Don't forget that NCBI has quite a reasonable API: eutils (http://www.ncbi.nlm.nih.gov/en...). It gets a lot of use in programming libraries (e.g. Bioperl) but for some reason, doesn't get much publicity or usage in web applications, mashups etc. - Neil Saunders

@Duncan I wondered if there is a recent paper using Biodas ? On my side, I've been trying to use the one from UCSC/Genome-Browser but the results where unuseable (not enough verbose, information missing, etc...) and I then went back to their anonymous mysql server. - Pierre

it is crawling flash already? - PauloNuin

Looks like it is (e.g. http://google.com/search?q=fil...) though I don't think this can explain the mysterious YouTube videos. - Eric Jain

it might, if part of the movie coding has segments of the sequence in it. - PauloNuin

Maybe it assumes that if someone just mashed the keyboard randomly and typed some very long strings, they are bored, so why not give them some videos to watch ? - Andrew Perry

I checked, any sequence of random chars, 130+ renders that list of videos. The same videos :) - Ricardo Vidal

Hidden DNA sequences in a Snoop Dogg video? We may be on to something BIG here :-) But note that any term that is too long appears to result in the same list of videos. Also, while Google may now be extracting text from Flash content, I don't think they process Flash video. - Eric Jain

Bill is right - I'm still an advocate of the general purpose wiki (Wikispaces in my case) for an online lab notebook. I know it isn't sexy and doesn't seem "cutting edge" but what is does well is let us represent pretty much whatever we need to record for experiments with the fewest assumptions. It is BECAUSE it is like paper that it works. - Jean-Claude Bradley

Jean-Claude: I noticed MediaWiki has some "forms" extensions, where users can create forms which fill out a template (like Semantic Forms). If this was simple enough to use, do you think this could be good hybrid approach between free-form and structured data in a wiki-based ELN ? For example, the powerusers could build forms+templates for standard experiments, which everyone could use. Extra data could be added to the wiki page after it was created from the forms+template. - Andrew Perry

Nice ideas Andrew. A few of the popular wikis have these form plugins (pmwiki, dokuwiki, mediawiki). I've thought before that they might provide a good environment for developing ELNs, LIMS and so on, but never had time (or sufficient positive feedback from potential users) to follow up. - Neil Saunders

There is one very good example of a Wiki-based production quality LIMS system (I haven't used it, but know folks who've taken a look at it). That's the WikiLims system from BioTeam ... so it's definitely doable http://blog.bioteam.net/tag/wi... - Deepak

WikiLims looks interesting; also a presentation here http://www.slideshare.net/gues.... I guess for wikis to work in this way, we need low barriers for developers and sufficient flexibility in the wiki backend. Otherwise you may as well code up your own web app in whatever language you know best. - Neil Saunders

That's definitely one of the plus points of MediaWiki. It seems fairly extensible - Deepak

Most of you know I'm part of the OWW team. So let me ask this question: Those that have used or seen OWW's lab notebook, what would you like to see added (or removed!) from it to make it more to your liking? As it has been said, MW is extensible and we are getting good at extending it, so let me know what you'd like and we can see what's possible. - Ricardo Vidal

I only keep a ELN. It's closed ;-0 It's dokuwiki install with a few modifications and plugins. As I spend all my time at the computer I have found this a lot better than writing/printing/cutting/pasting. I started of using mediawiki but had problems getting the 3rd party plugins (gnuplot, math etc.) to function. 2 of 12 in our lab use an ELN fulltime. I'm unsure of the Universities policy on ELN's, but i'm not concerned given that 2 Masters students just submitted without keeping any formal documentation. - Mitchell J Stanton-Cook

That's another good point; many wikis have some great plugins for research (when they work): plotting, formulae, BibTeX and so on. My "ELN" is basically a Trac + SVN installation, since most of what I do is generate file revisions (code, input/output, papers in LaTeX). It's "semi-open" in that parts of it are browse-able but file view requires authentication: https://predikin.biosci.uq.edu.... - Neil Saunders

Added wiki + forms = LIMS/ELN etc etc idea to Biogang projects: http://openwetware.org/wiki/Bi... - Neil Saunders

The other thing I like about the wiki is the discussion page. Supervisors/PI's can read and make comments at their own leisure. I would love to have "virtual meetings" on my ELN - that way when it comes up "what ! you did it that way !?!?!" "But we spoke about that.." "No we didn't..." situations are eliminated. - Mitchell J Stanton-Cook

Neil: What about those of us absolutely unable to "code up your own web app" in any language at all? We need someone to make those templates for us... - Heather

Ricardo: I definitely would like the content of each lab notebook *entry* to be searchable. For some reason, this <sitesearch>title=Search this Project</sitesearch> only seems to search within the page titles, at least for me. I'd also like a way to make image entry possible from within the pages one is editing (ie. a notebook page), the way Wordpress does when you are making a blog post. I might be asking for the moon... - Heather

@Heather - by "you", I mean "programmers", obviously! A good thing about wikis is that they are accessible to anyone. If a programmer wants to make them do more, they have to decide whether learning how to hack the wiki is a good use of their time and how extensible the wiki software is. The question is: how many wikis offer this extensive customisation? For a web developer, it can be faster just to code in what they know than learn a new framework. - Neil Saunders

@Ricardo: I signed up for a lab notebook just to play with it (my boss is very conservative, I can't use it for anything real...yet) and managed to break it by including an apostrophe in my "lab" name. I got email from the dude who looks after the notebooks, but he never did get around to fixing what I messed up... - Bill Hooker

Andrew - in a sense we use "templates" on the Wikispaces notebook since students often copy a previous similar experiment and delete the unrelated stuff. - Jean-Claude Bradley

Mitchell - one of my favorite features on the online notebook is being able to point out problems or ask questions directly on the page in bold and italics. When the students address the issues they can remove my comment. I have found this to be much more useful than the discussion tool since it is much harder to point to the exact section in the text. - Jean-Claude Bradley

@Bill I'll fix it up and let you know via email. - Ricardo Vidal

@Heather I believe that the search is working properly. It performs a restricted search within your lab notebook. As for the images, you can add images inside but I see what you are looking for. It is totally possible and I'll suggest it to be implemented :-) - Ricardo Vidal

Sorry to trouble you, but I don't get why it doesn't. Not browser-dependent... for example, if I search http://www.openwetware.org/wik... for the string "Sophie", I get this message: There is no page titled "Sophie +"Etchevers:Notebook/Genomics of hNCC" -"Lab Notebook"". - Heather

@Heather, you are right. It was buggy and we're fixing it. MW's search sucks and we're making it better via Google. It should be working better later today. - Ricardo Vidal

Thanks Ricardo. No hurry, mind you, since I'll only be playing. But of all the ELNs I've looked at, OWW is the only one that comes with a community, so I'd really like to give it a good workout before considering others. - Bill Hooker

@Bill, I'll let you know once your playground notebook is fixed. Meanwhile, you can fool around with this demo one: http://openwetware.org/wiki/Us... - Ricardo Vidal

Thanks! No native Linux yet though. I don't do Wine :) - Neil Saunders

Seems it might be on the way. Meanwhile, Wine it must be. - Ricardo Vidal

I begged for an invite in your comments to ensure you have my email :) - Andrew Perry

@Andrew invite sent :) - Ricardo Vidal

Danke ! - Andrew Perry via fftogo

Here's me begging as well. I signed up, so hopefully I'll be able to distribute some myself. - Mr. Gunn

Mr. Gunn, just sent your invite :) - Ricardo Vidal

Got it. The comparison to MP3 sharing is apt, with all the implications that entails. A hot feature for them would be online backup integration, so you're not limited to running it from one PC and so people could share references without having to actually mail the PDF. - Mr. Gunn

I want in too. If possible ... obrigado. - PauloNuin

Ah, reading the license terms: "You may (at your option) use our Software to make a regular back-up copy of your Academic Papers to our servers so that you can access your Academic Papers using the World Wide Web and you hereby grant to us a limited licence to upload, copy, store, use, modify, display and reproduce your Academic Papers for the sole purpose of providing our back-up service to you." I like this very much. - Mr. Gunn

We may from time to time provide interactive services on our Site, including, without limitation: "facilities for the uploading and sharing of users’ and members’ Academic Papers with other users or private user groups you have created" This is perfect! The social networking angle of the online service, linking people via authorship, looks really nice and pretty much kills SciLink. - Mr. Gunn

Don't mean to live-blog my reading of the license here, but I should include: "You may use our Site and our Software only for lawful purposes. You may not use our Site or our Software: to send, knowingly receive, upload, download, use or re-use any academic papers or articles without the permission of the copyright owner." - Mr. Gunn

Finally, "You may link to any of our publicly available pages, provided you do so in a way that is fair and legal and does not damage our reputation." I'm going to blog my review, just as I have with 2collab and Connotea. I hope they don't close my account because I say something too critical. - Mr. Gunn

Mr. Gunn, how about a blog post about the license terms? Sounds like you have some opinions about them. - Ricardo Vidal

That's coming, once I get some hands-on time with it. The import from Connotea is putting the doi in the notes field instead of the doi field, which is apparently Connotea's fault. Two killer features I hope they add soon: automatic download of PDF once metadata is added and adding to library via bookmarklet. If they don't have the second feature, I'll probably still use Connotea or something and periodically update Mendeley, provided. It needs to be easier to select a range of papers in Connotea by date - Mr. Gunn

Mr. Gunn - "I hope they don't close my account because I say something too critical." We sure as hell wouldn't! We know that we still have a lot of work to do, so our technology as well as our license terms are far from perfect - both will be modified based on our users' feedback. Any ideas are appreciated! Just one remark regarding the current license terms: As you can tell from the language, they were largely written by our lawyers with the main intention to protect us from lawsuits... - Victor

The license terms quite strangely resemble readable prose, so props for that! I'm still trying to find an import format that works 100% for Connotea/2collab -> Mendeley. I takes about 20 sec on my machine to import 550 records. It's becoming apparent to me, and probably has been for a while to Ian et al, that RIS kinda sucks. Every app seems to expect things like DOI and URL and notes to be in a different field. - Mr. Gunn

Thanks - we tried to intervene and rephrase where possible, but our lawyers were adamant on some points! To be honest, we hadn't planned with a Connotea/2collab import specifically; we just tried with BibTex and RIS files generated by Google Scholar and EndNote XML... If you feel so inclined, it would be enormously helpful if you entered any import/field mapping problems into our bug tracking system: http://mendeley.com/trac?compo... - Victor

I tried it yesterday. I think I imported around 400 articles. There were several errors in import but these are understandable. However I wanted to go through the errors and add tags etc but it was a bit to slow so working on it was a bit frustrating. Is it just me or is it slow for other people as well ? - Pedro Beltrao

Hey Victor, any way to get an invite? Thanks ... - PauloNuin

I second Paulo's question for an additional invite.. - Daniel Jurczak

Paulo, Daniel - I feel rotten for having to turn down your request, but unfortunately, we can't currently invite new testers. Sincerest apologies! The reason is that we've got our hands full fixing the bugs and implementing the feedback brought up by the current testers. I know it seems arbitrary, but there's also a waiting list of people who signed up on our website (www.mendeley.com). May I ask you to register there? You'll be notified first thing we go public beta... - Victor

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

We are so screwed. :-( - Bill Hooker

"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