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Webel - a web service based python library for chemical information - http://baoilleach.blogspot.com/2009...
Deepak Singh, Rajarshi Guha and Peter Miller liked this
Potentially a nice simple library for implementing in AppEngine based web services and/or Wave robots. Simple text search, MW, SMILES etc. Or I could finish wrapping the ChemSpider API properly...
- Cameron Neylon
Reflections on Science 2.0 from a distance - Part II - http://blog.openwetware.org/science...
Jan Schmirmund, Steve Koch, Neil Saunders and 5 other people liked this
I like your description about linking between different ontologies derived (and utilised) within different contexts. IMO shoehorning standards to fit leads to dogma, not innovation.
- Ant Beck
how easy is it to reconstruct your lab work if it used a just-in-time or transient ontology?
- Alec
I don't know - and there isn't really anything to compare it to either in terms of ease. There are many things that make it hard to use our lab records and we need to work on all of them.
- Cameron Neylon
One for the language geeks. What's the plural of lingua franca?
Matthew Todd and Michael Kuhn liked this
if we're being snobbishly latinate, linguae francae.
- D0r0th34
Hah! I guessed right then...reckon I'll be snob :-)
- Cameron Neylon
I think 'oxymoron' might get close ;)
- Pete
Reflections on Science 2.0 from a distance - Part I - http://blog.openwetware.org/science...
Mr. Gunn, Benjamin Tseng, Steve Koch and 6 other people liked this
Interesting point - could only track down Jon's tweet via Friendfeed. Possibly an argument for piping mine back in - or perhaps setting up a secondary account for archiving...
- Cameron Neylon
a secondary acct for archiving is a good idea.We tend to pull the RSS from tags on the day of any event and stick them in FF or google reader. Having an RSS feed of your own tweets into GR could work too. Tweetstream is definitely pretty transient these days.
- Jo Badge
I use FF as a searchable repository of my tweets, at least for now.
- Bora Zivkovic
The third para of that post was delightful. I also use FF exactly as Bora does, and to search for the tweets of some others. In fact I've toyed with setting up 'imaginary friends' of people / corporate tweets which don't have an FF account for this purpose but haven't got round to it yet. I really don't use FF enough!
- Jo Brodie
Love it: "...the natural unit of science research is the blog post".
- Bill Hooker
Next-gen PhDs fail to find Web 2.0's 'on-switch' - http://www.timeshighereducation.co.uk/story...
Jo Young, Cesar Sanchez, Joe Dunckley and 12 other people liked this
Why am I not suprised...?
- Cameron Neylon
saw the press release for the original piece of work behind that yesterday here: http://www.rin.ac.uk/our-wor...
- Jo Badge
Like as in "I share your...concern? Despair?"
- Neil Saunders
Ah I missed that - also interesting in the context of the NIH grants - anyone tracked any more information on those projects?
- Cameron Neylon
I don't really despair but assuming that group culture and practice will change because some young people come in isn't suprising. Search happens with a single person, so they will use those tools, but social bookmarking requires groups acting together. This means that you at least need critical mass within the group, or more likely, active encouragement from the top.
- Cameron Neylon
Change is happening, But ... very ... slowly.
- AJCann
hmm, just skimming the report (from Brisith library) says that librarians need to reconnect with scientists - errr, when were they connected?
- Jo Badge
I'll set the librarians on you.
- AJCann
and here we are. what? oh, well, it's a given that people contact their friends first before the librarian - that's been found in our literature for probably close to 100 years. i'm thinking that search engines probably are above friends now... .what's really great is if you're friends with a ton of your scientists and engineers so even if they don't call "the library" they say, "well I'll just call Christina" (I get that a lot)
- Christina Pikas
but about the article - I'm happy to see this because it supports the findings of the first wave of articles on the uptake of ICTs in science from the 90s. 1)it's not just a matter of time, 2) it isn't necessarily a matter of age (not all youngsters want to try or know how to use all new technologies), etc.3) usage across areas of science will differ
- Christina Pikas
*bays at the moon* *sniffs* *catches a whiff of scientist* AROOOOOOOO! *chases*
- D0r0th34
From Jo's comment, an outside observer would have to ask: Is it that science librarians make no effort to connect with researchers (which, given people like John D. and Christina P., I find VERY hard to believe) or that researchers show no interest in a connection? "You can lead a horse to water" and all that... but what do I know, being neither a scientist nor a librarian?
- Walt Crawford
I think another aspect of this is the plain old fashioned 24 hour day. My students -- and yes, they are undergrads -- are absorbing so much content information that they MUST learn or they fail, and doing so much volunteer/shadowing that they MUST do or they cannot get into grad school, and even those doing research are so busy learning western blots and how not to screw things up that...
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- Mickey Schafer
I'm wondering what our generation is going to say the one after us is failing to adopt. Seems to me like there's an unspoken assumption behind the question - either there has to be mass uptake for it to be useful or something along the lines of "What's the business model?" These questions invariably seem to come as people are trying to justify the use of web20 tools to themselves or...
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- Mr. Gunn
Distributed Science, Part 2 - http://scienceblogs.com/commonk...
'Mummi' Thorisson and Graham Steel liked this
John Wilbanks nails it - no surprises there then :-)
- Cameron Neylon
When access to the internet becomes a human right, is it against the Universal Declaration to switch it off. - http://blog.jaggeree.com/post...
Daniel Mietchen liked this
Reflective FriendFolios - http://scienceoftheinvisible.b...
Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world - http://www.citeulike.org/user...
Claudia Koltzenburg, Daniel Mietchen, 'Mummi' Thorisson and 2 other people liked this
Really must figure out how to set the citeulike feed so as not to push my own papers through to here :-)
- Cameron Neylon
Nowt wrong with publishing in multiple channels for different audiences.
- AJCann
Try doing a FF search for "citeulike" and then say that again! :-)
- Fergus Gallagher
Yes, my concern is that I'm publishing the same content in on aggregated channel to the same audience...I guess this is why people like posterous as a central wrangling house so much
- Cameron Neylon
Social programming should be a feature of a language - http://amix.dk/blog...
Daniel Mietchen and Christopher Granade liked this
Open Source Science? Or Distributed Science? - http://scienceblogs.com/commonk...
Jean-Claude Bradley, Steve Koch, Deepak Singh and 2 other people liked this
BMC Awards: A good opportunity to promote an Open Science research paper? Any suggestions? http://www.biomedcentral.com/researc...
The trouble with getting a domain name is that I actually need to figure out how to organize my online life...
Khader Shameer, Dan Hagon, Jason Winget and 3 other people liked this
I've been at it for years and still haven't figured it out
- Deepak Singh
It's a lot of work. Probably easiest to have a clear landing page that says "here are all the other places to find me".
- Neil Saunders
Yes, more or less figured that out. Question of how to set that page up at the moment. I do want to aggregate some stuff back to one place though. OpenIDs, FOAF, draft documents, that kind of thing, and some view of the streams that I'm generating. Aside from anything else I need to learn how to actually run/deploy/setup these things.
- Cameron Neylon
On a related note: It seems you used to be able to generate FOAF for your Friendfeed subscriptions using http://friendfeed.com/<username>/subscriptions?output=foaf .. but unfortunately it doesn't seem to work now.
- Andrew Perry
A domain name is just a name so if you've got some content hosted elsewhere already you can just use it as an alias - however I think the problem you're actually talking about is hosting that content. Assuming you're not already tied into one particular hosting company (as part of the domain name registration) I'd advise looking at a few content management systems (although they're...
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- Dan Hagon
Wait, friendfeed FOAF doesn't work anymore? Data portability fail there! I hope that's not a facebook-mandated change.
- Mr. Gunn
Cameron, I'd look into delegating your domain URL as an OpenID URL. Verisign has a pretty cool profiles service: http://williamgunn.pip.verisignlabs.com/ and there's also Google Profiles.
- Mr. Gunn
@Mr. Gunn - fancy stuff, this, very cool. Coverflow-style scrolling borrowed from OS X. Methinks I should switch from MyOpenID (http://mummi.myopenid.com)...
- 'Mummi' Thorisson
Yep, openID is coming. Think I'll be doing something quite simple with a Wordpress install as a starting point.
- Cameron Neylon
"Head in the Clouds" - A paper on Web-native lab notebooks in a new BMC journal: http://www.aejournal.net/content...
Mackenzie Cowell, Jason Morrison, Pawel Szczesny and 13 other people liked this
A change in the weather? - http://network.nature.com/people...
Björn Brembs, Duncan Hull and Mickey Schafer liked this
I worry a bit more about the mob element and also the selectivity of the community. Much negative response and little positive. The temptation to create a twitter storm to push a point without requiring much thought or even evidence will be great. In public life, as in science, we need to develop a much greater evidence culture.
- Cameron Neylon
Interesting article. Perhaps there is an element of society that hasn't been engaged in this sort of discussion before. I am of a generation that rarely (very very rarely) reads a newspaper and my news comes from the bbc website or twitter these days. Perhaps we have actually reached the stage of twitter as the citizen journalist? Will it be any better than the traditional media...
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- Jo Badge
This was a very interesting read -- ambiently-produced knowledge; ambiently-directed action. I find myself with the same sense of cautious optimism that Curry mentions by the end of the post.
- Mickey Schafer
Thanks for the comments folks. I do share your concerns Cameron. There was a more negative take on this in The Independent today: http://www.independent.co.uk/news.... I agreed with some of Glover's points - Twitter is more amenable to blind...
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- Stephen Curry
Clay Shirky had a good piece on a bad twitterstorm - http://www.shirky.com/weblog...
- Anders Norgaard
Stephen - agreed. I just meant to say that I got the impression that my sense was a little more towards the negative than yours seemed. Still very many strong positives here. We certainly live in interesting times...but then perhaps everyone does :-)
- Cameron Neylon
No, no - I'm pretty sure the Dark Ages were a crashing bore. *Much* more interesting nowdays! Then again isn't "may you live in interesting times" a Chinese curse!?
- Stephen Curry
Transitions, transitions - http://freelancingscience.com/2009...
Thieme Announce Access to DOI’ed Primary Analytical Data Available - http://www.chemspider.com/blog...
Steve Koch, Jean-Claude Bradley, Claudia Koltzenburg and 3 other people liked this
Yeah. That's the way to go :) FTA: "..Thieme have actually managed to pull off quite a coup and I commend them for their efforts." second that, times two.
- 'Mummi' Thorisson
DOI resolution works like a treat for the example given: http://dx.doi.org/10...
- 'Mummi' Thorisson
Ok - I have all the tweets from last weeks Leicester talk in an XML doc. Quickest way to convert to nice text/html in forward time order? - http://dl.getdropbox.com/u...
Claudia Koltzenburg and Mike Chelen liked this
Easier to start with the csv from http://twapperkeeper.com/uolneyl... ?
- AJCann
twapperkeeper doesn't seem to do it retrospectively...unless someone set one up in advance?
- Cameron Neylon
Do what? Convert to html? Hashtag is archived at http://twapperkeeper.com/uolneyl...
- AJCann
ok stand corrected - it does appear to be retrospective - or is this one that you set up previously?
- Cameron Neylon
I didn't set it up, maybe Jo did?
- AJCann
I did set one up a few hours back but it didn't seem to have gone back in time at that point. Maybe it just took a while. Getting closer, but now how can I put the links in? Hmmm
- Cameron Neylon
Ok, into Excel and now inthe right order - but how to format nicely for Wave? And will I have to write a Robot to do it...? Maybe I should just write a robot to pull the csv from TwapperKeeper...
- Cameron Neylon
Cameron, give me 5 minutes to convert this into HTML with XSLT
- Pierre Lindenbaum
@yokofakun rides to the rescue again! :-D
- Cameron Neylon
@Pierre A whole 5 minutes? Sheesh. You're getting slow. ;-)
- Chris Lasher
Chris, do not disturb me please :-)
- Pierre Lindenbaum
OK, done: sent on your mail at stfc
- Pierre Lindenbaum
Cool - will spend train trip home figuring out how the xslt works. Thanks for that! Good tutorial material.
- Cameron Neylon
Considering ways of aggregating information around a presentation into Wave in case that wasn't obvious. Inspired in part by Eva's comments on http://network.nature.com/people...
- Cameron Neylon
Unfortunately I didn't catch this in time to register the hashtag with 'what the hashtag'. It gives the best transcripts in my opinion... really easily. Here is an example from yesterday:
- Anne Marie Cunningham
Become independent of peer review - http://www.daniel-lemire.com/blog...
Rudolf Olah and Branwen Hide liked this
Quoted from Edsger Dijkstra: "Not only does the mechanism of peer review fail to protect us from disasters, in a certain way it guarantees mediocrity: the genius has no peers. And to make matters worse, his publication record does not reflect his work either. At the time it is done, truly original work —which, in the scientific establishment, is as welcome as unwanted baby— is very hard to publish as it takes at least another ten years for the appropriate journal to be founded."
- Daniel Mietchen
"I wonder if Journals shouldn’t encourage authors to set up blogs or even better yet wikis sites to write their article and get others to contribute." - comment #4, by Bradley Shoebottom. Yes!
- Daniel Mietchen
First Biology on SANS2d - http://www.slideshare.net/Cameron...
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Steve Koch, Benjamin Tseng and Jean-Claude Bradley liked this
nice toys
- Jean-Claude Bradley
Neil Swainston: We are the Robots - http://neilswainston.blogspot.com/2009...
Peter Miller, Daniel Mietchen and Mike Chelen liked this
Neil Swainston builds a Google Wave robot to hit the proteomics service at Manchester CISB for Uni_Prot names and return data that is available.
- Cameron Neylon
is there one that does Brenda?
- Anna Croft
Slides From DevDays Talk in Toronto Oct 23 - http://pyre.third-bit.com/blog...
Richard Akerman and Jean-Claude Bradley liked this
Women in Open Science - http://akcscience.wordpress.com/2009...
Mike Chelen and Daniel Mietchen liked this
Today's PhD seems apropos: http://www.phdcomics.com/comics...
- Christopher Granade
Beyond the Pale - http://www.inkspotscience.com/blog...
Daniel Mietchen, Bill Hooker and Jean-Claude Bradley liked this
Added McIntyre to http://en.wikipedia.org/wiki... He's controversial but appears to be all about the analysis of the raw data
- Jean-Claude Bradley
Nguyen on ‘hidden legal barriers’ to research - http://sciencecommons.org/weblog...
What is the Cost of PhD-level Intellect These Days? - http://openphd.wordpress.com/2009...
post title is a bit of a misnomer -- it's really about the cost of Ph.D certification. Ph.D level intellect is all over the place, with and without actual Ph.Ds.
- D0r0th34
I agree. There are plenty of people smart enough to get a PhD who were also smart enough to realize that they don't need to do so. Basically, I don't judge intellect by what degree someone has attained.
- Katy S
Ahhh, but it is not really about the cost of a PhD. The entire blog is about an Open PhD - in other words achieving the "PhD intellect" or proof thereof - without spending a penny. This particular post was to show that the ridiculous amounts of money spent on tuition from one institution as compared to another doesn't guarantee or define the quality of the doctoral candidate - it merely defines the quality of his or her wallet.
- Lisa Chamberlin
If you could start with a blank sheet of paper… - http://gov2.net.au/blog...
Richard Akerman liked this
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