focused on the information sharing aspect, appropriately so. - Mr. Gunn
I had a long talk with David today - there could be great synergy with our work on anti-malarials and certainly with the Open Science community - Cameron he's on your side of the pond - Jean-Claude Bradley
Ah - then I should defintely make contact with him. Left a comment on his blog this eveing about the open source drug discovery thing. - Cameron Neylon
Each new site should have a "why we're different/better than all the others" statement, because I'm not seeing it. Saying they're first is blatantly untrue, isn't it? - Mr. Gunn
Calling yourself the first when you're not: FAIL - Ricardo Vidal
true it is a bit misleading - if you feel isolated as a grad student join the blogosphere - plenty of grad students with blogs - Jean-Claude Bradley
Exactly, JCB! A network of bloggers is a social network, in fact it's the original social network. Facebook is just training wheels. - Mr. Gunn
Some very good points in there: "Whilst there are clear benefits to be achieved from providing teachers and students with the opportunity to share ideas in the context of stimulus artefacts, many hold reservations about 'giving away' their intellectual property." [...] "Their main concern is to access reliable, relevant content and information, but the ability to form connections between these resources is one way of adding value to the collection." - Thomas Brox Røst
many people concerned about "giving away their IP" need to have a talk with a VC. Was it Kawasaki that said something like "Nothing is novel anymore, and if someone has never thought of your idea before, it's probably because it's a dumb idea."? - Mr. Gunn
I've also had some contact with people preparing a report on Web2 and science so I need to talk to them and then point them here :) - Cameron Neylon
Insightful rant - it's better to define a job more by it's output than by what's actually done day-to-day. That's why "Movie Director" is better than "Project Manager". - Michael Nielsen
Cool! Should add that to my other FOAF file... - Egon Willighagen
It's had that for a long time (get the Semantic Radar extension, detects all FOAF friendly sites). MyBlogLog has that too - Deepak
I wanted this from Nature Network: would be far more interesting to get such an automatic FOAF profile with publications, locations, tags (=interest), network... Many tools could be built from this informations: "I'm looking from someone who know somenone in germany who worked on HIV..." - Pierre
cool, who wants to write a spider for this? - Mr. Gunn
Jonathan, you should title one of those upcoming PLoS papers "Tree of Life" and we'll all link to it and cite it feverishly! http://is.gd/Kxk - Duncan Hull
You may not worry about having the term "Tree of Life" lost to Hollywood, but when the next Angelina Jolie movie is titled Nodalpoint lets see what you do .. - Jonathan Eisen
yes, that wouldn't be good. Speaking of nodalpoint, I'm surprised Bosco Ho http://boscoh.com and Greg Tyrelle http://tyrelle.net aren't to be found wasting time on friendfeed... we should invite them to join the party... - Duncan Hull
"Wasting time"?? I resemble that remark! - Bill Hooker
We actually stole Nodalpoint from William Gibson. As for Greg, ironically for a web pioneer, he maintains almost no web presence whatsoever. Too busy in the Taiwanese corporate biotech sector. - Neil Saunders
This is a great piece, but I have a minor quibble: data is not so central to day-to-day practice in some scientific communities. Certainly, it's less central in much of theoretical physics, economics and computer science than it is in (say) observational astronomy. - Michael Nielsen
Michael, I use "data" in a rather loose sense of the word. It could be publications of common interest, or some other lower level concept that people can coalesce around. - Deepak
Well, at least FOF's aren't hiding you. - Tom Landini
I follow Josh Bancroft who follows you, so I saw your post. Which is a nice feature of FriendFeed. Initially I thought having friends of friends show up in your stream would be a mess, especially if you've subscribe to some attention moguls, but it works pretty well. - Adam Turetzky
I'm paying attention. Here's a comment (half an hour late, oops) - Lee Adkins
And in the end, the love you take...or is it make? Heck, I forgot... - Ontario Emperor via fftogo
This is definitely interesting. So if you are a FOF, and you comment here, do YOUR friends see that? FOFOF? - Andru Edwards
I don't follow you but you pop up as (friend of Robert Scoble). I'm not sure if I see everything you post but I see you passing by in the river quite frequently - Jon Dillon
Still over 50% of people replying are people who hadn't yet followed me. So the new followers and the people who are engaged...but what does that say about my original 150 or so followers? :) - Andru Edwards
i checked friendfeed for the first time this month and here's yours at the top. do i still count - Nate True
There have been a few conversations around this -- JCB uses WikiSpaces, Cam uses homebrew blog/wiki, and iirc a couple others were suggested but that's about it. - Bill Hooker
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
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
I realise I'm way late on this but I thought I'd add my two pieces. Our approach is blog based and (we think) neatly solves the problem of the issue of 'free text' via form based input by enabling users to set up templates using the standard markup language with some wildcards in it. I desperately need to do some screen casts of how this works but you can see some of it in the talk I gave at Drexel last year (http://drexel-coas-talks-mp3-p...). - Cameron Neylon
This enables the non power user to easily set up templates that then generate forms that can be filled in. Our user interface is ropey at the moment and as Bill points out we don't have a community using this as yet but we're working on both of those! - Cameron Neylon
I used Wordpress for a couple of years - would probably use that or Drupal (for structured entries) nowadays. - hubfeed
I really learned a lot from Jean-Claude's presentation that he delivered during Drexel University Libraries' Annual symposium on Scholarly Communication. Please also refer to http://scholar2scholar.wikispa... for notes taken during the 'Roundtable Discussion' and 'Further Reading' section for web resources on Web 2.0 and Scholarly Communication when you get a chance. - Jay Bhatt
There was recently a Brazilian paper using the h-index to show the Brazilian scientific productivity. I will find the link but I don't know if it is in English. - PauloNuin via twhirl
Thanks for pointing this out Bill and commenting on there - it is interesting the level of animosity the concept generates for people who speak before they read. - Jean-Claude Bradley
At least it is an opportunity to clarify some misconceptions - Jean-Claude Bradley
I just don't get people. It's not like anyone is saying that ONS is the only way of doing science. It's "a" way, and a perfectly fine one if someone so choose, but then if anyone equates science to just wet lab work is hopelessly lost - Deepak
Yeah, I don't get the animosity either. I do know it's very common in science though, and I don't understand why that should be. Shouldn't researchers be both *curious* and *positive* about new things? - Bill Hooker
I am not sure it is even worth responding anymore. The whole strategy of that blog seams to be to irritate people enough to comment and come back to the "discussions". - Pedro Beltrao
I take back this last comment. Whoever writes the blog does have interesting and useful blog posts in there. I don't get it why once in a while he/she has those posts full of insults that clearly look like flame bait. Just for the fun of it here is a link to a rinsed version of the RSS feed of DrugMonkey (http://www.feedrinse.com/servi...) - Pedro Beltrao
There's an art to using a combative, abrasive style in this way. Personally, I think RPM at ScienceBlogs has it and this guy doesn't. I just find it very tedious and go elsewhere. - Neil Saunders
@Neil: absolutely agree there's an art to it, but I like PP and think RPM should dial it back a few notches, because he has lots of good stuff to say but just doesn't have the gonzo style down. - Bill Hooker
On a related note --- what do people recommend for electronic lab notebooks in general - either the closed kind or the open kind? I am trying to move my lab to all electronic notebooks with the long term goal of posting a lot of stuff openly but I need to start with a good electronic notebook ... - Jonathan Eisen
@Jonathan - can of worms, mate! There is no good, free/open-source, one-size-fits-all ELN solution. Most people here are using wikis, blogs or a combination (blikis). - Neil Saunders
@Bill - question of personal taste, I guess. I'm not a fan of science bloggers who feel the need to project a contrived writing style. It just obscures the message for me. - Neil Saunders
Thanks Neil. The problem with the wiki/blog option is getting non techno people to use it. We have a lab wiki. Still hard to get everyone to use it for lab notebook stuff. Will check out smartnote - Jonathan Eisen
Jonathan - as you know I'm still a big fan of the general purpose wiki as lab notebook. One of the advantages of Wikispaces is that it has a decent visual editor and a highly simplified WikiText. But not matter what you use it will take more than technology to get your group members to enthusiastically use it. - Jean-Claude Bradley
Agree, Jean-Claude and Jonathan. My attempts, even with a visual editor and a training course, have failed to encourage lab members to edit our internal lab wiki. It was set up initially to only share our small sequence datasets, with the idea that this could be a pathway toward lab members using the wiki for protocols, and maybe even migrate to an open space like OWW eventually. It seems to be a real difficulty for the non-techno crowd, and it seems that they won't even try. - Andrew Perry
We get some use from our lab wiki and a LIMS that I hacked together, but only under great duress - basically the boss demands participation. Unwillingness to try is a source of continual frustration and incomprehension to me. The benefits are clear (I hope), the users are not stupid (I hope), nor computer-illiterate (if they can set up and manage Facebook, they can manage a wiki). It's either not a priority for them or else they're just lazy. - Neil Saunders
The problem we are having is integrating multiple formats - handwriting (e.g., lab notes), pictures (e.g., non digital images), digital images, analysis, etc. It is not that people are technically fearful, it is that getting people confortable with the idea of doing everything on the computer and changing practices (e.g, taking notes on the computer not by hand) will take some time. - Jonathan Eisen
I sometimes wonder if the free-form nature of wikis confuses some people. It means that they have to define their own structure for storing data. This is why I think the world needs a good, free, open-source ELN (and a LIMS) with flexible, but defined form fields: date/time, title, aim, upload (image/spreadsheet/text/whatever), notes and so on. - Neil Saunders
I think that's a big part of it, Neil: it took me a long time to grok wikis, and (by labrat standards) I'm a geek. Add to that the baffling tendency of scientists to sneer at anything they don't understand (I swear, outside their research, this is true -- and I have no idea why it should be so), and you have a recipe for Luddism. - Bill Hooker
A lot of reluctance is not related to technology - it is just human nature. Most students that I have had would not even keep a decent paper notebook without constant vigilance on my part. Some get it - and those who do of course will end up on top after they graduate and carry their skills to the workplace. - Jean-Claude Bradley
