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Daniel Mietchen › Likes

Mackenzie Cowell
RT @diybio: @biobus is a mobile biophysics lab operated by PhDs w/ fluorescent microscopes for highschoolers running on solar & biodiesel
Brain morphometry
MRI Measures of Alzheimer's Disease and the AddNeuroMed Study. - http://www.hubmed.org/display...
Brain morphometry
Perceptual and Semantic Contributions to Repetition Priming of Environmental Sounds. - http://www.hubmed.org/display...
Duncan Hull
Vocal learning
Human-specific transcriptional regulation of CNS development genes by FOXP2. - http://www.hubmed.org/display...
Vocal learning
Sleep, off-line processing, and vocal learning. - http://www.hubmed.org/display...
Research Funding 2.0
Stephen Peterson
Moon-Bombing Mission Finds Significant Amount of Water in Lunar Soil - http://www.popsci.com/science...
Mr. Gunn
Our Team | World Association of Young Scientists - http://www.ways.org/en...
Our Team | World Association of Young Scientists
"Daniel Mietchen - Open Science Policy Director" Congrats, Daniel! - Mr. Gunn from Bookmarklet
Thanks. As for the site being cluttered, we welcome suggestions. - Daniel Mietchen
Just an initial impression: "Oh, this is a site talking about some initiative. Oh, wait, there's a forum and a place to register so maybe the...wait, here's an activity stream from members!" Seems like the front page is going in a bunch of different directions at once. - Mr. Gunn
You certainly got a point there but the site is indeed an umbrella platform for initiatives that go into very different directions, e.g. http://pyrn.ways.org/ and http://giraf-iffd.ways.org/ , and the parent site aggregates that content and provides the forum to discuss matters of interest across the different initiatives. - Daniel Mietchen
I like what you're doing there, but I think you may want to think about usability. What does a prospective member think when they land on the page? Is the value proposition clear, or will it be just another site they'll have to sign up for, track activity on, etc. - Mr. Gunn
Mr. Gunn
I need some feedback/career advice.
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
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
Michael Nielsen
Polymath and the origin of life « Gowers’s Weblog - http://gowers.wordpress.com/2009...
Tim Gowers has some very interesting ideas for an open science project to come up with a simple theoretical model where self-replication organisms are likely to spontaneously arise. In this post he tries to formulate a question or questions such a project could feasibly attack, and discusses what would count as a success. - Michael Nielsen
I can't do justice to this post here in this short space - the whole post and the discussion thread that follows are both full of interesting ideas - but I think it'd be very interesting to get input from chemists and biologists. The spirit of the proposed project has something of the flavour of the Urey-Miller experiment. - Michael Nielsen
Michael Nielsen
Charlie's Diary: Designing society for posterity - http://www.antipope.org/charlie...
"So. You, and a quarter of a million other folks, have embarked on a 1000-year voyage aboard a hollowed-out asteroid. What sort of governance and society do you think would be most comfortable, not to mention likely to survive the trip without civil war, famine, and reigns of terror?" - Michael Nielsen
An interesting problem. But it seems problematic - if all our institutions (except ay the church) are of approximately single generation time spans, how do you go about hypothesizing that society X will last stably for 1000 years. - Rajarshi Guha
Jean-Claude Bradley
Liz Lyon on Open Science at web-scale - http://usefulchem.blogspot.com/2009...
Make that a 'like, like, like' :-) - Graham Steel
Michael Nielsen
The Law of Unintended Consequences - http://money.cnn.com/magazin...
"From 1992 to September 2003, pharmaceutical companies tied up the federal courts with 494 patent suits. That's more than the number filed in the computer hardware, aerospace, defense, and chemical industries combined. Those legal expenses are part of a giant, hidden "drug tax"--a tax that has to be paid by someone. And that someone, as you'll see below, is you. You don't get the tab all at once, of course. It shows up in higher drug costs, higher tuition bills, higher taxes--and tragically, fewer medical miracles. So how did we get to this sorry place? It was one piece of federal legislation that you've probably never heard of--a 1980 tweak to the U.S. patent and trademark law known as the Bayh-Dole Act. That single law, named for its sponsors, Senators Birch Bayh and Bob Dole, in essence transferred the title of all discoveries made with the help of federal research grants to the universities and small businesses where they were made. " - Michael Nielsen
Highly recommended to anyone with an interest in open science. - Michael Nielsen
Björn Brembs
Language evolution: The importance of being human - http://www.citeulike.org/user...
Nature, Vol. 462, No. 7270. (11 November 2009), pp. 169-170. The FOXP2 gene is implicated in the development of human speech and language. A comparison of the human and chimpanzee FOXP2 proteins highlights the differences in function in the two species. Some genes find instant favour in scientific culture and, like popular celebrities, remain under the close watch of their devoted following. FOXP2 has many of the qualities of an in-vogue gene — relevance to human disease, evolutionary significance and a prominent role in brain development. Martin Dominguez, Pasko Rakic - Björn Brembs
Michael Nielsen
Math Overflow « Combinatorics and more - http://gilkalai.wordpress.com/2009...
Gil Kalai's impressions of Math Overflow, the new question and answer site for mathematicians. - Michael Nielsen
Science in the long run
It is one of the rarest giants of the ocean, and it has been caught on film for the first time.
Science in the long run
Culture Clash – the biopolitics of popular culture - http://2020science.org/2009...
Science in the long run
Impact of home management of Plasmodium falciparum malaria on childhood malaria control in sub-Saharan Africa. - http://www.hubmed.org/display...
Science in the long run
Björn Brembs
Women scientists: biological drive vs. scientific passion - http://bjoern.brembs.net/news...
I think you're underemphasizing some cultural factors: namely, it is FAR more socially acceptable for men to abandon their children 12h/day than it is for women. Likewise, it is FAR more socially acceptable for women to say "I'm giving up on [career] to have kids" than for men. My personal opinion is that until men step up to a fair share of childcare, nothing changes. - D0r0th34
I agree with D0r0th34. Plus, it seems to me that there is something wrong with a career/professional culture that requires these work hours. Perhaps if more people were hired to work in the lab, it wouldn't be necessary for others to take on these work loads. - Katy S
also, "biological drive"? puh-LEEZ, says this no-kids-nuh-uh-not-ever woman. - D0r0th34
This is cultural rather than biological. US and UK are very very poor examples for women in science from what I have gathered so far. I would prefer to see statistics from somewhere like Sweden, which appears to have much more civilised maternity/paternity regulations. - Anna Croft
There's plenty statistics on this, no time right now to look it up, but there are norwegian studies. On the post-doc level I believe we are closing in on 50/50 share between men and women. Maternity leave and social benefits when you have small children do make a difference. That said, I believe that the distribution is skewed towards men when it comes to tenured positions also in scandinavian countries. - Nils Reinton
@D: I try not to emphasize neither biology nor culture. As a neurogeneticist, I find the dichotomy to be useless anyway - which I try to allude to in brackets. Social acceptance is certainly part of the mix. - Björn Brembs
@Katy: I think this is at the core of the issue: where do these long hours come from? Personally, every morning I look forward to coming to the lab and in the evening, I've organized events (sports, social) simply to have a deadline by which I MUST leave the lab. A quote from our prof emeritus here springs to mind: "When I married, I lost my Sundays in the lab. When our first child was... more... - Björn Brembs
@Anna: Of course, childcare is an issue in many cases, no doubt. However, I'm asking myself (as the issue will come up next year): how do I fit a 12-13h workday with a child that will be awake for (at least for some years) less than that time. If I have a child, I'd like to raise it and educate it at least for some of the time and not delegate that to 100% to strangers. Why have a child... more... - Björn Brembs
It might be interesting to look at what arguments emerge from looking at career path figures on men in science who do not raise children (or do any other daily care work for others alongside their jobs) compared to women in science who don't, either. - Claudia Koltzenburg
when they had me, my parents both took a year off, first mum then dad, before doing the daycare thing. that's what I plan to do. @Bjorn I think on average mothers probably do want to spend more time with their baby than fathers, but I doubt the effect is substantial or general. as Nils says, Scandinavian countries are closer to 50/50 thanks to a different culture re ma/paternity leave (though it's far from equal, and maybe it never will be, but i doubt there's any harm in trying). - Christopher Harris
@Björn I could make a number of comments to the nature of 'society' response to this, but given they relate to instances in my current job this is probably not the place (not relating to me in terms of childcare btw). My partner otoh, has indicated he is eager to take on any childcare responsibilities when/if the time comes (and thus considers this extremely seriously) - however, I suspect he is in a reasonable minority. Hopefully this will change. - Anna Croft
Science in the long run
Oil Prices and the Financial Crisis - http://rs.resalliance.org/2009...
The Financial Times suggests that the IEA agrees with Herman Daly (at least a little bit), in  Did oil cause the latest recession? IEA weighs into the debate: A feature in the draft executive summary of the IEA’s World Energy Outlook, which will be published tomorrow, revisits this argument and comes to a rather worrying conclusion. It [...]
Duncan Hull
Research grants: Let’s end this shared madness by Wellcome Trust director Mark Walport, Times Higher Education - http://www.timeshighereducation.co.uk/story...
Applying for a research grant entails an elaborate folie á deux between applicant and funding agency. The applicant describes in meticulous detail a programme of work, half of which has already been completed and the other half which probably never will be, at least not in the way that is proposed. The more original and important the research question, the more likely it is that this future half will never reach completion, because there is no road map into the unknown. There are of course exceptions, such as clinical trials, sequencing projects, epidemiological studies and genetic analyses, where it is reasonable to expect that what is proposed will be carried out. The current peer review process reinforces this approach to the funding of science. Referees and panel members are complicit with applicant and funder in judging the work of fiction that characterises many grant applications. - Duncan Hull
chaz2b
The Origin of Species by Charles Darwin (happy birthday, u were published 150 years ago today) - http://www.talkorigins.org/faqs...
The Origin of Species by Charles Darwin (happy birthday, u were published 150 years ago today)
Scientists' Next Big Discoveries Predicted in Online Report on the 150th Anniversary of "On The Origin of Species" http://www.nsf.gov/news... - chaz2b from Bookmarklet
Yeah just don't forget he recanted his notions on his deathbed. - Aaron Kendrick
Wow, I think I've just spotted a creationist:) You're not even supported by the nutcases over at "Answers in Genesis" on this one, Aaron: http://www.answersingenesis.org/article... - Eivind
he recanted due to pressure from the church, dont judge a man by his dying wishes, :( - chaz2b
thankyou eivind for the link, a great read - chaz2b
Mike Chelen
Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life - http://www.biomedcentral.com/1471-21...
"We describe the system architecture and template design of "Scratchpads", a data-publishing framework for groups of people to create their own social networks supporting natural history science. Scratchpads cater to the particular needs of individual research communities through a common database and system architecture. This is flexible and scalable enough to support multiple networks, each with its own choice of features, visual design, and constituent data. Our data model supports web services on standardised data elements that might be used by related initiatives such as GBIF and the Encyclopedia of Life. A Scratchpad allows users to organise data around user-defined or imported ontologies, including biological classifications. Automated semantic annotation and indexing is applied to all content, allowing users to navigate intuitively and curate diverse biological data, including content drawn from third party resources. A system of archiving citable pages allows stable referencing with unique identifiers and provides credit to contributors through normal citation processes." - Mike Chelen from Bookmarklet
pretty slick - Jean-Claude Bradley
Bosco Ho
The bioinformatic-journal/software hydrid - http://boscoh.com/protein...
Yes, yes. Very much like. - Neil Saunders
Bosco, this is a superb idea. Along with starting up a new journal/software hybrid, it will be great if existing journals insist users to submit source code, executable or VM of a bioinformatics software / database / server to a centralized repository like 'biohub.org'. - Khader Shameer
This is a good idea. - Michael Barton
While not linked to an actual repository (but rather, provides a snapshot of the s/w and data for the article), Journal of Statistical Software, does pretty much this - Rajarshi Guha
I would take this further and the article text remains in the revision repo. The reviewers are sent to the article, not the other way around and it can be forked in just the same way the software can - Frank from iPhone
@Frank, this makes sense, since otherwise the paper would be static and refer to old versions. But then this assumes that as the s/w is updated, so is the paper - Rajarshi Guha
@Rajarshi not neccessarily the paper should state which version/revision it refers to. It does not have to keep up with the sw. That is what documentation is for :) - Frank from iPhone
me likey too - Deepak Singh
The more I think about it, the more I think some big-wig bioinformaticians should do a deal with Google Code to edit a journal. That might even align with Google Scholar. - Bosco Ho
@Frank, in that case, why bother with a VCS? Why not just put a tarball with the source code for the version that goes with the paper? - Rajarshi Guha
Great idea, but I can't see it working for data sets. Yes data sets evolve and should track provenance somehow, but having been in and around standards groups for some time now, this is an impossible task for a publishing group to take care of, especially considering the nature of big-data bioinformatics. Plus if goes against best practices for software source control (use factories, don't store your database...) - delagoya
There are some interesting and non-trivial questions around this kind of idea as to what peer review should look like. Should such a journal provide virtualisation environments so that the code can be run? Example data should be a requirement presumably? Are peer reviewers expected to evaluate code "quality". Anyone thoughts on this would be extremely useful...and help guide a project like this into reality. - Cameron Neylon
My answers to Cameron's points: (1) no, (2) yes, sample data would probably be used to run tests which should pass, (3) quality is somewhat subjective - minimum requirement should be that code runs and generates output as expected - but reviewers could certainly suggest code improvement where appropriate. - Neil Saunders
So if the answer to 1) is no, does that mean that you can't necessarily expect referees to actually run the code? Or compile it? Or just that you pick referees appropriately? Or conversely that "refereeing" becomes a process of building up enough positive comments or karma points in the repository...? It seems to me that you want to bring the best of versioning systems and best practice... more... - Cameron Neylon
Referees should certainly be able to run code - I'm just not sure that virtualisation through the web interface is the way to do it. Seems like an additional layer of complexity that might get in the way of making this idea work. - Neil Saunders
@Cameron & Neil: If it could be figured out how to to handle the virtualization (or having remote access to machines), I think that'd be a highly valuable addition to peer review. Easy for me to say (not knowing how to implement it), but I think it's a great goal to strive for. It doesn't seem too crazy to have the journal have a bunch of machines on hand so the authors can remotely upload / install code and referees could then remotely log in to look at and try out code. - Steve Koch
I can't figure out where to jump into this thread. Personally, I think we just need a place to publish locations, i.e. the code is here, data is there and this is the version we used, etc. That must be maintained and being able to maintain that should become part of the funding process. Since funding agencies are the ones who are funding this research they need to include the ability to... more... - Deepak Singh
My feeling is that being able to run the programs somewhere on a server without downloading them is important - but that is very much a user's perspective. I often look at useful things that are made available and just have no clue how to actually make them work. A good range of downloadable executables would probably do the job for me though. Additional question: what are the standards for web services? - Cameron Neylon
Which is why VM's and cloud services are such a big deal for demo's and provenance now. You can package up a VM with the exact stack that you want and make it available, either as a service or a VM you can launch yourself. It's too easy not to do it - Deepak Singh
@Deepak : Cloud + VM is an an interesting combination, but should have an accessible pricing that is affordable to a larger research community - Khader Shameer
I think there should be strict guidelines while reviewing bioinformatics software / database / servers to test the resource. I had a recent experience : a reviewer wrote extensive list of points to reject a server that we developed with out trying what exactly it is doing or to know how does it differs from other existing resources. I strongly support the hybrid journal model, also it... more... - Khader Shameer
Let's talk specifics. VM images are great, but you are tying your release to a particular release of a particular platform. A better approach is to start from a base OS (like a linus distro ISO) and have a set of build instructions for system set up and application building. My favorite of the moment would be Chef. - delagoya
Second, academics love to solve a problem with a novel algorithm and then move on. In fact it is in their best interest to move on after milking a project for all it's worth, publication wise. Maintenance, or even robust testing (couch... Tophat ... cough ... Bowtie .. cough ) is not even on the radar. Frankly I am not so sure it should be. Maintenance requirements may slow the pace of... more... - delagoya
@delagoya, good point. If I have made significant improvements, why update the old paper? better to try for a new paper! - Rajarshi Guha
delagoya, chef's fine too. Find a common medium/mechanism that works for the community. The resources are certainly there. It's a matter of trying things out. As someone I know says, start simple, and iterate - Deepak Singh
Khader, that's where the funding agencies come in. They need to provide mechanisms for sustainable funding here. - Deepak Singh
The nice thing about a hybrid journal is that it might be possible to have new dois/database entries for "significant" updates. Not perhaps just place holding papers as is the case sometimes in the NAR database issue but when something has changed significantly you can get a new paper without needing a new algorithm or service. I like the idea of funding to support "orphan" code and services as well. Make it worth money and people will do it. - Cameron Neylon
Delagoya - as a naive user I disagree. I really don't want to have to build, I want to use in the lowest stress way possible and a hosted VM seems like a good way to enable that - as well as allow for longer term preservation. We may not be able to run linux on future hardware but will probably be able to handle VMs for longer (actually having written that I'm not sure its true - would be interested in more expert perspectives) - Cameron Neylon
I almost missed this discussion. I really like the idea but I wonder how discovery type projects fit in. I mostly use code to look for trends. If anything I might make some predictor to enhance existing data. For these reasons most of what I do is one off scripts around perl and R. Maybe this sort of project does not belong in a bioinformatics journal at all. - Pedro Beltrao
Pedro, great question. Personally, if we included all glue code, small scripts, etc this would be unsustainable and defeat the purpose of peer review as well - Deepak Singh
@Pedro, I don't see a journal/software hybrid as replacing all bioinformatics journals. I think there's a place for journals that discuss pure algorithms and ideas. These would do exploratory type programming. Normal journals service these papers quite well. For me, a hybrid model targets specifically those papers that describe a program that is meant to be used by other people. In that... more... - Bosco Ho
Bosco, you're thinking along the lines of a communications journal aren't you. And then people can go to work on the code if it is on github or something - Deepak Singh
@Deepak. Yep. The disconnect I see is that pragmatically, it's the open-source project that counts. The article in the bioinformatics journal is so that we can get a place-holder to collect citations that contribute to our academic CV. The journal/software hybrid provides the most efficient way to this goal. - Bosco Ho
Very nicely summary of the problem. Really, the whole concept of a journal article about software is stupid. What does an academic article do? Alert people to a new finding/discovery. But in the case of software - well, the software is the finding. And people are "alerted" by finding it on the web, downloading it and using it. As Bosco says, the sole role of an article here is a CV tick - hence the hybrid approach. Non-academic programmers must find all of this very odd. - Neil Saunders
Michael Nielsen
Barack Obama's Work in Progress - http://www.gq.com/news-po...
Many interesting tidbits on how Obama writes. - Michael Nielsen
Many interesting tidbits on how Obama writes. - Michael Nielsen
Michael Nielsen
Open Knowledge Conference (OKCon) 2010: Call for Proposals - http://blog.okfn.org/2009...
"We welcome proposals on any aspect of creating, publishing or reusing content or data that is open in accordance with opendefinition.org. " - Michael Nielsen
Shirley Wu
Why do some people sneeze when they look at the sun? » Scienceline - http://www.scienceline.org/2009...
I have a mild photic sneeze reflex :) - Shirley Wu from Bookmarklet
I'm a sun sneezer, as are both my sons. - John Dupuis
I don't even have to look at the damn thing -- if I go from shade to bright light and warmth, I sneeze my fool head off. - Bill Hooker
It's all visual as far as I can tell, for me. Just looking at a brightly lit spot if I'm in the shade is usually enough to tickle my nose. I don't think temperature change matters for me. Not sure if it has to be sunlight vs. artificial light, but if it does, that's a very interesting question of "why?" - Shirley Wu from twhirl
It's also called "Autosomal dominant Compelling Helio-Ophthalmic Outburst syndrome", or ACHOO for short ;) - Shirley Wu from twhirl
I'm not sure about temperature either -- I've never tested sudden temperature changes without accompanying changes in light levels, dust levels or something else that could cause the sneezery. - Bill Hooker
Looking at a lightbulb works for me. Thinking about it now it occurs to me that it might be getting less pronounced as I get older. - John Dupuis
I am glad to see that I'm not alone! Never considered the genetics (or not). To me, it feels like the squinting squeezes my upper nose (making it run slightly) and that sets it off. - Neil Saunders
Michael Nielsen
O'Reilly Answers - Ask, Answer, Share - http://answers.oreilly.com/
Question and answer site that brings to it a ready-made community: the community around O'Reilly media. Looks a bit too broad to me, but it'll be interesting to watch develop. - Michael Nielsen
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