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Cameron Neylon
A collaborative proposal on research metrics - http://cameronneylon.net/blog...
When we talk about open research practice, more efficient research communication, wider diversity of publication we always come up against the same problem. What's in it for the jobbing scientist? This is so prevalent that it has been reformulated at "Singh's Law" (by analogy with Godwin's law) that any discussion of research practice will inevitably end when someone brings up career advancement or tenure. The question is what do we actually do about this? n opportunity has arisen for some funding to support a project here. My proposal is to bring a relevant group of stakeholders together; funders, technologists, scientists, adminstrators, media, publishers, and aggregators, to identify needs and then to actually build some things. - Cameron Neylon
Wonder whether Andrew Treolar might have insight to contribute http://andrew.treloar.net/ - Kubke
AT certainly has experience of the problem and also seems to be collecting a lot of data... - Cameron Neylon
He was strong about making data sets a primary citable object at the data matters meeting where I met him, to make the 'use' of the data as trackable as any publication - Kubke
Yep, I think that's a key theme. Need to make sure have Dryad and Datacite involvement with this. - Cameron Neylon
He suggested giving the 'data' a DOI and tap onto the search/link/tracking that already exists for paper publications as something which could provide an initial viable solution - Kubke
Essentially this is what the DataCite project are doing. I think Dryad is connected with them as well. I worry about using dois for this because I would rather URLs [ducks in case geoff bilder arrives to pummel me (-; ] but the reality is that the scientific mindset seems to be doi = real so I think it's going to be the way we move forward in practice. - Cameron Neylon
The redirection mainly. Essentially it breaks a whole set of fun things that you can do with URLs. None of which to be fair are very commonly done. Also in principle they could be enabled through the doi redirect. Essentially its a minor quibble that it doesn't add anything technically and breaks some stuff. But the reasons for dois are fundamentally social not technical. - Cameron Neylon from twhirl
I'm a big DOI fan. Just yesterday I ran into a few duplicate papers in the Mendeley library. One reason is that there are several URLs associated with a paper: PubMed, Journal HTML page, Journal PDF, institutional repository URL,... Not to mention that many URLs break over time. - Martin Fenner
And DOIs would really help to automatically find science blog posts associated with a paper. The Journal of Neuroscience editorial about supplementary information in August has no DOI. Almost impossible to find all blog posts (there are many) that talk about this editorial. - Martin Fenner
All true but I guess my problem is that fundamentally dois are a special system so that generic web tools (and yes particularly semantic web tools) will break over them and the info won't get incorporated into the wider web. e.g. Martin's problem could be solved by an owl:sameAs which would mean that it would be transparent to other web systems. But with dois someone has to build... more... - Cameron Neylon
None of which changes the reality. DOIs are dominant and are here to stay as far as I can tell so I just need to get over it and move on... - Cameron Neylon
Just added a comment and we need to do more than offering incentives for "re-use". - joergkurtwegner
While I am a big fan of finer-grained measures of contribution (e.g. peer review), I am not convinced that the current proposal should be stretched to cover such measures. It seems to me that what is wanted here is a hard-nosed, outcome-focused project designed to answer hard questions about ROI. For that purpose, a close focus on re-use is probably optimal. - Bill Hooker
Nice proposal. It currently focuses strongly on funder needs. Useful, perhaps necessary, but it means delayed and indirect rewards to the jobbing scientist. Would it make sense to work in a more direct focus on "jobbing scientist needs" too, with possible hacks of automated reuse-metric CVs and reuse-metricful tenure packages? - Heather Piwowar
Joerg - I commented on your comment back at the proposal. Two things really. My view is that the "measuring re-use" idea covers things like review. A good review needs to be "cited" in some way and that re-use measured and rewarded. I'm not quite sure where you're going with the micropayments thing. A kind of micropayments has been tried by EPSRC in the UK where they pay £50 or... more... - Cameron Neylon
Heather, good point. Although the response I've got suggests that people are interested enough in the possibility of getting credit for a more diverse range of things that thats enough at the moment. But yes, the CV is a very good place to realise some benefits. Need to talk to someone inside VIVO I think to see if there is some low hanging fruit there. - Cameron Neylon
@Bill , @Cameron - I understand your views and the ROI question is important. As long as we agree that there is some measure, recognition, and reward scheme I agree. So, a re-use needs to be tracked otherwise, we need to prevent ab-use of re-use. - joergkurtwegner
So if I'm reading you right your core point is that we shouldn't assume that simply by measuring something that the rewards will flow from that. That it is important to consider explicit reward schemes, which might include payment or aggregated micropayment? - Cameron Neylon
Actually it strikes me that both Joerg and Heather are pointing in the same direction here. Keeping up the issue of direct benefits. - Cameron Neylon
Cameron, what is your timeline for the proposal and what sort of additional help would be useful at this point? The current draft doesn't have references: do you need any? Other help? - Heather Piwowar
References (both to literature and to other projects) would be a big help. Contacts with funders would be useful if anyone has them. And proof reading still valuable. I'm currently checking with the funder whether this is heading in the right direction and then I'll start pulling in contributors more. Timeline is really about a week though the quicker the better I suspect. - Cameron Neylon
Also anyone got a good contact on the inside of VIVO? I know that Mackenzie Smith is on their advisory board but don't have any good contacts on the inside. It would be an obvious source of data. - Cameron Neylon
Sounds good. I've added (REF) indications where it seems like references might be appropriate, to facilitate crowdsourcing. Cameron, please edit as needed based on the intended document length and number of refs expected by the funding body? - Heather Piwowar
Yep, still working on those last two questions... ;-) - Cameron Neylon
what came of this? - Claudia Koltzenburg
Got the money, running the workshop: http://beyond-impact.org - Cameron Neylon
Interesting - is this the Friendfeed replacement? - http://mashable.com/2010...
Interesting - is this the Friendfeed replacement?
"LinkedIn Signal is a content consumption application with more filters than we could possibly ever need. Signal pulls in both Twitter and LinkedIn updates from LinkedIn connections and presents them in a style similar to the Facebook News Feed." - AJCann from Bookmarklet
Well, if they let users feed other stuff in there besides Twitter (e.g., I block all Twitter without like or comment on FF), it seems very powerful! - Björn Brembs
Closed beta at present so we have to wait to get our hands on it. Then it's a question of whether this community will migrate or fragment. - AJCann
Personally, I'm beginning to like http://lifestream.aol.com/ although essentially no-one is there yet. Encouragingly, AOL did just buy the Brizzly team in order to work on this. - Matt Leifer
I keep my LinkedIn for work-related network... I do not even want to think about mashing that up with the stuff I put now up on FriendFeed... it would ruin the LinkedIn to me. I'm already ignoring the groups, as they have become dumping places of noise already... - Egon Willighagen
It is the filtering of FF that is a winner to me... I'm really not interested in the photo's people make, and often hide them... I have seen beautiful nature photographs (that, btw, must go into Wikipedia), but after seeing them I often 'Hide' them... sometimes I even decide to Hide a particular feed of someone... this is the functionality that makes FF work for me... but LinkedIn is... more... - Egon Willighagen
Martin Fenner
Do you read the papers you cite? "No: I only cite my own work" one possible answer in survey by The Scientist http://blog.the-scientist.com/2010...
The conversation between Martin and Christian Specht is a gem. This is what the internets are *for*. - Bill Hooker
Hey you gotta be honest... - Benjamin Tseng
Also a nice anecdote from Jan Velterop. I think there is material for many more blog posts. My latest post (about Citation Style Language) of course also cites the Laemmli paper... - Martin Fenner
There's another problem here. I often cite a paper for a number or a piece of data. I'll check that number or comment in the paper but will often not read the whole paper. Does that count? - Cameron Neylon
how do you know that paper has the number or comment you want? surely you have to at least scan it? - Christina Pikas
Google...so yes, I skim but I wouldn't call it reading...not in the sense I think is meant in the survey - Cameron Neylon
I actually read every article I cite. Even go through the trouble of having articles translated for me when I don't know the original language when the article has precedence over a specific finding. - Kubke
I fall between Cameron and Fabiana; I will cite papers for a number or single observation or whatever, but I do read enough of the paper to be sure it says what I think it says about that particular datum. (Actually I suspect this is what Cam does as well -- "skimming".) I definitely don't give a close reading to every paper, checking references and scrutinizing controls and statistical... more... - Bill Hooker
I don't think I could cite something I didn't read, how would you know if that paper actually shows what you are claiming in your statement ? Citations serve as foundation for the research problem, methods or discussion. Assuming that you are not constantly changing topics those citations are not going to keep changing dramatically either so getting up to ~100 well understood papers is not that hard .. even at 1 day per article. - Pedro Beltrao
"Assuming that you are not constantly changing topics": schistosomiasis --> HIV replication --> iron homeostasis --> Ebox signaling networks --> HIV diagnostics. In the first two (phd and first postdoc) and in the Ebox work (last postdoc), I probably did have e.g. 100 well understood papers that I had read carefully and cited regularly. But that was the foundational stuff; there are... more... - Bill Hooker
Björn Brembs
'Supplement' is an anachronistic pejorative for 'essential information' - http://bjoern.brembs.net/news...
Björn Brembs
Social filtering of scientific information - a view beyond Twitter - http://bjoern.brembs.net/news...
The fruits of our collaborative effort at http://ff.im/beKZB . Special thanks to the other co-authors http://friendfeed.com/danielm... and http://friendfeed.com/allyson - Björn Brembs
@Frank: you should try the Readability bookmarklet: http://lab.arc90.com/experim... -- works wonders :) - Michael Kuhn
Cool! Subscribed to some of those, thanks! - Björn Brembs
sure :] .... posted this to http://friendfeed.com/friendf... - here you can complain about Friendfeed :] ... .... http://friendfeed.com/mashabl... - pb:
Very nice, has anyone tried to set-up and using the open source'd FriendFeed, called Tornado? http://www.techcrunch.com/2009... - joergkurtwegner
Awesome! I did not know of Tornado! This will come extremely handy should my grant get funded! Thanks! - Björn Brembs from iPhone
Björn, when do you hear about the grant. Jeremy was asking yesterday and assuming it hadn't been funded but I had a vague memory you wouldn't hear until ~March? - Cameron Neylon
All they said when we submitted was "not before 2010". There you go, now you know as much as I do :-) Which reminds me to maybe give the lady a ring and ask how things are looking... - Björn Brembs
Just got off the phone with her. She said it's still under review and she wouldn't know anything further before the end of March. - Björn Brembs
Which reminds me: is anybody here in contact with the two groups receiving NIH funding to develop FfS? http://www.nih.gov/news... - Björn Brembs
Not really - last time I looked there was precious little real information out there. It would make me much more confident of the value of the projects if the proposals were put out for public discussion. - Cameron Neylon
I am in contact with the Cornell/UFL one which will focus on people, though not in a way very similar to facebook (the Harvard one is focusing on research infrastructure). Both have a national focus initially, but at least the former envisions to go global eventually, to collaborate with existing platforms if that makes sense to them (especially in terms of RDF compatibility), and to produce open source code. - Daniel Mietchen
@Daniel: I'd imagine the DFG would appreciate it if we told them we are in close contact with these two groups. Let me know if any of these guys show any interest towards us. Is there any public information about the projects so I could contact them as well? - Björn Brembs
Björn, I forwarded our mail exchange to you. - Daniel Mietchen
Great! Thanks a lot - do we have contact with the other group in Harvard as well? - Björn Brembs
Not that I know. - Daniel Mietchen
heiko hebig
dear facebook. the news feed / live feed separation is... just wrong.
Jean-Claude Bradley
Brent Friesen compares grading lab reports with sex :) - Jean-Claude Bradley
So, male students should be good at getting better grades, because they are cross-trained by faking love and engagement? - Oliver Schuster
Communicating Chemistry: http://www.nature.com/nchem... Nature Chemistry 1, 673 - 678 (2009)
By Theresa Velden and Carl Lagoze: "New web-based models of scholarly communication have made a significant impact in some scientific disciplines, but chemistry is not one of them. What has prevented the widespread adoption of these developments by chemists — and what are the prospects for adoption over time?" - Hilary
With a discussion of the role of open access, data sharing, electronic lab notebooks, preprint servers, and blogs in chemistry communication. - Hilary
I think the latter part of the article by Velden and Lagoze hit the nail on the head albeit sideways. There is a lot of chemistry disciplines and the pharmaceutical and beauty industry would be especially open to espionage. There is also the issues of security with the organic chemistry field as research from that branch could be turned into catastrophic weapons of mass destruction. The... more... - Aaron Kendrick
Aaron: is that scenario realistic? the knowledge and facilities required to make nuclear or biological weapons are considerable. simpler methods such as guns or explosives may still be a more effective and reliable means for violence - Mike Chelen
it is confusing that this article states "Hardly any established scientists maintain a blog" then cites an article http://dx.doi.org/10... which says "they contribute to the current practice and reputation of science as much as, if not more than, any popular scientific work or visual presentation" - how could blogs be so influential with supposedly no participation from established scientists? - Mike Chelen
Full whitepaper here: http://hdl.handle.net/1813... (I would have liked to see this linked to in the article). Also http://ff.im/bU7ae - Hilary
Security of biological weapons is a much more serious issue than for chemicals. Mustard gas is nasty but limited in spread, and most seriously nasty chemicals are natural in origin anyway. On top of that I think its been reasonably well established that security in e.g. cryptography is best served by an open approach. Espionage similarly is a separate issue. What we have at the moment... more... - Cameron Neylon
i definitely don't think the issue is about weapons/weaponization, an undergrad in chemistry (or a high school kid who can read on the internet) should know enough to make some serious bombs. Velden talked about her dissertation research at 4S. It was interesting how the members and PIs of the labs carefully do not reveal details of their work. They've had things scooped by other labs with more money/people so they don't talk about the details at conferences. - Christina Pikas
This talk of "dangerous science" is a red herring for a discussion on Open Science. It could leave one not familiar with the chemistry publication process with a very false impression. With very rare exceptions, all the information required to synthesize explosives and other dangerous compounds is already contained in regular research papers. If anything Open Science could make science... more... - Jean-Claude Bradley
Finally got round to reading the Nat Chem article. Can we stop talking about weapons in this thread - totally irrelevant. The article makes some excellent points, particularly in the section "Chemistry distinguished". The "focus on creation" paragraph will irritate many, but there is an element of truth there, as anyone will acknowledge who spends much time reading organic synthesis or catalysis papers. When/where is the second workshop? - Matthew Todd
Mat - if there is any follow-up meeting it will be discussed in the Google group http://groups.google.com/group... - Jean-Claude Bradley
Bora Zivkovic
From the comments, @brembs: "I found the best advice to be that you spend as much time in the lab as you *like*. If the lab pulls you out of bed in the morning and you have to find some activity (sports, music, friends) to drag you out of it in the evening, you’ll be fine. If some clock rules your lab hours, something is wrong." --hands-down the best advice to an intending grad student that I have ever seen. - Bill Hooker
Funny how I liked that comment the best myself. - Bora Zivkovic
Mind the caveat, though: today, there are fields which are ruled by the clock and their number is growing. - Björn Brembs
Is any job a 9-5? None I've worked at - Deepak Singh
Well, my inner clock works me more like 10-7 but I believe 9-5 is plenty if you WORK. Much better than hanging around day and night to be seen by the supervisor, but doing nothing. You have to be able to cope with the 24-7 folks' comments though... - Oliver Schuster
Chris Patil
Has anyone used Web 2.0 tools like FriendFeed, Twitter, etc. to initiate or implement collaborative science? I'm writing a series of pieces about new technology in scientific communication, and I'd love to talk to someone who's actually used these sorts of tools to do actual science. Let me know!
If you'd rather take it straight to email, you can email me at the address listed here: http://ouroboros.wordpress.com/about... - Chris Patil
And by the way, this is for a journal, not my blog. - Chris Patil
Thanks Pierre. I will definitely follow up with the people involved in that thread. Keep 'em coming, folks! - Chris Patil
I'm not sure this counts but the biogang (http://biogang.openwetware.org/) was sort of founded/created via Twitter/FriendFeed interactions. Lots of projects there. Also, the bioinformatics survey was also propelled by T/FF if I recall. - Ricardo Vidal
Jean-Claude Bradley started a spreadsheet where he wrote this kind of information : https://spreadsheets.google.com/ccc... - Pierre Lindenbaum
This is really amazing, you guys. Thank you. JC, the spreadsheet is incredible. - Chris Patil
There are so many examples on discussion boards like ScientistSolutions, Molecular Station, etc. (Disclaimer, I work for SSI). I could give a you a list of at least 50 specific threads on our site. Here's a recent favorite http://www.scientistsolutions.com/t8853-h... - Rusty Bishop
I just added to the spreadsheet re: the help I got with CSV munging shell scripts earlier. Would discovery of papers through social bookmarking be considered collaborative science? - Mr. Gunn
@Mr. Gunn - no, i don't think so. Collaboration suppose to be productive - if discussion about papers within the group brought all participants to consensus that could be collaboration via social bookmarking with discussions. But bookmarking sites don't provide discussions. Even they would, it will take for a long while for scientists to start discuss about papers online - simple online collaboration. My thoughts also here - http://hematopoiesis.info/2009... - Alexey
Chris - Carmen Drahl made a nice video showing how FriendFeed is used to collaborate with scientists (second vid on the right) http://pubs.acs.org/cen... - Jean-Claude Bradley
Pierre - thanks for posting the spreadsheet - it is nice to see these little projects get re-use - Jean-Claude Bradley
Concretely, the References Wanted room (http://friendfeed.com/rooms...) has really been useful in writing up articles so I can rapidly get my hands on hard-to-come by references in journals to which my institution does not subscribe. But I'm not sure this is a great thing to bring up in your article, except in a vague way; we're not quite clear which side of the law participating re-distributors are on (fair use, or not?) It's not quite the same as discovering papers as per Mr. Gunn. - Heather
Sci-Mate is a very recently opened collaboration to develop Web 2.0 tools for the benefit of researchers. http://www.sci-mate.org/ - Christopher Dyer
I have recently started a project shared on a wiki + google code + zotero but it is still early days http://openwetware.org/wiki... - Pedro Beltrao
open notebook science should qualify, thinking about usefulchem as example of wiki and google spreadsheets like http://spreadsheets.google.com/ccc... - the list on wikipedia is helpful http://en.wikipedia.org/wiki... - Mike Chelen
I Added the GeneWiki paper in Jean-Claude's spreadsheet https://spreadsheets.google.com/ccc... - Pierre Lindenbaum
Chris - if you are asking for a more technical answer - UsefulChem and the ONSchallenge run mainly on a combination of wiki/blog/Google Spreadsheets - Jean-Claude Bradley
Pierre - thanks for the addition - Jean-Claude Bradley
Maybe this is where Google Wave will turn out to be useful once we all realise that we're not flying around Beginners Island naked like in Second Life ;-) - Sally Church
Sally - do you have a link to the island where everyone flies around naked? Sounds like fun :) - Jean-Claude Bradley
Of course I'm naked but my feline fur hides that pretty well - Jean-Claude Bradley
Michael Nielsen
nice solution to the multiple author problem - Jean-Claude Bradley
Really great story! Congrats Michael, Timothy, and the rest of the team! - Steve Koch
Pedro Beltrao
The EMBO Journal makes the referee reports available - http://www.nature.com/emboj...
The EMBO Journal makes the referee reports available
"starting with manuscripts submitted in 2009, The EMBO Journal will publish online an editorial process file alongside each published paper. (...) It will also contain all pertinent communication regarding the manuscript between the corresponding author and the editorial office, including the referees' comments as part of the decision letter." - Pedro Beltrao from Bookmarklet
Jean-Claude Bradley
Browser-based chemistry is here - its name is ChemDoodle Web Components - http://baoilleach.blogspot.com/2009...
Mr. Gunn
A brilliant use of twitter. - http://dilbert.com/strips...
A brilliant use of twitter.
I might have to try that sometime, if I ever have a boss again ;-) - Mr. Gunn from Bookmarklet
Josh Lam
HideIpVPN: Free UK and US VPN (50 Invites!) - http://joshlam.com/2009...
Björn Brembs
"Frontiers will launch two new indices, incorporating usage data, as well as social network data, to allow readers and users of data to shape the impact of articles. The Academic Excellence and Social Relevance Indices will provide the most advanced measure of the impact of an idea, an article and an author on the research community and on society." - Björn Brembs from Bookmarklet
Another quote: "Frontiers (fortunately or unfortunately) is indexed in Thomson ISI and an IF is expected in 2011. Perhaps by then, the impact factor obsession that has become so widespread in the past ten years will have been replaced by a more reliable approach to the analysis of "your impact on human thinking" and we can move beyond "where you publish" to "what you publish"." - Björn Brembs
The piece is strangely formatted, though, which prohibits it being forwarded to those that should read it. - Daniel Mietchen
On a related note: I just had such a discussion via email with a senior colleague whose scientific advice I value highly, but whose views on matters like impact factor I do not share. Excerpt from the conversation: Me: "I honestly wish the time will come when committees would stop counting papers and instead actually read, say, the top two or top five of each candidate. " Reply: " The... more... - Daniel Mietchen
Jean-Claude Bradley
Group chemistry - Inside Higher Ed - http://www.insidehighered.com/news...
Learning chemistry in groups with no paper and no computers. - Jean-Claude Bradley
sounds like there is specialized computer usage - "one is in charge of logging the group’s work in a blog" - Mike Chelen
that's true - I guess they can't use any other programs on the computer - Jean-Claude Bradley
yup it looks like calculator only, although calculators are still a specialized type of computer. another interesting aspect is the way the roles are divided and rotated - Mike Chelen
I like the idea, while I don't know (yet) how to adjust it to my needs. Most chemistry courses are not based on calculations. - Oliver Schuster
Yes I find it hard to imagine doing this for organic - it is an unusual approach - Jean-Claude Bradley
Interesting - we just had a visit from the guys who developed POGIL. I'm thinking of giving it a try next year. Lecturing can sometimes feel very inefficient. But yes, I think organic chem benefits from a pen and paper. - Matthew Todd
Mat - I look forward to seeing how POGIL works for you. For organic synthesis, I have also used the Wheel of Orgo game, which students can play on a TabletPC - http://edufrag.wikispaces.com/orgofra... - Jean-Claude Bradley
Cameron Neylon
David Mitchell: Pointless studies are the key to evolution | Comment is free | The Observer (via Philip Moriarty) - http://www.guardian.co.uk/comment...
Don't know how many overseas people would know who David Mitchell is (Peep Show, That Mitchell and Webb look, also did the PC part in UK "PC and Mac" ads) but main point being it takes a comedian to make the serious point effectively. - Cameron Neylon from Bookmarklet
Finally, some sense about the REF :-) - AJCann
Brilliant: "That breakthroughs often come by accident rather than design, from a desire for knowledge rather than a gap in the market, is so well established it's a cliche – it's one of the things that every schoolboy used to know. Why doesn't anyone at the Department of Education? Is it linked to the fact that nowadays every schoolboy barely knows how to count to the number of A*s he's just been awarded?" - Björn Brembs
Wow! This is the first time someone makes my cocktail party argument publicly: "Public money should be made available for research that would otherwise not happen. Research of economic value is outside this category". Fantastic! http://bjoern.brembs.net/comment... - Björn Brembs
Very true! In addition I think an academic`s main assignment is to teach students. It does not really matter what the subject is - as long as it is demanding. If a new discovery can be made it's even better, but not necessary. Having said that, I fear application driven research tends to be mind numbing screening of process parameters rather than challenging and cutting edge. I'd like to leave that to the engineers... - Oliver Schuster
Bill Hooker
Citation Tracker: Monitoring Citations to your Publications - http://behind-the-enemy-lines....
"a tool that can augment Google Scholar and monitor Google Scholar (and other services like Libra, CiteSeerX, SSRN), and also monitor the Web (Google, Bing, Ask) for mentions of the paper. You can access a pre-alpha version at http://www.citation-tracker.com" - Bill Hooker from Bookmarklet
working ok for me in FF3.5 - Cameron Neylon
ok, what did you figure out. i'm stuck on the start page, too. - Christina Pikas
ah, you noticed that it put your e-mail name in the login instead of your user name. got it. - Christina Pikas
at a first glimpse it doesn't really work for me being an organometallic chemist. it's easier to check scifinder (chemical abstracts) to see if someone cited me or use the journal's citation alert. i assume since scifinder is a commercial product it's not possible to implement it? - Oliver Schuster
Mike Chelen
"NMRShiftDB is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. Please consult the documentation for more detailed information." - Mike Chelen from Bookmarklet
With plenty of room to store your OpenData. And if you want free NMR prediction of rare nuclei, just email me papers with spectra of those NMR nuclei. I just love adding uncommon chemistry... - Egon Willighagen
I recently did some statistics on the content: http://chem-bla-ics.blogspot.com/search... - Egon Willighagen
And new molecules tracked on FriendFeed: http://friendfeed.com/openche... - Egon Willighagen
having fun playing with the SPARQL queries from http://chem-bla-ics.blogspot.com/2009... and the endpoint http://pele.farmbio.uu.se/nmrshif... is helpful to know about - Mike Chelen
Bora Zivkovic
Why Do We Sleep? http://neuroskeptic.blogspot.com/2009... mammal-centric-think: exaptation vs. adaptation: "functions" for sleep evolved after sleep itself
The more pressing question for me at the moment is: Why am I NOT sleeping. Good night... - Oliver Schuster
'Mummi' Thorisson
Most researchers agree that open access to data is the scientific ideal, so what is stopping it happening? Bryn Nelson investigates why many researchers choose not to share. In 2003, the University of Rochester in New York launched a digital archive designed to preserve and share dissertations, preprints, working papers, photographs, music scores — just about any kind of digital data the university's investigators could produce. Six months of research and marketing had convinced the university that a publicly accessible online archive would be well received. At the time of the launch, the university librarians were worried that a flood of uploaded data might swamp the available storage space. Six years later, the US$200,000 repository lies mostly empty. - 'Mummi' Thorisson
If sharing requires any deviation from a minimum workflow it will be very difficult to implement - even for those who agree to sharing in principle. If you want people to share drafts of manuscripts don't ask them to submit drafts - just have them write on a public wiki. - Jean-Claude Bradley
Most data stores I have seen do an excellent job at putting the data in... but have you ever tried to get the data back out?? That would be my bet on reason number one why repositories have not taken off yet... - Egon Willighagen
@Egon - sure, I can imagine that's a big reason, but surely also (in some cases anyway) a lack of tools to get data in that fit into scientists' workflow (as jcbradley said). Or if the tools are there and not a pain to use, but fundamental reason who people are reluctant to use them: e.g. no way to attach a suitable license (though Creative Commons taking steps in this direction: http://creativecommons.org). - 'Mummi' Thorisson
...and my own pet interests as of late - no way to i) easily and unambiguously link one's data contributions to one's identity nor ii) others can't cite the work in a robust way. Which is where contributor IDs (http://dx.doi.org/10...) and dataset DOIs (http://www.datacite.org) are intended to help in the long run. - 'Mummi' Thorisson
Steve Koch
Open Notebook Science @ UNM Physics, Round 3 -- If you have technology for us to try, let us know - http://stevekochteaching.blogspot.com/2009... (via http://friendfeed.com/steveko...)
If its a public RSS feed then preparing a service that talked to the OWW MediaWiki API to post the image shouldn't be too hard. Making it properly secure would be a nightmare though and there is the question of where it should go obviously. - Cameron Neylon
As for where it should go: OWW has things set up with lab notebook pages by date...so I think just putting things on pages by date added to RSS feed would be good enough. What is the big security risk? I've been wanting "email to wiki" for a long time now, but it's been put off due to risk of spam. Is spam the risk you're thinking of? If so, one solution I have in mind is that all of... more... - Steve Koch
Steve, although not really sexy technology, I'm curious if you have students create annotated bibliographies of some sort? I see that you have recommended readings..and that individual students have publications saved (I was confused by this at first; I thought "publications" referred to their own publications! Perhaps consider using the word "bibliography" or "(re)sources"?) -- but... more... - Mickey Schafer
Mickey -- That is a really great idea (though I haven't looked at the specific tech you're mentioning yet). The students only write one formal lab report with citations, and we go through a rough draft / feedback process. So, actually, I think there's a bunch of room to learn how to use the best electronic citation tools. Sort of obviously important now that you've mentioned it, but I... more... - Steve Koch
Great initiative Steve! Your students may not appreciate this fully now but when they are applying for positions or scholarships it is handy to be able to provide a public link to showcase their work. - Jean-Claude Bradley
"...a public link to showcase their work" is a very good idea. Many students are required to submit writing samples as part of their graduate application -- and most are quite surprised by this. I don't think they are getting this info ever before they hit the application process and for some, that's awfully late. To simply begin incorporating the expectation that students will have... more... - Mickey Schafer
Steve, again, not trying to burden your students:), but the reason I suggested a "lab bibliography" is that I've had students create such docs for their labs. All my students in every class have to do ann. bibs and write reviews (science pub model, not solely lit reviews); some use their reviews as intros to theses, a few go onto to publish them, and some have given them to their labs... more... - Mickey Schafer
Hey Jean-Claude and Mickey, Thank you for the feedback and ideas! Sorry for my delayed response: my 3 year old son and I went on an adventure to see friends in VT and my phone got doused with water while my body was being used as a trampoline by a bunch of children. So, I was disconnected but having fun. Going to work on making this a better class for the students as Mickey and others... more... - Steve Koch
Mike Chelen
Science Online London 2009: Online communication of science by institutions and organizations on Vimeo - http://www.vimeo.com/6390075
Science Online London 2009: Online communication of science by institutions and organizations on Vimeo
"How can research and educational outreach organizations use online tools such as blogs, Twitter, etc. to communicate science? In this audience participation session, the speakers will use real-world examples to spark discussion about some of the issues involved, including overcoming resistance in the institution, tone of voice, and constraints around talking about animal research or other sensitive topics. Ed Yong, Henry Scowcroft, Paolo Viscardi, Simon Frantz" - Mike Chelen from Bookmarklet
Mr. Gunn
Peer review and its alternatives « GETTING PUBLISHED - http://gettingpublished.wordpress.com/2009...
"By no means has this been the only experiment but to date no credible alternative to peer review has emerged. In short, what Churchill said about democracy applies equally to peer review: it is a lousy system, but to date all the alternatives have been even worse." - Mr. Gunn from Bookmarklet
If you target journals that allow pre-prints you can comfortably participate in the peer review process while still being able to share your work no matter how long it takes to review. - Jean-Claude Bradley
@J-C agree. Sorry for the lazy question, but is there a list of journals (maybe ranked by perceived prestige) that allow pre-prints? - Steve Koch
Steve there might be some lists out there but they may not be completely up to date - and sometimes you might be able to get an exception by contacting the editor. We've just been looking at journals that would best fit our content and then looking into their policies. It doesn't take that much effort. Most OA journals should be fine - we submitted to JoVE, J. Cheminformatics, Chemistry... more... - Jean-Claude Bradley
Mat Todd was trying to pull together such a thing a few months back and we tried to make contact with SPARC but didn't get a response. We were trying to ask a wider question - not just pre-prints but also data, discussion of data, presentation, pre-submission public review but it didn't get very far. My understanding is that NPG are fine, PLoS are fine, and BMC are fine. ACS are not and I'm not sure about Elsevier, Springer or Wiley. Often the information is not clearly available. - Cameron Neylon
Also as I recently discovered the rules for peer reviewed papers and "front matter" may be different so if you're doing the latter then check in advance for any publisher. - Cameron Neylon
Thanks, Jean-Claude & Cameron - Steve Koch
Hopefully some publishers will recognize the opportunity to make use of this new form of "free advertising". As authors start to see the value of retaining copyright (or allow pre-prints), journals that might otherwise remain obscure will get a lot of promotion from a very vocal group of scientists. In the past few months I have been part of discussions to select publishers for book... more... - Jean-Claude Bradley
Björn Brembs
Do you know how to manufacture a biface? - http://bjoern.brembs.net/news...
Björn, could you please increase the size of your font in your blog. That would make my eyes happy :-) - Pierre Lindenbaum
Of course, I could easily do that, but so far you're the first to complain. Why not just hit ctrl + '+' when the focus is on your browser window (or whatever the combination is for non-firefox browsers)? - Björn Brembs
He is right though. The font is difficult to read. - Daniel Lemire
alright, alright. Howze dat? - Björn Brembs
I was going to nominate this guy, but I see he's improved things greatly since I last visited. http://theamericanzombie.blogspot.com/ - Mr. Gunn
Jean-Claude Bradley
Working and Communicating in an Online Environment Presentation Slides John McQueen, Matthew Jager, and Alexandra Stone, Department of Horticulture, Oregon State University http://docs.google.com/present...
Very useful content - Jill O'Neill
Cameron Neylon
ChemSpidey Rides the Wave Courtesy of Cameron Neylon - http://www.chemspider.com/blog...
My comment at Tony's post: "Thanks for the shoutout. Probably worth pointing out that mouseover functionality won't be straightforward at the moment as there isn't any direct way of doing that via the client. It would require a gadget for each chemical compound which might get complex. Would need to think in a little more detail about it in any case. The selection of choices is really important and a general problem for this kind of markup - access to the internals of the system that make the spell checker work will make that a lot easier." - Cameron Neylon
Egon Willighagen
Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards - http://www.slideshare.net/egonw...
Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards
Jean-Claude Bradley
The star-nosed mole's amazing appendages - http://scienceblogs.com/neuroph...
Looks like the predator. - Andrew Lang
Disgusting-looking. But fascinating. - Steve Koch
Star-nosed mole against Luca Turin: who would win? - Steve Koch
I wonder if the mole can distinguish deuterated molecules - Jean-Claude Bradley
I wonder if it can distinguish enantiomers? - Bill Hooker
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