Just noticed a few glitches - ref 15 from the preface is missing and Antony's bio is missing from the print version. These problems don't show up on the LuLu preview but they do on eReaders, as reported by Abigail on her Nook. So the eReader can serve as a way of checking formatting before print.
- Jean-Claude Bradley
FF doesn't meet all your requirements but it does seem to work well compared to the specialized services - at least in some fields
- Jean-Claude Bradley
Well I guess that's not surprising given my biases - at some level I'm more interested in what people think I've missed than my own predjudices though. FWIW I think a clever combination of DropBox, FriendFeed and some of the elements from StackOverflow, with perhaps a bit of the coordination ability of posterous would go very close to the mark. Still need better network and filter management tools though - somehow they need more configurability but less configuration...
- Cameron Neylon
OpenWetWare is looking to make a major overhaul in the next couple months, and has a bit over 1 year of funding left. I feel like this is an opportunity to at least try to do some of the things that most people think are necessary for SS4S. Not perfect, but better so that we'd have a better idea of what is really needed. I think the time frame (now; already funded) makes "not perfect" a...
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- Steve Koch
I really like what you said in point 10. It's something that I've seen far too many scientists being cavalier about. Federation, open protocols and specifications, along with open source, are very important to science.
- Christopher Granade
Might be worth seeing how far sourceforge meets your criteria. Certainly it's totally based around objects, i.e. software projects, and there are lots of high quality open source science projects whose code is hosted there. Although it has community/social networking tools I've personally never really used these and most visits I've had to sf have either been fleeting (to download...
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- Dan Hagon
Steve, absolutely we need to keep evolving with the resources available. OWW is a great place to do that.
- Cameron Neylon
Dan, there was a conversation around using Github in a similar way some months ago and I think these things have a lot of potential as a back end. I think federation is important enough that you'd want to use a DVCS rather than SVN as a back end though.
- Cameron Neylon
Sourceforge has several DVCS options in addition to svn these days. Although github is great I would be wary of anything that requires scientists to learn the intricacies of git. hg and bzr are much more friendly to non-developer types that don't need the full flexibility of git. I've had some success using them to collaboratively author LaTeX documents.
- Matt Leifer
Matt, ok, I'm behind the times (nothing new there!). The intracies are less of an issue as this would only be a back end. No SS4S that any significant proportion of scientists use is going to look _anything_ like a code repository. To start with your average scientist is never going to touch a command line. If you're dealing in Latex you're already talking about a minority I'm afraid....
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- Cameron Neylon
There are several wikis that use DVCS as a backend. This could be a starting point for developing the type of thing you are interested in.
- Matt Leifer
LaTeX isn't the minority in whole areas of math, CS, physics....I guess that brings up the same old complaint: "science" is defined as all biomed, all the time. I'll try to come up with some more substantive comments though
- Christina Pikas
Christina, didn't mean to say it should be excluded just that a non-command line system is non-negotiable so most online VCS aren't going to be good enough as a front end. Support for Word, Excel, video, images, XML and Latex are all non-negotiable characteristics of any such system.
- Cameron Neylon
Matt, not sure that a wiki is the right starting point - the document model doesn't seem right to me, although I'm way behind on the most recent developments in Wikis so I may be out of date on that as well. What is in my head is a DVCS back end with APIs providing access from e.g document authoring systems, databases, publishers, whatever. A feed system that looks a bit like friendfeed...
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- Cameron Neylon
I wasn't suggesting actually using one of the wikis, just that they have already done a reasonable job of abstracting the version control functionality (in fact, some of them support more than on DVCS in this way) so there may be some things in the codebase that are useful. It is also an example of taking a command-line DVCS and giving it a more user friendly interface. In addition, if...
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- Matt Leifer
Ah good to know - which do you think are the best examples of these wikis? I should take a look. In any case at this stage I'm just throwing ideas out. Have no resource to actually a build anything at moment.
- Cameron Neylon
Is there actually a need for social software for scientists? Or should scientists use and customize the existing social networking tools (FriendFeed, Facebook, LinkedIn, etc.)?
- Martin Fenner
I'm beginning to think the main issue will be that business models for consumers services are incompatible with what researchers need. So yes, customise might be better than build but if we have to go down that route we may as well have a good idea of whats required. One person's customisation is another person's build.
- Cameron Neylon
I'd be curious what you think of HubZero, Cameron.
- D0r0th34
Depends a bit on server setup. For Mercurial I like Hatta, but it requires persistent python processes, i.e. no good for most shared hosts that only allow CGI. There is a list of RCS backed wikis here: http://hatta.sheep.art.pl/Similar projects
- Matt Leifer
Cameron, I love and absolutely agree with the necessity of "scientific objects". If you lack those, then (as Martin points out) just use the general purpose sites. In that principle, I think there are some viable networks -- DVCS systems around scientific code, Mendeley around scientific publications, (eventually our BioGPS around genes). But I think we should be developing specific networks appealing to specific groups of researchers, rather than trying to serve the needs of all scientists...
- Andrew Su
Andrew agreed, but if these are federated then they can all still talk to each other. I'm thinking more framework than site or single service. Ideally all of these things can be plugged in or wired up together...my concern with general purpose sites is primarily that they don't provide the level of trust and stability that we would expect for "research enterprise"
- Cameron Neylon
Just one comment. There are protocols out there that allow different social networks to talk to each other. There are protocols out there that allow web resources to talk to each other. It's not really that hard if everyone supports some basic standards. RESTful API's, OAuth, OpeniD/Facebook Connect/Friend Connect, etc. IMO what's more important is that any sites we design have the...
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- Deepak Singh
@D only really had a chance to have a quick look. First impressions are that it is very slick but looks as though everything has to be on the inside - I don't see much mention of pulling stuff in and out. The multimedia talks are nice but why not pull them in from e.g. slideshare to pick an example.
- Cameron Neylon
completely agreed, federation through standards...
- Andrew Su
Twitter is far from perfect, but look at the infrastructure that has evolved around it e.g. 3rd party apps, services). You don't get that kind of traction around a social networking site just for scientists. Imagine what email or the WWW would look like if there were separate versions just for scientists.
- Martin Fenner
from iPhone
Absolutely but that actually means we can build something better, and as long as it hooks into Twitter (RSS/OAuth...Deepak's list basically) we get all the benefits and all of the functionality we want - as well as a way of drawing people in. Assuming this framework is any good of course. Imagine PubMed if it had been built for the consumer web (actually maybe not such a good example...
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- Cameron Neylon
Sort of responding to Deepak a few comments earlier. Something like a social network is useful for at least one reason: recruiting scientists who aren't ready for open science, or cannot communicate openly for one reason or another. So, a reasonably secure way of making data private and shared with a limited network is a good thing, I think. I think ultimately that will lead to much more open science (my own lab started out with a private wiki before doing ONS)...
- Steve Koch
Steve, but does it have to be a social network per se, or a site for say sequencing geeks (I am looking at you SeqAnswers) with the appropriate features built in. Social networks don't have to be all in the open. Facebook is a social network. 90% of my communication on there is private and you should see how much of my Twitter usage is DM's
- Deepak Singh
Deepak, I think I was just using terminology incorrectly. I was assuming Facebook = social networking.
- Steve Koch
The US gov is inviting comment on the Public Access to Science and Technology. http://friendfeed.com/mrgunn... I know we have some comments, can we draft a quick letter?
Will be happy to contribute and carry work load. Would it be worthwhile to write an 'international' letter that could be forwarded to individual govts (a letter that would be put forward globally, and simultaneously, with signatures from around the world).
- Kubke
Can look over drafts and do tinkering if it is useful...or just sign if it isn't
- Cameron Neylon
Cool, I'll start something on Etherpad.
- Mr. Gunn
question is: should we have 2 letters - one from US residents (whether citizens or whatever) and one from interested international folks? I don't know if they get sorted into different piles or what.
- Christina Pikas
I dont see a need for two letters. The signatures could be separated into US scientists and international support.
- Kubke
Thank you to everyone who helped and encouraged on this and offered future support! Among many things, one thing I'm a bit embarrassed about is the lack of details in the "broader impacts" and open science parts of the proposal. Definitely it needs more planning and better writing, and the panelists are going to point that out. Hopefully you all understand that it's a product of spending all my time trying to make the research parts as good as I could.
- Steve Koch
Thanks everyone! I sort of dropped off the map after submitting the proposal. One of my most successful attempts at actually vacating during a vacation.
- Steve Koch
Bummer! Just found out tonight that the proposal was not funded. I have done one read-through of the reviews. First of all, I am once again amazed at the time and effort the reviewers put into reviewing my proposal. There were 6 reviewers in total and they all had a page or more of feedback. And they all pretty much agreed on the main points: (a) interesting proposal that is worth...
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- Steve Koch
Thank you Jean-Claude, Andy, Cameron, and Drew for the Open Science support letters! I am sure that was key to the very positive reviews for Open Science. Thank you to everyone else on friendfeeed who supports me and our other lab members. We now have 7 months to obtain the preliminary data and get a couple publications, and indeed we are now poised to do so. I am confident the lab members can do this, and by eliminating (b) and (c) above, all signs point towards this being a very strong proposal next time.
- Steve Koch
well done all 'round! next time you'll knock 'em dead.
- D0r0th34
for the CAREER third time is often the charm - good luck for next round
- Jean-Claude Bradley
Thanks, Jean-Claude and Dorothea. The CAREER "3rd time's a charm" effect is part of the reason I submitted without strong preliminary data. (But I also thought we'd be able to generate the data in time for the 2nd submission. Now, though, I'm SURE we can before July :) )
- Steve Koch
After thinking about it for a couple days now, I am still very happy that they viewed the open science so positively. I think that's a big deal.
- Steve Koch
absolutely Steve - very good feedback about OS being a positive to the funders
- Jean-Claude Bradley
Steve, this looks really really promising. If you can come up with interesting data for the next resubmit, I think you have a great chance to get funded. Congratulations!
- Bill Hooker
I must admit that until 48 hours ago, I never realized the Met Office data was secret. I'd always assumed it would be in the public domain. Silly me.
- AJCann
You basically have to send them an email saying what you want and what you're using it for. If you are an appropriate accedited researcher you can get access to the thing you want, but not distribute it I think. Its a classic demonstration of public domain benefits in some ways.
- Cameron Neylon
blimey - I never knew that met office data wasn't public record. Is the idea that Ordinance Survey introduced deliberate small mistakes into their map to protect their copyright? Or is that an urban myth. Depressing is about right.
- Jo Badge
I've heard from people who do mapping type stuff that the OS errors are real. Can't say I've ever checked myself though.
- Cameron Neylon
in the US NOAA NWS data is open, but there's a cost recovery model for some of the historic data sets. I think the art around these parts is to combine NWS stuff with Navy stuff and stuff from the literature, but that's just my impression.
- Christina Pikas
My understanding was that most of it was provided at cost - but a lot is in formats that are not terribly useable or useful so they charge for transfer to media and some reformatting. Bottom line is that most of it is government data and therefore in the public domain by definition.
- Cameron Neylon
Some interesting comments on the blog itself - first time I've had that many comments in ages!
- Cameron Neylon
It was an inspiring talk Tony - thanks for taking the time. In all the talks we had at U of Ottawa 20 years ago I don't think we could have guessed that this what would be happening to chemical information today.
- Jean-Claude Bradley
I like the way you can click on different parts of the InChIKey and have it do searches automatically - I didn't know that before - very cool.
- Andrew Lang
JC...if you'd asked me almost 20 years ago whether I'd be working on a project like ChemSpider the answer would be a big no. I certainly wouldn't have envisaged the progress that we have seen in computer-based chemistry....the internet wasn't even a term we had heard back there in Ottawa!
- Antony Williams
yes we actually physically went to the library back then :)
- Jean-Claude Bradley
Rajarshi Guha presents at the final fall 09 Chemical Information Retrieval class at Drexel University on December 3, 2009. The audio for the first 45 seconds is a little off but the rest is fine. Implicit and explicit molecular representations in 1D, 2D and 3D formats are introduced. Approaches to quantifying molecular similarity using fingerprinting are discussed, such as the Tanimoto index. The relevance of these methods to drug design in terms of virtual screening and QSAR is explored. The concept of scaffold hopping is presented as a way of speeding drug discovery. Finally, ways of comparing the similarity of molecule libraries are detailed, stressing the importance of generating diversity.
- Jean-Claude Bradley
#qotd "New scientific truth usually becomes accepted, not because opponents become convinced, but because opponents die, and because the rising generation is familiar with the new truth at the outset. "
- Duncan Hull
thank you for sharing, sounds very interesting, Cameron, Q: is this 'Impact summary' just one summary among others for this project proposal or is it the only summary?
- Claudia Koltzenburg
ah :-) on text one, some more points emerge: -- it is unclear to me what CRU refers to; -- in 1) "The proposal will also work towards" - I guess this is intended to say "The proposed project...; -- in 2) "Will will" should maybe read "We will"; -- does the structuring 1) 2) 3) correspond to the work packages of the proposal? if not, how *does* the summary structure relate to the main...
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- Claudia Koltzenburg
re text two "easy to use tools that get out of the researcher’s way" - do you mean "tools that are so good that researchers do not realize they are using these tools"?
- Claudia Koltzenburg
Re: text 2 absolutely - that is the aim - probably not quite attainable but a worthy goal. Re: text 1 - yes organization needs improving as to what the point of the three points is. And my sentences are too long. CRU is the Climate Research Unit at East Anglia of leaked emails fame which I will actually take out as a direct reference because it will just get people's backs up for the wrong reason
- Cameron Neylon
Should also point out that we're aiming to make stuff available, not necessarily completely tackling the usability question. Might be best framed as "how many research objects and how much metadata can be collected without bothering the user?"
- Cameron Neylon
from twhirl
agreed, well framed, sounds to the point, it seems to me. Yet: "the user" - what threshold level of experience are you implying for each of the areas you are addressing? is there a phase aspect to what "the user" is, e.g., is this entity made up of other sub-entities at the start of the project than by the time it ends? (am referring to "driving adoption and uptake" in text 2)
- Claudia Koltzenburg
The user in this context is the individual research scientist. Was using it interchangeably with "researcher" to try and keep some variety but its a good point that its ambiguous, particularly when I talk about crowd-sourcing at the end. The "audience" for this document is a panel of primarily biological scientists but the person "handling" the proposal can be expected to have some reasonable IT or information management expertise, as should the referees
- Cameron Neylon
There are 30 different ways to number a die. By stereoisomer do you mean a pair of opposite sides have switched numbers whilst all the other sides are the same?
- Andrew Lang
No, opposite sides have to add up to 7. Stereoisomer here means different spatial arrangements of spots on the faces or arrangements of the faces themselves. Same connectivity, different in space.
- Matthew Todd
Rzepa applies the anthropic principle to amide bond rotation. [Note to self - how do dipoles help explain the Me inequivalence of dimethylformamide?]
- Matthew Todd
from Bookmarklet
Couldn't you change the parameters in the model he mentions to see what chemistry would be like in a 'different' universe? I think that would be very interesting.
- Andrew Lang
Space ships powered by dark matter or baby black holes could enable reaching Andromeda in a human lifetime - fun little article http://www.newscientist.com/article...
The piece mentions Bussard's ramjets which is much more sensible than using dark matter or black holes. Reminds me of the Elite-type fuel scoops on Stargate Universe. :)
- Andrew Lang
Are you talking about when the SGU ship goes inside a star to get fuel?
- Jean-Claude Bradley
Scientific American: Splitting Time from Space--New Quantum Theory Topples Einstein's Spacetime: Was Newton right ... http://www.pheedcontent.com/click...
"AcaWiki is like "Wikipedia for academic research" designed to increase the impact of scholars, students, and bloggers by enabling them to share summaries and discuss academic papers online. AcaWiki turns research hidden in academic journals into something more dynamic and accessible."
- Daniel Mietchen
from Bookmarklet
Good idea, but unlikely to take off, IMHO.
- Björn Brembs
To my understanding it all rests on the willingness of people to write summaries of articles far more substantial than the already available abstracts.
- Jean-Claude Bradley
Why do you think academic PI's would prefer put summary on acawiki but not in blogs?
- Alexey
from iPhone
Alexey - I can see situation where people who don't have blogs would post on AcaWiki - but I don't know if there is a critical mass of people willing to do that
- Jean-Claude Bradley
I think there would need to be some sort of reward. I suggested perhaps for literature reviews (plenty of thesis chapters out there that never get published) that providing a doi and submission to the new Rapid Research Notes database might be interesting in that regard.
- Cameron Neylon
Interesting. DOIs cost money, but a fund for assigning DOIs would be good to have.
- Jodi Schneider
@Jodi, they do, but not that much. If it's worth the CV fodder then I don't think a small payment for a doi is a big problem (if its around e.g. the $10 mark)
- Cameron Neylon
Jenny Carpenter sounds so much like Joanna Scott - I love the sound effect of getting hit by a bus at the start ... FTW Canadian Radio!
- Jean-Claude Bradley
Anna - yes cost is an important consideration. But currently there is no free true substitute for SciFinder and Beilstein and I was pleased to see how CAS takes curation seriously. Over the next few years I think the quality of free databases will start to rival the commercial solutions though. Even now you could do a lot of good research without these tools but you are much more likely to miss some important papers and have to be careful.
- Jean-Claude Bradley
yes, just read the article and was quite impressed with their response. However, since we no longer afford CAS or Scifinder at our university, its all a bit irrelevant to us. They can be proactive, but I will never see it. And trust me, we are highly aware of the risks, but we have to negotiate with non-scientists on this one, who don't see scientific credibility as an issue. :(
- Anna Croft
Anna - that is interesting and another powerful reason for publishing OA - so that your articles will be found by your peers. Does anyone have stats on what percentage of PhD granting institutions have a subscription to SciFinder?
- Jean-Claude Bradley
OA yes! The problem then can be reversed though with only the rich able to afford papers. Most of our grants don't cover publication charges (otherwise one of our articles would have gone directly to PLoS neglected diseases probably) - so the best I can do at the moment is publicise the abstracts and hope someone asks me for the article :) Really need to get using acawiki or related.
- Anna Croft
Anna - have you tried asking to waive the publication fee? We've had good luck with that.
- Jean-Claude Bradley
I feel bad resorting to that; to my mind it should be reserved for truly poor nations, like the developing world. Guess I could though :/ Afterall, this is stuff where the results are already attracting interest without publication, but we already hit 'my computer is bigger than yours' referees on last submission.
- Anna Croft
Anna - Bora posted some interesting stats lately - I think only about 10% of authors requested a waiver. I don't know if the 90% pay the fees via NIH or with some help from their institution - it would be interesting to see that breakdown.
- Jean-Claude Bradley
Ok, well I am at least thinking about it. Was considering the position if one offers to review extra articles, but then this would create a time divide - people who can afford to buy time away from refereeing vs those that need to to get published but have no money; and thus have less time for writing papers. => rich institutions getting richer and poorer ones doing all the work.
- Anna Croft
wow - amazing talk on knowing the universe is flat, civilizations evolving in 50 billion years will see no evidence of the Big Bang, the total energy of the universe is zero and the mass inside of protons is in the voids
- Jean-Claude Bradley
Yes, Krauss gave a talk at Sydney last year, and I was surprised by that idea that future civilisations will have no decent evidence of the Big Bang.
- Matthew Todd
Mat well to be more precise: they won't have any evidence using the techniques we've been using for a few hundred years at most. Lots of people are famous for claiming that things are impossible only to be proved wrong by using methods previously unimaginable. Still this doesn't make the talk any less powerful.
- Jean-Claude Bradley
Andy- yes he had some good material - a few Bush jokes never hurt
- Jean-Claude Bradley
IMHO, it is one of the best presentations on YouTube
- Björn Brembs
I think the IUPAC name is going to be great. Markus let me test this before it was made public. Avogadro will soon gain a structure->name system.
- Geoffrey Hutchison
Actually, I would say the main advantage is that absolutely no technical ability is required. In contrast, adding a Jmol applet of benzene to your website is not trivial.
- Noel O'Boyle