated to non-OA article sharing leads to an est. saving (loss) of $1.4M. Nature articles=most-requested - http://www.ispub.com/journal/the_internet_journal_of_medical_informatics/volume_5_number_1_52/article/opening-the-non-open-access-medical-journals-internet-based-sharing-of-journal-articles-on-a-medical-web-site.html (via http://ff.im/aEm6b)

October 28 - Comment - Like - Share

HT Noah Gray - Heather

References Wanted: Sally Church

http://www.ncbi.nlm.nih.gov/pubmed...

October 27 - Comment - Like - Share

Unbelievable - they wanted $15 for an old Science magazine article :( - Sally Church

2 more comments

Email http://is.gd/fH7i please, many thanks! - Sally Church

On its way. But it's not so old? - Heather

Well earlier this year but old as in not current. Thanks, Heather. - Sally Church

The Life Scientists: Brian Krueger - LabSpaces

Fwd: Is it inappropriate to thank god at the end of a scientific talk in the acknowledgments? (Student in lab did, boss atheist)

October 15 - Comment - Like - Share

Pierre Lindenbaum liked this

I'm not devoutly religious, but I think this is a issue of free speech. My boss says that the university works hard to keep god out of all communications, but I think that's more of a business matter. He's since told the student that its wholly inappropriate and unprofessional to thank God. - Brian Krueger - LabSpaces

17 more comments

I'm not overly religious as well but I agree with your group leader here. To me, it's not so such much a matter of free speech but more a breach of professional ethics. I also disagree with political statements being made in scientific presentations. People attend scientific talks for the science, not the presenter's political or religious views. There are plenty of other channels (and contexts) more suitable for that purpose. - Ricardo Almeida

I agree that it's a bit of a question of what is appropriate. The student should be made aware that such a statement will make the majority of his/her audience highly uncomfortable. What if s/he had said "thanks in particular to my main squeeze for that really great blowjob last night, that relaxed me for this presentation" - it would be out of place, as well, and make listeners uncomfortable. On the other hand, I'm uncomfortable with an outright ban on thanking God per se. (And I'm atheist, too, FWIW.) - Heather

While in general I agree with Heather, It could also be cultural. In some cultures, it would be perfectly appropriate to do so and no one would even notice unless someone went on a rant - Deepak Singh

Haha, I'm not sure the support someone receives (or at least the perceived support), is comparable with a blow job :P This is a very religious person, so her perceived support from God is extremely high. I also don't think it's preaching, but maybe others would. It's just a personal statement, and if she feels it's appropriate, then how can I have a problem with it? - Brian Krueger - LabSpaces

if the talk was about Evolution, it would be a problem :-) - Pierre Lindenbaum

Or about Richard Dawkins :) - Deepak Singh

I've only seen this happen at the end of dissertation defenses, where there is a little more leeway given to the acknowledgements section. It's unclear from the OP whether or not this was the case? At a "normal" talk it would be a little weird for sure. - Jason Winget

I say inappropriate, according to both science and religion. "And when you pray, do not be like the hypocrites, for they love to pray standing in the synagogues and on the street corners to be seen by men. I tell you the truth, they have received their reward in full. But when you pray, go into your room, close the door and pray to your Father, who is unseen. Then your Father, who sees what is done in secret, will reward you." Matthew 6:5-6 - Chris Miller

(FWIW, I'm an atheist, but enjoy quoting the bible to make a point to religious folk) - Chris Miller

So is it wrong to thank god when a long and boring talk comes to an end? :-) - Eric Jain

Hah hah - I think Heather hit the nail on the head here - the student was giving a talk, not receiving an award, so thanking God is just as weird and unprofessional as thanking your Mum and Dad. I think the student has misunderstood what the acknowledgments section is for - for attributing the work done and advice given (and hopefully God himself has not been contributing directly to the science). - Ben Blackburne

Don't ban it. I'd rather know who among my colleagues is prone to belief without evidence. - Bill Hooker

There should no censure on what students say in presentations- better to have the discussion on what the presentation is "for" and whether inclusion of personal beliefs / opinions furthers this aim (we're scientists right?) - Richard Badge from Nambu

Eric++ ! :-)) - Pierre Lindenbaum

I have zero problem with thanking god at the end of the talk... I would notice the author presenting a slide with results carved in rock on a mountain and present that as his scientific results... - Egon Willighagen

Acknowlegements in talks , thesis etc are where speakers / presenters get an opportunity to reveal aspects of their personality which their science may not convey so its not uncommon to see people thank their base jumping buddies, their cat , parents etc so I see no problem with people thanking God either. - Hari

Base jumping buddies? :) - Deepak Singh

+1 Hari. - Chris Lasher

References Wanted: Pedro Matos

Looking for http://www.nature.com/nrmicro... thank you

October 16 - Comment - Like - Share

on its way. - Heather

thank you! - Pedro Matos

References Wanted: Jim Hardy

Metabolism of prednisolone by the isolated perfuse...[J Steroid Biochem Mol Biol. 1991] - "PMID: 2069869" - http://www.ncbi.nlm.nih.gov/sites...

October 13 from Bookmarklet - Comment - Like - Share

email to http://is.gd/4iv52 please - Jim Hardy from Bookmarklet

3 more comments

No luck. More direct link here: http://www.sciencedirect.com/science... - Heather

@Heather, thanks for the direct link. @Jim, check yer email :-) - Graham Steel

Thanks to Abhishek, who also sent it to me! So if Jim, you didn't get it through Graham or Abhishek... drop a line. - Heather

Heather, got it. Thanks a lot. Jim H - Jim Hardy from email

References Wanted: Heather

Another one of mine - and the corresponding author is now dead. http://www.springerlink.com/content... once more, to http://is.gd/mailto:...

October 15 - Comment - Like - Share

Strange, when I put the is.gd link, it's automatically translated back into what it was originally? At least on my screen, and mouseover refers to the shortened link. - Heather

Sent. - Bill Hooker

Thanks to both Bill and Abhishek! - Heather

References Wanted: Heather

My own article :-( http://www.tcmonline.org/article... - please send to http://is.gd/mailto:...

October 15 - Comment - Like - Share

Sent -- but it's humongous, so let me know if your email (or mine) chokes somewhere along the way, and I'll ftp it to a super secret location and email you the address. - Bill Hooker

Thanks so much, Bill. It came though just fine. - Heather

Heather to Heather's feed, The Life Scientists, Science 2.0

What do you think of LabCollector? Have you heard of it? Other lab management software to which you are partial, with easily implemented "module" templates that already have been drawn up by someone? http://labcollector.com/index...

October 12 - Comment - Like - Share

Paul Bacchus, Claudia Koltzenburg, george and Mary Canady liked this

First glance ... not bad, OK UI but interesting feature set - Deepak Singh

We are giving it a try here and had time to evaluate it. Not bad given similar tools cost an arm and a leg. However they could improve their user interface a little bit more to look more web 2.0. They seem to focus on easy deployment setup on Windows platform while in reason sense, you need a *nix deployment setup - george

I'm sure that's a marketing decision, but I'd have been happy to have a *nix setup, true. It would have been another good reason to keep the dual-boot of which only I ever make any use. Sigh. - Heather

The Life Scientists: Chris Patil

Has anyone used Web 2.0 tools like FriendFeed, Twitter, etc. to initiate or implement collaborative science? I'm writing a series of pieces about new technology in scientific communication, and I'd love to talk to someone who's actually used these sorts of tools to do actual science. Let me know!

March 6 - Comment - Like - Share

george, Oliver Schuster, Mary Canady and 22 other people liked this

If you'd rather take it straight to email, you can email me at the address listed here: http://ouroboros.wordpress.com/about... - Chris Patil

22 more comments

And by the way, this is for a journal, not my blog. - Chris Patil

example: http://tinyurl.com/63vurc - Pierre Lindenbaum

Thanks Pierre. I will definitely follow up with the people involved in that thread. Keep 'em coming, folks! - Chris Patil

I'm not sure this counts but the biogang (http://biogang.openwetware.org/) was sort of founded/created via Twitter/FriendFeed interactions. Lots of projects there. Also, the bioinformatics survey was also propelled by T/FF if I recall. - Ricardo Vidal

Jean-Claude Bradley started a spreadsheet where he wrote this kind of information : https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

See also this post: http://friendfeed.com/e... - Pierre Lindenbaum

This is really amazing, you guys. Thank you. JC, the spreadsheet is incredible. - Chris Patil

There are so many examples on discussion boards like ScientistSolutions, Molecular Station, etc. (Disclaimer, I work for SSI). I could give a you a list of at least 50 specific threads on our site. Here's a recent favorite http://www.scientistsolutions.com/t8853-h... - Rusty Bishop

I just added to the spreadsheet re: the help I got with CSV munging shell scripts earlier. Would discovery of papers through social bookmarking be considered collaborative science? - Mr. Gunn

@Mr. Gunn - no, i don't think so. Collaboration suppose to be productive - if discussion about papers within the group brought all participants to consensus that could be collaboration via social bookmarking with discussions. But bookmarking sites don't provide discussions. Even they would, it will take for a long while for scientists to start discuss about papers online - simple online collaboration. My thoughts also here - http://hematopoiesis.info/2009... - Alexey

Chris - Carmen Drahl made a nice video showing how FriendFeed is used to collaborate with scientists (second vid on the right) http://pubs.acs.org/cen... - Jean-Claude Bradley

Pierre - thanks for posting the spreadsheet - it is nice to see these little projects get re-use - Jean-Claude Bradley

Concretely, the References Wanted room (http://friendfeed.com/rooms...) has really been useful in writing up articles so I can rapidly get my hands on hard-to-come by references in journals to which my institution does not subscribe. But I'm not sure this is a great thing to bring up in your article, except in a vague way; we're not quite clear which side of the law participating re-distributors are on (fair use, or not?) It's not quite the same as discovering papers as per Mr. Gunn. - Heather

Sci-Mate is a very recently opened collaboration to develop Web 2.0 tools for the benefit of researchers. http://www.sci-mate.org/ - Christopher Dyer

Check out: http://www.dental.pitt.edu/informa... - Heiko Spallek

I have recently started a project shared on a wiki + google code + zotero but it is still early days http://openwetware.org/wiki... - Pedro Beltrao

open notebook science should qualify, thinking about usefulchem as example of wiki and google spreadsheets like http://spreadsheets.google.com/ccc... - the list on wikipedia is helpful http://en.wikipedia.org/wiki... - Mike Chelen

I Added the GeneWiki paper in Jean-Claude's spreadsheet https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

Chris - if you are asking for a more technical answer - UsefulChem and the ONSchallenge run mainly on a combination of wiki/blog/Google Spreadsheets - Jean-Claude Bradley

Pierre - thanks for the addition - Jean-Claude Bradley

Maybe this is where Google Wave will turn out to be useful once we all realise that we're not flying around Beginners Island naked like in Second Life ;-) - Sally Church

Sally - do you have a link to the island where everyone flies around naked? Sounds like fun :) - Jean-Claude Bradley

Of course I'm naked but my feline fur hides that pretty well - Jean-Claude Bradley

References Wanted: Sally Church

Looking for this: http://www.nature.com/nm... and the accompanying editorial: http://www.nature.com/nm...

October 14 - Comment - Like - Share

I signed in but still couldn't see beyond the first paragraph. Email http://is.gd/fH7i please, many thanks! - Sally Church

Done - on their way. - Heather

Wicked cool, thanks Heather! - Sally Church

Heather

Back to school - http://network.nature.com/people...

August 15 from A Developing Passion - Comment - Like - Share

Mike Chelen liked this

Thanks, Mike, Can't say I like it much myself, given I still have to prepare for it. :-) - Heather

hehe, well the writeup is a helpful summary of the differences, the educational systems can definitely sound rather complicated :) - Mike Chelen

References Wanted: YGC

http://www.natureprotocols.com/2007...

September 24 - Comment - Like - Share

Email guangchuangyu@gmail.com , thanks! - YGC

Sent - looks good! - Heather

thanks - YGC

Heather

Big day - http://network.nature.com/people...

October 9 from A Developing Passion - Comment - Like - Share

Mike Chelen and Claudia Koltzenburg liked this

congrats :-) - Claudia Koltzenburg

thanks, Claudia. Big relief. She gave her talk again today in our seminar series, much more relaxed, it was pretty good indeed! - Heather

References Wanted: Bill Hooker

Global Incidence and Epidemiology of the AIDS Pandemic, Distribution of HIV Subtypes, and Epidemiology of Hepatitis C Infection Among HIV-Positive Individuals in Current Clinical Neurology - http://www.springerlink.com/content...

October 9 from Bookmarklet - Comment - Like - Share

cwhooker AT fastmail DOT fm - Bill Hooker from Bookmarklet

2 more comments

No can do, Bill. - Graham Steel

Yeah, this is a tough one, a book chapter. Thanks for trying. - Bill Hooker

me, neither ;-( - Heather

Mike Chelen to Mike's feed, Bioinformatics, Science 2.0, OpenSci Info

Bio-Linux 5.0 — NERC Environmental Bioinformatics Centre - http://nebc.nox.ac.uk/tools...

September 7 from Bookmarklet - Comment - Like - Share

DanDan, Cass Johnston, Endre Sebestyen and 18 other people liked this

"A dedicated bioinformatics workstation - install it or run it live. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base." - Mike Chelen from Bookmarklet

31 more comments

Neat idea- but how much of the 4gb USB stick remains for holding data / analyses: need a bigger stick? - Richard Badge from Nambu

This was one of the first (and probably best) of these distributions (think there was a BioKnoppix at one time?) It's been around at least 6 years. But a software suite is only half the battle. The biologist needs to know how to use the packages, store and interpret the output. Which is why we have bioinformaticians and IT staff. I've never been convinced that "bioinformatics on a stick" is much use to biologists compared with expert advice/support, but I may be wrong. - Neil Saunders

Are these targeted towards biologists, or informaticians? Don't see biologists getting much use from such a distro, but do see computational types making good use - Deepak Singh

Target market is what has always confused me. I'd assume that bioinformaticians are happy to install their own software locally and for biologists with limited tech skills, a live CD doesn't help much. But I'm happy to be proven wrong by success stories. - Neil Saunders

I gave it to one of my students - we'll see what he has to say. - Björn Brembs

Neil: making the software easier can help decreasing repetitive tasks, allowing more efficient use of expert advice and support, which is definitely the most valuable and scarcest resource. newcomers can often manage to boot the OS and start playing with some software, and experienced users can check if their software of choice is included, and save a little time when setting up new machines - Mike Chelen

Deepak: looking at the package list http://nebc.nox.ac.uk/tools... some favorites of both fields stand out, for example a biologist may run a BLAST search regarding a DNA sequence they are studying, while an bioinformatist could develop applications with Bio-Java and Eclipse IDE - Mike Chelen

Richard: data could be stored on a network drive, or a larger flash disk could be used, since there are 8, 16, and 32gb USB sticks available now pretty inexpensively. also, additional USB drives can be plugged in limited only by the number of USB ports on the machine - Mike Chelen

Björn: cool, would love to hear how useful others find it. the software packages can also be installed in current Ubuntu systems by adding their repository http://nebc.nox.ac.uk/tools... - Mike Chelen

Follow on question? Would a VM be equally useful? For example, I use VMs a lot to learn stuff and configure environments. - Deepak Singh

Deepak: yes absolutely! for exactly the reasons you mention, experimentation and reliability. found a VirtualBox VDI image: http://friendfeed.com/bioinf... any more formats such as VMware or EC2 AMI would be great too :) - Mike Chelen

there's a bunch of good EC2 AMI's that I will be highlighting either here or somewhere else soon (from familiar names), but more the merrier - Deepak Singh from IM

@bjorn please do get your student to feed back to NEBC, a long time ago Bio-Linux was my baby and my full time job. It's come a long way since I left it and I'm very happy to see that it's still going. It has its rough edges, and things which could be done better, but out of the box it's a well set up system ready to go. It's already been used as the base for other more focused... more... - Daniel Swan

@Neil with Bio-Linux I can happily say that we turned a few biologists into informaticians, and one into a programmer when I was with the team! Even last week a biologist walked into my office, asked me to help it getting up and running in VM on his laptop so that he could do some work. The Live-CD version was really just a distrubution method, we used to send out a bootable cd-rom that would netinstall a Linux image from our servers. Inefficient at best :) - Daniel Swan

Good to hear. I remember when NEBC were setting up many years ago, Dawn contacted me regarding compilation of Phred/Phrap under Cygwin after I mentioned it on Nodalpoint. The early days of the bioinformatics social network! - Neil Saunders

Deepak: thinking about combining the Bio-Linux packages with some of the standard Ubuntu EC2 AMIs from http://alestic.com/ since they are optimized already, and contain other common tools - Mike Chelen

Mike, that would be brilliant. Lots of our customers ask for starting points in this space and being able to point to something that they might be familiar with would be great. Let me know when you do that. I am thinking about writing up a post on all the available bioinformatics AMI's on AWS - Deepak Singh

Mike - you might want to talk to Tony Travis about this (ajt@rri.sari.ac.uk) he has interests in taking the Bio-Linux base in a more 'cloudy' direction, and I'm sure Dawn and Bela and co. at NEBC would be happy with any feedback along those lines. - Daniel Swan

Deepak, getting the bio-linux packages installed can be done with a bash script http://github.com/mchelen... and maybe used with runurl http://alestic.com/2009... or to generate an AMI - Mike Chelen

Daniel, almost all the packages install okay, are there any particular applications that would be important to test? here is how the desktop looks on ec2: http://ff.im/8fb8j - Mike Chelen

Great idea. Anything to reduce the tedium of wget; ./configure; make; make install is welcome and helps lower the entry barrier for people into the field. - Todd Harris

Todd: it would be nice to start an instance with the least manual input, especially when running a particular application. for example software set up to use a biology AWS dataset http://developer.amazonwebserv... - Mike Chelen

<-- pure biologist, willing to install on top of current Ubuntu to give it a try. Agree with Todd on extra installs. I essentially only use a java-based app to chomp on big files, also Bioconductor on rare occasion. Neil's point about need for expert advice is well-taken, but I find that a biologist, willing to use a linux platform, right away gets more targeted feedback when asking for help. - Heather

Heather: that's great, did you find it easy enough to add the repository? here's a script that can save a little time, it is only a few lines though: http://github.com/mchelen... - Mike Chelen

The ideal way to install the repository would probably be a .deb containing the apt sources and signing key. This is used for example with Ubuntu One https://one.ubuntu.com/support... and PlayDeb http://www.playdeb.net/updates... (expand the instructions). Maybe someone could prepare this given the existing NERC repository info? - Mike Chelen

Deepak: the Bio-Linux image from JCVI http://www.jcvi.org/cms... really looks great, anything that helps this project can benefit other researchers interested in running bioinf software on EC2. maybe a repository mirror within EC2/AWS cloud, or a public AMI, would help too? - Mike Chelen

Mike that is a public AMI, ami id is ami-6953b200 - Deepak Singh from IM

Deepak: found the wiki page now http://sourceforge.net/apps... thanks! - Mike Chelen

anytime - Deepak Singh from IM

does this image include a desktop environment? the screenshot sort of looks like remote x. in most cases that is probably best, it could be nice to have a desktop version as well. thinking about slower internet connections, where some compression (such as freenx) is usually needed for remote desktop - Mike Chelen

Not sure, you'll have to ask Bioinfo ... My guess is no, since I think it's built on a server image, but I could be wrong - Deepak Singh from IM

Deepak: that's good, been trying to find a way to get the bio-linux packages installed on 64bit instance. desktop could be handy for learning and testing - Mike Chelen

Cesar Sanchez to Cesar's feed, The Life Scientists, Biology

Britain's Nobel winner condemns science funding reform - includes flat bicycle tyre and elaborate Swedish prank - http://www.guardian.co.uk/science...

October 8 from Bookmarklet - Comment - Like - Share

Deepak Singh, Jan Aerts, Tom Walsh and 4 other people liked this

"When the head of the academy came on the phone, I said, 'I don't know who you are, but you certainly have a good Swedish accent.' - LOL - Cesar Sanchez from Bookmarklet

3 more comments

I like the new spelling: "rhibosomes". From article: "The three scientists were awarded the prize for making detailed atomic maps of "rhibosomes", the complicated biological machines lurking inside cells that translate genetic code into complex life, from bacteria to humans." - Cesar Sanchez

An editor who got them mixed up with "rhizomes" probably. - Heather

They've fixed that already - Andrew Clegg

though "ribosomes" still has quotes around it which I'm not sure is entirely correct... - Cameron Neylon

Hilary to Hilary's feed, The Life Scientists, Science 2.0

The Tranche Project - citable sharing of large datasets: https://trancheproject.org/about...

October 6 - Comment - Like - Share

Andrew Perry, Jill O'Neill, Heikki Lehvaslaiho and 11 other people liked this

"Tranche is a free and open source file sharing tool that enables collections of computers to easily share data sets. Designed and built with scientists and researchers in mind, Tranche can handle very large data sets, is secure, is scalable, and all data sets are citable in scientific journals" - Hilary

11 more comments

The hashes seem to be a bit long to use as references, though... - Jan Aerts

Hook'em up with DOIs for referencing, like peanut & jelly in a sandwich... - 'Mummi' Thorisson

This is the endorsement from Nature Biotechnology that they mention on their website, Democratizing proteomics data - http://www.nature.com/nbt...: "The lack of raw data sets associated with proteomics and molecular-interaction papers is a long-standing and pernicious problem[...] This has begun to change, however, with the advent of the International... more... - 'Mummi' Thorisson

Jan - +1 on the hash URLs; would be good to at least have a URL-shortening alias thingy on there, like FriendFeed offers. - 'Mummi' Thorisson

even better if it were a preservation-quality redirector such as an ARK or handle - D0r0th34

what's different between DOI and ARK? long hashes are aren't too bad since a search URL... more... - Mike Chelen

Exactly - the short URLs would just be for convenience: DOI registration for each dataset would be a natural extra component to add to this system (along with a few other features I can think of, like feeds for new/updated datasets, OpenID login etc.). - 'Mummi' Thorisson

BTW from dict.org: tranche = ' a portion of something (especially money)' - 'Mummi' Thorisson

@Mike - apparently an ARK (Archival Resource Key, http://www.cdlib.org/inside...) does something akin to what a DOI does in terms of identifier persistence and whatnot. An ARK is an actual URL, whereas DOI by itself does not specify the resolution protocol (hence the http://dx.doi.org resolver service). Not too clear on in which domains ARKs are used, have never actually come across one of those in my work. - 'Mummi' Thorisson

Mummi: wonder if the hashes could be resolved by multiple servers as well. thanks, that helped explain things a lot. - Mike Chelen

Thanks for sharing, Hilary! Looks ideal for sharing of raw data from high-throughput sequencing, which has been a problem for us across multiple sites. And tranche in French is a slice of whatever - in the case that best springs to mind, brioche. - Heather

So the hashes contain an MD5 and an SHA-1 and an SHA-256. Hope the rest of the system makes more sense :-) - Eric Jain

References Wanted: Heather

Can anyone access Cell Tissue Research? for the following review: Biogenesis and function of fibrillin assemblies. Ramirez F, Sakai LY. Cell Tissue Res. 2009 Jun 10. http://www.springerlink.com/content...

October 8 - Comment - Like - Share

http://is.gd/44C5n - Many thanks in advance. - Heather

sent! - Björn Brembs

w00t! thanks, Björn. - Heather

References Wanted: Daniel Mietchen

Hippocampal volume as an index of Alzheimer neuropathology - http://www.neurology.org/cgi...

October 7 - Comment - Like - Share

http://is.gd/fPLI - Thanks! - Daniel Mietchen

2 more comments

No access either, sorry! - Heather

Sent, while sitting in UCL library .) - Andrej

It arrived safely - thank you! - Daniel Mietchen

References Wanted: Sally Church

Looking for: http://jco.ascopubs.org/cgi...

October 7 - Comment - Like - Share

Email http://is.gd/fH7i please, many thanks! - Sally Church

Amazed we had access. On its way. - Heather

Michael Nielsen

PLoS Biology: Real Lives and White Lies in the Funding of Scientific Research - http://www.plosbiology.org/article...

September 14 from delicious - Comment - Like - Share

Robert Spekkens, Cesar Sanchez, Geoff Wozniak and 31 other people liked this

"The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group... They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking." I agree with much in this article. Some years back I constructed a list of papers I especially admired, and was surprised to discover that with only a few exceptions they were produced from unfunded research. This was sobering, since it suggest that receiving research grants was (at least according to my judgement of scientific quality) anticorrelated with doing work of the highest quality. Grants seem to be good at sustaining an established area, but not very good at all at producing the conceptual innovations that start new subfields. - Michael Nielsen

12 more comments

It's very clear that some scientists are just really good at getting money - good salesmen I guess, like you say. They are not always the best scientists yet seem to do well in the jobs market, as universities love scientists who bring in money. - Sarah Kendrew

"She looked for a job in science publishing or in the granting agencies—both of which, ironically, offer better working conditions and much better security of employment than research." - Duncan Hull

Depressing - Rajarshi Guha

@Rajarshi Good to see the issues given a higher profile though... - Duncan Hull

@Duncan, oh absolutely. The idea of long contracts (5 - 7 years) makes sense. But these approaches will really require systemic changes - even if I could get by with small amounts of money (say for 1 student), the university won't like the fact that I'm not bringing in gobs of money to pay for electricity - Rajarshi Guha

I agree with Duncan that although the situation is depressing (and quite accurately represented in there), seeing it gain higher profile is refreshing. - Daniel Mietchen

Pushing these issues more and more is vital if we want things to change - even if we don't agree on the solutions, awareness of the problems is a prerequisite for change. - Björn Brembs

Interesting that similar sentiments have been expressed earlier in engineering. See my write-up Individual and Empire in Academics (on a research article) http://unrulednotebook.wordpress.com/2008... - Arunn

To be nitpicky, I'm afraid that the following suggestion is as open to abuse and laziness as the current one: "Everyone should get slotted into a funding category and assessed every five years. If you're productive, you get five more years of resources. If productivity is down, you are moved down a category. If it is high, you can apply to move up. Starting PIs are in a different... more... - Heather

Hmm. can't write English today. The suggested improvement to the system is subject to abuse, as much so as the current system - dead wood will be carried along. No room will be made for younger people moving up the ranks. And I meant "effective". - Heather

Lest we forget: http://www.nytimes.com/2008...: "Trained as a biochemist, Dr. Prasher, 57, was interested in the chemistry of how certain animals are able to glow. In the late 1980s, he applied to the National Institutes of Health for a five-year grant to track down the fluorescent protein gene...'I knew it could serve as a genetic marker and it would be really, really useful, which it has turned out to be.' That application was turned down..." - Richard Klancer

Michael Nielsen wrote above: "Some years back I constructed a list of papers I especially admired, and was surprised to discover that with only a few exceptions they were produced from unfunded research. This was sobering, since it suggest that receiving research grants was (at least according to my judgement of scientific quality) anticorrelated with doing work of the highest quality.... more... - Bora Zivkovic

I don't have a blog post about it. To make the judgement I used a large fraction of what I know as a scientist. I couldn't easily reduce that to a short list of criteria. - Michael Nielsen

Heather › Comments