I program in python (and use NumPy, matplotlib, biopython etc.) and I think it is great. And if you use a modern GNU/Linux distribution with a large package database - like Ubuntu/Debian or Gentoo you don't even need this kitchen sink package. Then the scientific python packages are just one command away. Eg. "apt-get install python-numpy python-biopython python-matplotlib" - Anders Norgaard
I am pretty convinced by now (based on other anecdotal evidence) that Perl's days as being the main bioinformatics language are numbered. - Deepak
@Deepak Really? I'm a Python evangelist and biased, but even so, I do not see Perl prevalence decreasing in bioinformatics. For example, the traffic to the Bioperl mailing list is twice that of the Biopython mailing list. And I wonder if Jason Stajich or someone with OBF can provide an estimated download count. Perl has simply snowballed as the de facto language of bioinformatics and despite my abhorrence for it, some really useful, powerful libraries have been written in it that I wish were in Python. - Chris Lasher
@Chris But what is the rate of new development? - Kevin D. White
@Kevin I don't know. That's a very good question. What metrics could we use to assess this? I can't come up with an apples-to-apples comparison at the moment. - Chris Lasher
Perl in general seems to generate less buzz these days (e.g. see http://www.google.com/trends?q...). But if "amount of buzz generated" is a predictor of future performance, the smart money would be on Ruby... Would be interesting to do a survey of what languages are used at major bioinformatics centers (and elsewhere)? - Eric Jain
@Chris, there is still Perl code around, but a good chunk of it seems like legacy code. A lot of the companies and dev groups that I have been around are using less and less Perl (more Python, some Ruby) - Deepak
Download counts are notoriously hard to measure since one can get code from SVN or as a package from CPAN or from obf site. Website gets about 1M hits a month FWIW. I don't think Biopython should be used as a measure for python in bioinformatics though - it seems like lots of ppl are rolling their own in python and maybe that's the problem? - Jason Stajich
@Jason re: rolling their own. Absolutely correct. This is a major issue that was discussed without resolution a year ago at SciPy 2007. It led to the creation of the Biology in Python list and group. http://bio.scipy.org/ There's been chatter, but it still doesn't feel like a unification of Python efforts in bioinformatics. - Chris Lasher
I don't know about all this Ruby and Python nonsense... but *real* scientific software is still written in Fortran. ;-) - Adam Kraut
Not very surprising and good news for OA. Lower impact publishing would exist anyway even without PLoS ONE and BMC. It is great that by covering the whole impact spectrum PLoS is financially viable. I hope PLoS can now focus their attention on what they set out to do with PLoS ONE, to have additional ways of doing post-publication peer review and promote those articles that deserve the attention. - Pedro Beltrao
My sample isn't very representative but PLoS ONE seems to enjoy a solid reputation amongst my silent (as in non-blogging) peers despite the "light" peer review. - Roland Krause
Yeah Pedro, I would like to see the post-publication review on PLoS ONE, i.e. the comments on the papers, to be emphasized more. That's a killer feature that is under utilized. Similarly, I often link up PLoS ONE articles on my blog and never once have my trackbacks worked... strange, given that PLoS ONE is one of the only journals I know that allows commenting and trackbacks on articles, but the trackbacks don't work. - Kambiz Kamrani
There was also the little interesting remark (from an unidentifiable source) stating that BMC is already profitable and for sale. It will be interesting to see if this is really true, who ends up buying BMC and what will happen to BMC in the future regarding their publishing policies. - Pedro Beltrao
PLoS ONE serves a valuable function; it publishes "sound science". Not amazing or ground-breaking, but solid and worthy of attention. The kind of work that the majority of us do, I imagine. Disclaimer: my boss is an academic editor and I'm a reviewer. I don't think "not ground-breaking" equates to "lower review standards". Didn't Bora mention on his blog that 50% of submissions are rejected? - Neil Saunders
I really don't get the negative spin on the good financial results. NPG is also diversifying a lot with a growing list of Nature branded journals that include for example Nature Protocols (an experimental lower tier version of Nature Methods?) along with many other journals that do not carry the Nature name (http://www.nature.com/siteinde...). - Pedro Beltrao
I've just read the comment thread to the Nature news story. There is outrage about the "slurs" the commenters feel are cast upon PLOS but no factual responses to the facts presented in the article. I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction because something is published that the commenter happens to disagree with but can't be bothered to support rationally. - Maxine
By the way, my disclaimer (comment above): I am an editor at Nature, the journal. - Maxine
A journalist writes: grass is green, sun is yellow, sky is blue. Declan writes: grass is green and that is BAD, sun is yellow and that is REALLY BAD, sky is blue and that is REALLY, REALLY BAD. He may have gotten all the facts right but he painted them in puking green in a way that suggests that good is bad, up is down and we are now in war with Eastasia. - Bora Zivkovic
Maxine, Paul Peters commented on the original, making a point that many have made (NPG has its own stable of "second-tier" journals). That's a fact, but you chose to obscure it in your response to Paul by focusing on the "Nature Whatever" group, which makes up about 1/3 of the ~60 journals published by NPG. It's not even (see Bora, above) a criticism of either publisher -- where did this idea come from that publishing solid science was bad? - Bill Hooker
Further, Butler seriously misrepresents the PLoS ONE review process, skirting the edge of disinformation in an attempt to paint it as somehow less rigorous than other journals. PO reviewers do not "only check for serious methodological flaws" as Butler claims. This is a petty smear, carefully worded to keep lawyers at bay but clear in its intent. - Bill Hooker
Sorriest (and most blatantly wrong) attempt I've seen by a for-profit publisher to debase the open-access movement. Incidentally, I do think there are reasons to have a different pricing structure for open-access than PLoS, but the attack on the review process at other PLoS journals while touting the lesser Nature journals rings hollow. Incidentally, it was a slanderous and misguided enough attempt to get me to join the commenting section of Nature and this website to talk about how bad it was. - Evans B
I've confused by your point about my reply to Paul Peters, Bill. I thought it was clear enough and it contained the URL (not a live link) to the numbers in question. I didn't "choose to obscure" anything, I am not that kind of person, I was correcting an error of fact that this commentator made. - Maxine
Bora, the news story didn't say green is green, etc, it had numbers in it. I haven't looked at the comments on the Nature site since this afternoon, but when I did, they were mostly of the "shock horror, Nature has run a news story about another publisher" variety. We often run news stories about scientific publishing/publishers. Do we need to write that we are one do you think? - Maxine
Sounds like it's all tits-up for toll access - Graham Steel
Yeah, no conflict of interest here. are Nature commentaries peer-reviewed research? - Timothy Driscoll via Alert Thingy
Maxine, thanks for the responses. Do the editors at Nature really miss the subtext of the following lines? "PLoS stays afloat with bulk publishing", "bulk, cheap publishing of lower quality papers", "PLoS One uses a system of 'light' peer-review to publish any article considered methodologically sound." The subtext is clear, that things are different in a bad way from how things are at Nature ... so where's that graph of Nature's financials? - Evans B
As a followup, are we really to believe that Nature recently added all the new NPG titles for any other reason than to capitalize on the very thing you condemn PLoS for doing? - Evans B
Yeah, sorry Maxine, didn't mean to say it quite like that. Mea culpa, I apologize. - Bill Hooker
My point, more carefully phrased, is that Paul's comment (though he made an error which I think effectively obscured the larger point) is just an example of a point that many have made: NPG has, indeed most publishers have, their Glamour Mags and their workhorses. Declan makes it sound somehow heinous to do this, but it's a standard business model. - Bill Hooker
What I'd like to see is a PLOS ONE with 0$ cost to the authors, where the light review puts it at a different level (counts for tenure points) from Nature Proceedings, but it still is free - community based - open access. The PLOS ONE reviewers don't get paid anyway right? So the only cost would be only for computing infrastructure, and a few people for organizing/moderating peer-review (infrastructure can be covered from donations, people can donate time). Imagine if this thing picked up like Wikipedia... - Ntino
factual points for maxine: a) the live link you (maxine) gave us only shows the impact factors of the "nature xxx" journals, not those of the >40 other lower impact factor journals that npg publishes. the PLOS accounts are public, and nature is entitled to publish the results of its sleuthing, but for the analysis to be convincing or useful, a comparison with the publishing models of other groups (or at least that of NPG) is essential. b) how exactly is evaluating a paper for methodological soundness "light" review ? and how does adding on a subjective assessment of potential impact somehow makes the review "heavy" (or "rigorous") ? more on all this in the original nature thread ... - mad -
Since not everyone has access to nature, I'll re-post my comment here: Why do we, with today's technology, still have about 20,000 different 19th century journals around? Nature Neuroscience editor Noah Gray points it out: "Nature Neuroscience aims to send 30-35% of papers out to review, so getting past that stage is the biggest hurdle." http://network.nature.com/foru... Why does this step come *before* peer-review? Shouldn't this come afterwards? Why is this considered "non-light"? : - Björn Brembs
Let scientists decide what is good science in their field and then have ex-scientists which usually are smart, knowledgeable, experienced and eloquent decide what is "hip" right now? Let's exaggerate our current system slightly: "non-light" peer-review is mainly a review by ex-professional scientists (either voluntary or involuntary ex-) for popularity. Publication in such journals usually decided who gets grants, tenure, a life. So basically, we have a system going in which ex-members (either members who left or didn't cut it) decide which members get promoted and which get fired. How many corpporate managers do you think would want to implement that in their company? Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One. - Björn Brembs
@Bjorn - Right now the different tiers of journals work reasonably well at sorting out the potential interest of an article. It is far from perfect but I don't feel I a missing important articles by not reading lower tier journals outside my field of research. Still I am interested in knowing the latest news on the very important discoveries in science. I agree that in principle this "sorting" could be done after peer-review and publishing but we don't have the tools to do this .. yet. - Pedro Beltrao
maxine wrote earlier: I'd be more impressed if one of the commenters pointed to a factual problem with the article, rather than the usual "internet outrage" reaction. ok.. now there are numerous pointed criticisms of the article, on the internet, much of which can be recapitulated by paraphrasing this thread. so now.. i'd be more impresssed if maxine/declan/one of the people at NPG actually responded to the most substantial of these comments in a factual manner, rather than merely cherry-picking the weakest links/arguments in rapidly posted comments and choosing to counter them. - mad -
In summary: should Nature journals write about the publishing business? I think the problem is that Nature see themselves as representing science; science publishing is a hot topic, articles about it in Nature journals are fair enough. Other people, however, see Nature as an arm of NPG with the business interests and conflicts of interest which that implies. It's always going to be controversial for them to discuss other publishers. - Neil Saunders
Timo Hannay at NPG has written a post at Nascent, one of the NPG blogs, about this news story on PLOS. It is being discussed by this FF group. - Maxine
Timo's article is even nastier than Butler's, if that is humanely possible. Where and when will Declan defend himself? All the damage control so far has been done by Maxine, Timo, Euan, Bob, etc. When will Nature give Declan a green light to defend his own words, his motivations, and his "information"? - Bora Zivkovic
Thanks. I just saw it and added it to the ever-growing linkfest. I had to go offline as we had another bad storm here so I wanted to unplug my computer. - Bora Zivkovic
The main worry I have about OA journals relying on government moneys is that they can be shut off at any time. When budgets get tight, philanthropic outlays for things like PLoS get dropped quickly. I also worry when a journal has to constantly apply for grants and moneys. What happens when that income begins to dry up? I think it is very important for PLoS to become financially independent, so the journals will remain for years to come. - Daniel Kulp
Oh the irony. You now have to pay NPG $8 to read the Declan Butler article - Graham Steel
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
The Wellcome Trust Sanger Institute has sequenced the equivalent of 300 human genomes in just over six months. The Institute has just reached the staggering total of 1,000,000,000,000 letters of genetic code that will be read by researchers worldwide - Duncan Hull
Science Progress is amazing. I subscribe to only the best posts via AideRSS, which I can't recommend highly enough for those of us without enough time: http://www.aiderss.com/rss/gre... - Donnie Berkholz
"Like" as in "I like that someone noticed this and is still pushing the issue". - Andrew Perry
Well, if it's tre that the odds of someone getting a tenure track position by 35 are only 7%, there's only one solution: make PhD programs a mandatory two decade ordeal! That should get most people past 35! - Todd Harris via twhirl
"In 2007, two hundred scientists received six or more NIH grants, and a single investigator won 32 grants, while many others got close to ten." This sounds ridiculous. It is clear that this investigator cannot be coordinating closely all those projects. - Pedro Beltrao
It's a classic catch-22. Increasingly, funding consists of large grants to established researchers with stellar track records. However, to become established and build a track record, you need funding - which you can't get. I'd actually like to see postdocs desert academia en masse; let's see where the big bosses would be without their slave labour. - Neil Saunders
I've always wondered how science would work with a more active 'union' for PhD students and/or PostDocs .... if they went on strike how would things pan out ... it's not like public transport employees or a big building project with tight deadlines ... the 'general public' probably wouldn't notice for years. Hence the level of exploitation that occurs (not saying every student/postdoc is exploited, but many are, and I think the lack of any power in a stop-work is a large part of it). - Andrew Perry
I still get a little bugged by the assumption that PhD = career in academia - Deepak
Yeah, I've often wondered how long it would take for anyone to notice if academic researchers went on strike :) - Neil Saunders
Thing is, the rules are different in academia. Basically, if you're not independently-funded, you don't count and are not free to pursue your own agenda. So we end up working for successful group leaders and furthering their careers, rather than our own. I personally think it's wrong that senior researchers get credit for minimal input, solely because they hold the grant, but that's how it is. - Neil Saunders
Neil ... one of the many reasons I wasn't interested in academia. In a good company, you get recognized (as does your manager) when you do well. In academia, it seems like the managers (PIs) get undue credit ... nothing wrong with academic science. I quite envy the freedom from time to time, but there's a lot more - Deepak
@Neil: don't disagree with you, but just to play DA: it's brutal to get and hold onto a lab as a PI, and once you're there it takes all your time and energy just to hang on. (Unless you're one of the silver-spoon Big Shots, but there are a lot more small, struggling labs than big fat ones.) So there's a PI catch-22 as well: you have to take credit for what your lab does, or you get no credit at all. I keep wondering whether Pawel and his freelancing ideas might not be a viable alternative model... - Bill Hooker
@Bill - don't disagree with you either. In theory, a PI is rewarded for their previous hard work, skills in organisation, directing research, mentoring and so on. Sometimes, it even works out like that :) However, I do think we've entered an era where the system actively favours established researchers and actively discriminates against young, early-career scientists. I think it's untenable and would like to see it proved so by people voting with their feet and getting out. - Neil Saunders
I think there's definitely a "rich-get-richer" thing going on. I also think that competition has reached the point -- 7%! -- where we might as well draw names out of a hat. (Sneaky self link: http://3quarksdaily.blogs.com/...) There's not much correlation any more between smarts+hard work and success. Something's gotta give. - Bill Hooker
@deepak: One problem is that academic training is done by academics. That's all they know. They aren't prepared to train people for careers in other environments. And as for grad students striking, it's been done, and doesn't really work for reasons mentioned below. Besides, aren't we all in it for the love of discovery? Are you really going to go on strike when your killer experiment you've spent a year setting up is coming to fruition, your bunnies need a bleed, or you need to read galleys? - Todd Harris via twhirl
Todd, I wouldn't disagree with that, but there are more than enough PhDs who move on to industry, where quite frankly I enjoyed the science I did. I think the stike that Neil refers to is people choosing industry over academia - Deepak
That is indeed the action I meant. The whole notion of striking PhDs/postdocs is ridiculous! If your job (any job) is really making you so unhappy, then look elsewhere. I'm acutely aware of "whinging postdoc" syndrome when we explore these issues. I have no time for those "life is so hard in academia" style of blogs. It really isn't. - Neil Saunders
Well, the strike I was referring to was a real strike, not a shift out of academia, but for reasons Todd (and I) have already stated, it wouldn't work, it would have to be a pretty bad situation before things came to that, and despite problems overall most junior scientists do love their work to much to do it. Because of this, it's one less bargaining chip that they have to improve their situation, unlike some other industries. So in reality, I guess a move to industry is a good alternative to a strike ... - Andrew Perry
Especially since it's often a pretty good alternative, and you get to build stuff and often, esp in a small company, get to do some very interesting research - Deepak
I came to this discussion late (ironically because I'm writing yet another grant) but thought I add anyway. I train people in my lab for academics or industry. Most have gone on to industry as it turns out. Since I've worked in both settings its easy for me to make the training fit either option. I try to give the person the chops for either and then let them pick. - Maureen
Since we are talking about alternative career paths it could be worth mentioning that scientific publishing is still growing at a strong pace. I think if I was not happy with research in academia publishing would be the place I would look for an alternative. - Pedro Beltrao
Postdocs: A 1960s invention because they didn't have enough professorships. Lame. Lame. Lame. - Mitchell Tsai
Comments came back today for a .au funding round. A comment directed at a senior researcher with 10 000+ citations was "very good track record but very no recent first author papers". Also last year the Platypus was not exciting, this year the reviewers are so excited they are creaming their pants. Two questions. Who are the idiots who review these grants (I hope it isn’t those who hold 10+ grants)? Are the only things that get funded something that's been big in the media? It appears very short-term hype focused vs long term vision - Mitchell J Stanton-Cook
This is the logical outcome of poorly synchronized boom-bust cycles in funding, training and the availability of scientific careers in any given place. On top of this, since science is now a transnational career possibility, problems are being exacerbated by even more short-sighted policies in other countries. Some interesting comments here: http://bigpicture.typepad.com/... - Heather
Reading this has rather put me off continuing in academia. I like doing research, but I'm not sure if I fancy spending most of my time writing grants if I become successful. Success in research = do less research ? - Michael Barton
Michael, I do think that to an extent it's a choice. I know a few PIs who still write their own code. Even in industry you can choose your track (technical vs. management). Most of my friends are still in the technical track and at least managing large projects if not right in the middle of them. - Deepak
"Success in research = do less research?" Depends in part on the field. A few years ago I started going to occasional math and philosophy meetings (I'm a physicist). I noticed the senior mathematicians and philosophers were a much more interesting and happy bunch than the senior physicists, on average. My eventual theory was that the relatively low level of funding in mathematics and philosophy was actually a boon for these people. Most senior physicists are machines for turning coffee into grants. - Michael Nielsen
@Pedro – yep, I can recommend publishing :-) BTW, we (=Mol Syst Biol) are still looking for a second editor... - Thomas Lemberger
@pedro re: one investigator with 32 grants - I think I read in a follow-up article in Science or Nature a few months ago that they didn't distinguish between types of grants, so that individual actually had a slew of conference grants and not research grants (he is the main organizer for a major series of conferences), so he was an outlier. Still, there are a distinct minority with the majority of research grants, so I don't disagree that the system needs to change.. - Shirley Wu
Nature had that article (Pubmed ID#: 18354436): 32 grants to Andy Robertson, Chief Scientific Officer of the Keystone Symposia; those 32 grants averaged $15,312 a piece. - dsbreak
Thanks, I've seen similar programs but they all stipulate that they are for visits to distant laboratories for training purposes, and tend to be in experimental biology areas. I'm looking for something more general that can fund trips to conferences or workshops, not exp bio related, not necessarily presenting a talk, etc... - Shirley Wu
I believe that many of the "institutional" conference organizers (CSHL, GRC, etc.) provide travel funds. I'm not sure about general funds for any conference (outside of the benefits that certain fellowships carry). Are you looking at anything in particular? - dsbreak
You mean like slush funds? It seems like it is rare for there to be a pot of money for unrestricted travel for students unless you get it through a general fellowship that gives a chunk of money that is unrestricted. I don't know if you can spend money from an NSF Dissertation Improvement Grant that way, but you have to get that funded for your research work. I think NSF Minority travel award might be another way, but only some qualify of course: http://rurl.org/u8o - Jason Stajich
Our graduate student association provides a few travel scholarships a year. - Mr. Gunn
I must admit that I was very underwhelmed by the article. Chris is a little out of his league isn't he? - Deepak via Bookmarklet
We were crunching the genome with huge clusters a decade ago. As we get more information, our models get better. To make more sense of this information our theory has to get better to as Lee Hood always says. Ah ... I am bugged. All Hypy with limited fundamental understanding - Deepak
I'd like to see someone try to sell 'correlation is enough' to the FDA or equivalent - Cameron Neylon
Cameron: lol In journalistic terms the essay is good, but it's science where being only trend sensitive is not enough. And Anderson has not much clue on what's going on in biology, but he is probably right on what's going on in physics, which we don't really know. - Attila Csordas
Am reading the paper version of Wired at this very moment! The cover uses the headline "The End of Science." Now that caught my attention as I pulled it out of the mailbox! But yes, underwhelming. I don't think scientists are going to stop asking "why?" anytime soon, the way the article makes it sound. - Shirley Wu
like I said last time this came through - it's a tad grandiose. Did he just learn about data mining recently? - Mr. Gunn
Ah - plane travel tomorrow which is usually when I buy a copy- mind you probably be last months on this side of the pond anyway :) - Cameron Neylon
I agree, Bill. Makes one think of the many propositions to replace wet lab experiments with in silico substitutions. You need both. - Heather
Chris still is onto something. In industry you can create value from correlations and "hunches" based on data. Even medical trials are just data and correlations. And in oder to save lives you don't really need to know why, just what. Science is a method, never forget that. Not a religion. And its limits are there, as well as its advantages. Other methods might be more efficient at doing something else, not? - dekay
Actually, that used to be the case. The focus these days is on the why, on the mechanisms. It's why VIOXX happens, cause you don't understand the why. Yes, you need statistical separation, you always have, even when you had limited data. More data only improves your statistics. - Deepak
For example, docking studies are increasingly trying to add more "physical" measures rather than rule based implicit, this is what the data tells us measures. Science is much too noisy, and the kinds of false positives you would get with Google are NOT acceptable. Is the scientific methods dogma. Can it change, yes, but not for the reasons that Chris is talking about - Deepak
Even Valleywag has an opinion on this, they are scientists too, and have a lab at the back: http://valleywag.com/5019748/w... "The problem here is that if we stop asking the question "why?" then we are basically making for the foundations of faith. You can always make statistics say nearly anything you want, it simply depends on the assumptions you make when you analyze and present them" - Attila Csordas
Attila - no, Anderson is definitely not right about physics, either. It's a strange article. Data mining isn't replacing the old scientific method. It's augmenting it. - Michael Nielsen
Agree with Michael. The writer seems to think that somewhere in a big pile of data lies "everything", waiting to be extracted using algorithms. That's just not how science works. It's the questions that we ask and the interpretations that we devise that make it science, not the raw information. - Neil Saunders
I created a slide at my previous job, which had all the data sources (expression, proteomics, genotyping, histopath, name it) that exist related to a study on the edges, with the emphasis on there being a ton of heterogenous data, and in the middle a big "?". The point. It's all about the question, NOT the technology or data type - Deepak
Chris' piece is provacative ... but the Ars Tecnica piece touches on some key points - was /.-ed a bit ago, so my apologies if this is old news: http://arstechnica.com/news.ar... - Kaitlin Thaney
Kaitlin, that is a great article. Hopefully it will help the masses understand why Anderson is wrong. It also leads to a worry I have had about Google. They don't really understand science at a fundamental level. Maybe I am wrong, but I get that impression all too often. - Deepak
Although I admit I don't quite get the cloud part. It almost seems incidental - Deepak
Hey Deepak. Don't tell Attila you don't think Google gets science. ;-) - Mr. Gunn
There's a good "rebuttal" on ArsTechnica (see comments to Wired piece for a link). Also discussion on Nature Network Cancerevo blog (on the computing clouds) and at the Researchers and Web 2.0 group which you are all warmly welcome to join (I sent round an invite just now with the link). - Maxine
so essentially, the phase of an exon depends on the summed length of the preceding exons and a division by 3.../me draws boxes - Neil Saunders
yep - just keep a running length variable as you putting together the CDSes and do mod 3 - Jason Stajich via twhirl
I can't believe how much pain this is causing; I mean, I'm sat here drawing segmented boxes...it must be Friday - Neil Saunders
Neil, think of me... I'm new to bioinformatics and am yet to know how to draw segmented boxes :P - Ricardo Vidal
Neil, I found this old code for you in my archive (copied and pasted in pastie.org) http://www.pastie.org/223229 . The code was used to find the amino-acid on a genomic sequence. Hope it will inspire you (A gene contains an array of transcripts, a transcript is defined by an ATG, Stop and an array of exon, an exon is just a pair start/end. will only work for translation in the forward orientation ! Pierre. - Pierre
CiteULike. Better support, better features (e.g. PDF upload), cleaner and more functional UI (in my opinion), more suited to bibliography as opposed to general bookmarking, responsive developers. Connotea is hopelessly slow, lacks basic features (batch delete, clear indication of # articles in library), has an ugly UI with little functionality (e.g. the display of a full, word-wrapped URL in the header; the fact that the bookmark is just a link with no abstract - unless you import BibTeX, then the abstract becomes an ugly front-page "note"), is buggy (duplicate URLs, struggles with certain author names), broken, needs a complete re-write and all that work falls to one person. - Neil Saunders
citeulike can easily be downloaded locally: simple clean, easy, doi matching, shared groups, LikeUCite can download all PDFs as well making a local library that I sometimes move into Paper (OSX) locally for archiving. I use Bibtex export for preparing papers. I also add a tag for a particular manuscript we are writing and then easily download the set. Collaborating with (willing) co-authors also makes it possible for multiple users (in a group) to add papers. - Jason Stajich via twhirl
I use the exact same approach for writing papers as Jason; works very well. - Neil Saunders
If I haven't invested yet in Connotea, can I import old Endnote libraries into CiteULike? - Heather
Heather: if you export your Endnote as RIS or BibTeX, you sure can. Just not the nasty, proprietary, good-for-nothing, binary EndNote (.enl) files. - Neil Saunders
I started my library with connotea but I think I would use citeulike now just for the pdf uploading tool.. I use this scientific-social-boorkmarking tool because they understand the DOI or the pubmed-id's. However, once a month, I transfer all my bookmarks from connotea to http://del.icio.us because, at the end, its 'network" option is the best tool for knownledge discovery : http://del.icio.us/network/lin... - Pierre
"Liking" this to remind me to try CiteULike. - Bill Hooker
Google Trends shows that CiteULike is more popular. Both could have better group features. - Martin Fenner
Pierre - Just today I was thinking again how Nature could try to combine Nature Network with Connotea to provide a page in NN for paper recommendations (based on the contacts libraries in Connotea). Also maybe analyze the papers published by the user to give recommendations based on a search for related papers (automated query to pubmeds related papers ?). To be a bit fancy they could give some options to filter them. Hide some of the users contacts or pick a selected group of journals to filter etc. - Pedro Beltrao
@Jason "Indecent liberties with the bioperl paper", I like it! I think citeulike is better, but only just and agree with Martin that they could both be better. Been using http://www.scopus.com a lot recently, and this plays nicely with citeulike, dunno about connotea though... - Duncan Hull
I'm going to try CiteULike soon. I tried it soon after launch and didn't have a good experience, but I understand it's come a long way. The only thing keeping me with Connotea is inertia, and the fact that I think citeulike is the dumbest name ever. Sorry, Mr. Cameron. I tried 2collab http://synthesis.williamgunn.o... but there are all kinds of weird design decisions that just don't make any sense to me and the import and export still need work. - Mr. Gunn
I use Connotea, but the problem with online ref. managers is when you try to access articles from journals that require subscription. Which has me going all the way around to login through the university library's proxy and then retrieve the article. The middle way I've found is by saving the pdf's locally through Zotero, and then uploading the references to Connotea via .ris or .bib file export from Zotero... So I get pdfs right there in my hands to read right away, and saving the refs online for Web 2.0 - Ntino
My impression is that 2collab is more of a social bookmark/discovery tool for papers than a bibliography manager. I liked Zotero a lot initially, but abandoned it in my quest to move as much stuff online as possible. When it supports synching to online repositories, I might come back to it. - Neil Saunders
Thanks, all. Giving citeulike a shot. - Chris Miller
I used to be a Connotea guy but this thread got me curious to check out CiteULike. Verdict: I like. The UI could be improved, I had a hard time figuring out how to edit the citations I submitted, but it works and I love the PDF uploading -- beats me having to email myself the PDF or carry around a memory stick when I find papers I wanna read. I also like the tagging the items either as "read." "to read." - Kambiz Kamrani
Funny, the tagging by importance of reading is my least favourite feature of CiteULike. I guess it's supposed to function as a recommendation - only the default is "might read" and everyone leaves it as that (go on, check the library of almost any user!) If I make the effort to save it, I assume that I either have read it or plan to at some point. Useless feature, for me anyway. - Neil Saunders
All I want is the webbyness of citeulike combined with the iTunes like interface of Mekentosj Papers, but cross-platform, rather than Mac only. - Duncan Hull
Why not combine Connotea and Nature Network? I see a lot of synergy. - Martin Fenner
Pedro has pushed the NN-Connotea integration at NN and other forums. Don't know if it's under consideration. Perhaps the priority is fixing Connotea first. - Neil Saunders
In related news, the long (January) overdue update to make Endnote work with Word 2008 for Macintosh was just announced. - Martin Fenner
We're aiming to set up an infrastructure that'll allow all our apps (and potentially external ones too) to share data with each other. NN-Connotea should be one of the first things to come out of that. Don't know about the timeframe though. - Euan
I'm at a network conference this week looking for techniques to help integrate into connotea for searching through the graph of information there to help with content discovery, lot's of good ideas here, and, oh, yes we are looking at nn-connotea integration, but that should not be too much of a shock. - Ian Mulvany
I use refworks because it's free for me, but it's so annoying. I can't even export all my papers at once because it can't handle the load. Fail. I'll bear with it for these last few months of my PhD, but if/when I start something new I'm going to use either Cite-U-Like or Connotea. - Eva
I think it means that bloggers get access to papers before publication like science journalists do, provided they don't break the news before the official release? Can someone clarify? - Neil Saunders
They have done that unofficially in the past, so looks like they are formalizing part of that process - Deepak
@Neil Yeah, you can't blog about it until after the embargo date has passed. - Euan
This is great. Levels the field for bloggers wanting to work as science journalists. - Pedro Beltrao
"Bloggers wishing to apply for inclusion in our press list should do so through our contact form including links to 6 blog postings written by them in the last 6 months discussing the content of primary research papers. " - Mr. Gunn
Very cool! Thanks for the heads up :) - Ricardo Vidal
Yes, it is already happening to some degree. I'm a blogger and PLoS sends me the same email announcing upcoming papers that they send to professional journalists. Often times they attach the real deal PDF to the article. - Kambiz Kamrani
Does it mean I can access cycles on Intrepid? Somehow I doubt it - Deepak
you have to apply to the U.S. Dept. of Energy (DoE), much like you would for any large research grant proposal, it's just you're asking for CPU time instead of money. http://hpc.science.doe.gov/ It seems to be pretty open(to academia & industry) although I haven't look at the previous allocations, I imagine the science has to be something relevant to the DoE's mission. - Cornelius Toole
That's a problem then. That's still essentially the old model (I used a ton of supercomputing time when I was in grad school). Even after that, resource acquisition was not exactly smooth (long queues and the like). What I want is utility supercomputing, where I can dial up a whole rack on a blue gene for a bit to run some massive simulations of a molecular motor or something like that. - Deepak
I think teragrid is like that - you can get cycle on bluegene at SDSC. http://www.teragrid.org/I found the system untenable for bioinformatics though - migrating data to local nodes is important for performance. I also often want to run many jobs at the granularity of each protein (refining gene models based on homology let's say) that make not take long individually, but some may take longer, why not spread across the cluster. - Jason Stajich
for teragrid allocations you still have to apply to the NSF for hundreds of thousands of units, they do have smaller allocations with shorter turnarounds( a couple of weeks). I think the 'open' in open science means you can get cycles for research that doesn't require you have DoE/DoD security clearances, and for basic research, as opposed to the applied research that DoE is interested in, which is normally concerning things that can be applied to nuclear stockpile issue, or homeland security... - Cornelius Toole
There's no market for utility HPC provided by private industry. The only orgs with big pockets and impetus for big metal are governments. Their priorities are nat'l security & then basic research, maybe economic development. And even though gov'ts are some of the few who pay for such expensive & scarce resources, allocations are made upon subjective criteria such as impact of science, mission relevance & capability, as opposed to who can buy cycles, which is a long, slow process. - Cornelius Toole
I don't know if it has to be private. The funding model needs to change. Even as a grad student it was very frustrating. You never new how much supercomputing time you needed, and how long you would need it and when, especially if its project based. Agreed, that for most of those task, commodity clusters/EC2 would be sufficient, but again, the access models were the same as for any HPC time. I've already run into limitations with licensing models since I am an individual - Deepak