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Duncan Hull to Duncan's feed, The Life Scientists, Semantic Web for Health Care and Life Sciences IG

The Semantic Biochemical Journal experiment « O'Really? - http://duncan.hull.name/2009...

December 10 from Bookmarklet - Comment - Like - Share

joergkurtwegner, Greg Tyrelle, Bill Anderson and 17 other people liked this

"There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia (http://www.getutopia.com) and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses: Blogs for biomedical science Biomedical Ontologies – OBO etc Project Prospect and the Royal Society of Chemistry The Chemspider Journal of Chemistry The FEBS Letters experiment PubMedCentral and BioLit [2] Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3] The Elsevier Grand Challenge [4] Liquid Publications The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it? The Semantic Biochemical Journal project with Utopia Documents [5] The review asks what advances these projects have made and what obstacles to progress still exist.... more... - Duncan Hull from Bookmarklet

22 more comments

Am I missing something here? I only seem to see a few popups when mousing over references? - Cameron Neylon

Interesting though getting started wasn't entirely transparent. Figs are interactive (pink background and menu) so, for example, data from Fig 9 can be replotted. Tended to spawn popups at an alarming rate. Fig. 13e appeared unable to load into popup. - Peter Miller

@Cameron, you need to download the Utopia client to get the full effect http://www.getutopia.com the animations are embedded in the PDFs and viewable within the client. It's not a browser based thing (yet). - Duncan Hull

Done that, looking at both the paper online in enhanced version and pdf I'm not seeing any visual cues or anything that take me anywhere much. Do I need to have the utopia client running as well? Ok you need to open the pdf in Utopia. That's really not immediately obvious I have to say, particularly with the "enhanced online version" getting billing front and centre. Ok I could have read the instructions but its only the mention that Utopia is a "pdf reader" that tells you what to do. Could be clearer. - Cameron Neylon

Have to say that the idea of a semantically enhanced pdf I have to download and open up in a particular viewer seems to be somewhat missing the point :-) - Cameron Neylon

Also seems odd that the enhanced online version doesn't at least include the links that are in the enhanced pdf - Cameron Neylon

@Cameron I see your point, I'd like to see a more web friendly version but there are some limits to what you can do in a web browser (especially when it comes to sequence alignment and molecular visualisation) - Duncan Hull

Yes, and that is all fair enough - you need to start somewhere but you'd think the links could be translated across pretty easily (e.g. Caspase-3 in paper 1, fig-1 legend is linked in the PDF to a wikipedia entry, why not in the online version?). Bring on HTML5 is what I say :-) - Cameron Neylon

@Cameron ... and yes, its an "experiment" too (normaly caveats apply!). The thing to look for is the little Utopia Documents icon embedded in the text once you've opened up an article (e.g. the review) in Utopia documents. Thanks for the rapid feedback... - Duncan Hull

Yep, found it eventually. I'd suggest changing the instructions to be much more explicit. i.e. Download Utopia, then download pdf, then open in Utopia. Most people will have pdfs set to autoload in something else so its not an obvious path - particularly to people used to plugins and overlays. Heh, next quetions can I leave a comment on the journal article to suggest this....mmmm.....that would be a "no" then... ;-) - Cameron Neylon

Dear Santa, Please can you provide Utopia for Ubuntu/Debian/Linux. Thanks :) - Allyson Lister

I just skimmed it initially - didn't note the requirement for this odd piece of software. Puts paid to it for me, I'm afraid. - Neil Saunders

From Philip McDermott: "ubuntu version in the works but just slightly delayed for launch. I'd have thought it'll be available next week sometime" - Allyson Lister

The idea of a specialized PDF reader for this means it's just a proof of concept at this stage. I'll mention it to the Mendeley people and see if they might like to incorporate some of this into their internal PDF reader. - Mr. Gunn

@Mr. Gunn thanks... - Duncan Hull

@Mr. Gunn thanks. Be interesting so know what they think of it, feel free to put them in touch with us :o) - Philip McDermott

I think that the initial confusion of PPLs website has confused a lot of web-oriented users. Try grabbing the app, the paper, and working through it, and you should get a feel for what we're trying to do. We're not saying web-based is bad, it's just that this is a little different. - Philip McDermott

@Philip see also commentary here http://digitalcuration.blogspot.com/2009... - Duncan Hull

As I understand it the PDF reader software is just an initial client for the backend which lets you annotate whatever - and from where all the annotations are fetched. If (when?) it gets opened up you could extend the existing client to read other files, write your own client, write a Firefox plugin, whatever... - Euan

@Euan yes that's right (and you put it much better than me). As for opening it up, you'd have to ask the Utopia team... it would make a lot of sense. - Duncan Hull

I like the concept of the Utopia reader. But the integration of references could have been done better. Why not use DOIs instead of linking to a Google Scholar search? - Martin Fenner

Dear Santa, like @Allyson I really hope your reindeer's can still pull the Linux version, too. - joergkurtwegner

Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9 - joergkurtwegner

Jonathan Eisen

Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution - http://phylogenomics.blogspot.com/2009...

Thursday from The Tree of Life - Comment - Like - Share

rowlikeagirl, Björn Brembs, Martin Fenner and 2 other people liked this

The Life Scientists: Neil Saunders

Life Scientists 2009 summary - http://nsaunders.wordpress.com/2009....

Wednesday - Comment - Like - Share

Jason Stajich, Yaroslav Nikolaev, Abhishek Tiwari and 19 other people liked this

This blog post is rather rough and ready - a work in progress - but I wanted to push it out before the holidays. Find out which items from this group in 2009 were most discussed (comments/likes)! - Neil Saunders

14 more comments

hey, good stuff: especially like the healthy diversity concerning the contributors of most commented/liked entries, do you happen to have a little stat on the most frequent contributors in terms of number of entries, likes, comments or all of them? - Attila Csordas

It's certainly easy to calculate per user contributions using the API data, but I haven't done it. Might be fun, but I'm more interested in what's discussed than who posts. Feel free to adapt my code! - Neil Saunders

what's the license for the code, and is there a way to download it other that copy+paste? looks cool, thanks for sharing! - Mike Chelen

Licence is "it's on my blog, you can copy it and do what you want" :-) - Neil Saunders

ok cool, that means CC-BY-NC-SA? - Mike Chelen

It means I don't take licencing of my posts very seriously :-) Although now I look closely at my blog, the relevant icon is top-right, just above the search box. - Neil Saunders

although NC and SA clauses are a bit restrictive, it is fine for the time being. since the code is useful, giving licensing some consideration may be worthwhile :) - Mike Chelen

If it were actual code for download, I'd think about it more. When it's text on an open, public web page, I just assume people will do with it what they will. Anything goes, except claiming that you wrote it :-) - Neil Saunders

copyright law prohibits duplication without your consent, regardless of whether it is on a website or in a repository. while some may break these laws, many of us are committed to working within its boundaries through the use of open-source licenses :) - Mike Chelen

I'm intrigued that things are so spread out - no one person has more than one entry in the top 10 list...good sign of collaborative effort IMO - Cameron Neylon

Facebook acquired FriendFeed on August 10. Am I right that there is no significant change in number of posts over the year or after the acquisition? - Martin Fenner

This is really cool Neil. When I saw readI immediately though if this could be done on a rolling monthly basis this could be the new version of BioBlogs. Maybe some sort of simple Sinatra app. - Michael Barton

Sample sinatra app on Github and hosted on Heroku :)? - Deepak Singh

Neil, I agree w/ you: most commented/liked entries are more interesting than the list of most frequent contributors (although that is interesting nevertheless) - Attila Csordas

I like the idea of automated monthly analysis as a web app! Tricky bit will be fetching only new entries and not missing any, but once a db structure is in place, shouldn't be too hard. I'll give that some serious thought. - Neil Saunders

Björn Brembs

Embedding 3D models of biological specimens in PDF publications - http://www.citeulike.org/user...

December 16 from CiteULike: brembs's library - Comment - Like - Share

Dan Hagon, Kubke, Mike Chelen and 5 other people liked this

Microscopy Research and Technique, Vol. 71, No. 11. (2008), pp. 778-786. By providing two examples, the option for embedding 3D models in electronic versions of life science publications is presented. These examples, presumably representing the first such models published, are developmental stages of an evertebrate (Patella caerulea, Mollusca) and a vertebrate species (Psetta maxima, Teleostei) obtained from histological section series reconstruction processed with the software package Amira. These surface rendering models are particularly suitable for a PDF file because they can easily be transformed to a file format required and components may be conveniently combined and hierarchically arranged. All methodological steps starting from specimen preparation until embedding of resulting models in PDF files with emphasis on conversion of Amira data to the appropriate 3D file format are explained. Usability of 3D models in PDF documents is exemplified and advantages over 2D illustrations... - Björn Brembs

7 more comments

Awesome 3D models, rotatable, zoomable, everything within a PDF with no extra plug-ins! Amazing! - Björn Brembs

I think they should have mentioned some Open Source alternatives to Amira/Adobe, my favourites being http://rsbweb.nih.gov/ij/ and http://www.ctan.org/tex-arc... . For the fossil part, see also http://www.virtualpalaeo.org/ (summary in http://newsletter.palass-pubs.org/pdf... ). - Daniel Mietchen

+1 Björn - this is a most impressive piece of work !! @Daniel, I'll check those links out tomorrow. - Graham Steel

Now I need to find out how to get the 3D model of our experimental setup into our PDFs! - Björn Brembs

Daniel: how is imagej used to embed 3d models? - Mike Chelen

imagej produces the 3D models, animate the embedding. - Daniel Mietchen

That is a great link Bjorn. My student has been producing similar models of brain/brain regions that are extremely useful since one can rotate the brain, remove regions, or "slice" it at different angles (great when trying to interpret histology and also to calculate stereotaxic approaches for electrophysiology). But it never occured to me he could publish the dynamic pdf. - Kubke

Does anyone know if Osirix can do the pdf trick? http://www.osirix-viewer.com/index... - Kubke

Cameron Neylon

What should social software for science look like? - http://blog.openwetware.org/science...

December 9 from Science in the open - Comment - Like - Share

Ruchira S. Datta, Meryn Stol, suelibrarian and 32 other people liked this

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

27 more comments

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... more... - 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... more... - 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.... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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

Neil Saunders

About | R bloggers - http://www.r-bloggers.com/about

December 12 from delicious - Comment - Like - Share

Jean-Claude Bradley, Martin Fenner, Wladimir Labeikovsky and 3 other people liked this

R-Bloggers.com is a central hub of content collected from bloggers who write about R (in English). The site will help R bloggers and users to connect and follow the “R blogosphere”. - Neil Saunders

'Mummi' Thorisson to 'Mummi''s feed, The Life Scientists, Science 2.0

Fwd: CrossRef joins ORCID initiative: Open Researcher & Contributor ID - http://www.crossref.org/01compa... (via http://friendfeed.com/mrgunn...)

December 12 - Comment - Like - Share

Pedro Matos, Jean-Claude Bradley, Steve Koch and 6 other people liked this

"CrossRef is pleased to announce that it will be participating in the recently launched Open Researcher and Contributor ID (ORCID) initiative to create an unambiguous identifier for scholarly and professional researchers. Our members will be aware that CrossRef has been exploring the possibility of creating an “author DOI” or “contributor ID” system. In doing so, it has become clear that the issues and use-cases involved in identifying researchers span a broad collection of stakeholders including libraries, institutions, funders, publishers and, of course researchers themselves. In short, this is not primarily “a publisher problem.” As such, we believe that the ORCID approach to creating an inclusive and open organization representing all the stakeholders in the scholarly communications process represents the best chance of creating a successful contributor identification system" - 'Mummi' Thorisson

8 more comments

Absolutely fantastic news on the researcher/contributor ID front! - 'Mummi' Thorisson

For those who are new to the topic, this has has been discussed extensively on FF before and elsewhere. Couple of links which may be helpful for background reading: A specialist OpenID service to provide unique researcher IDs? http://ff.im/GbM8 http://blog.openwetware.org/science... http://network.nature.com/people... - 'Mummi' Thorisson

Finally, it was about time! Good. - Björn Brembs

Am I allowed to be amused that we're IDing orcs? Many logos suggest themselves... - D0r0th34

But of course, D0r0th34! what else could this possibly be about!! !? :) [BTW apologies to fellow FriendFeeders who are not also Tolkien-fans and do not find this amusing at all.. ] - 'Mummi' Thorisson

Mmmkay, so now we have ORCID. Where do I sign up and claim my papers? - Björn Brembs

+1 D0r0th34 Maybe if you're lucky, they'll figure out a way to offload most of the workload to librarians ;-) - Mr. Gunn

Funny thing about that. I spent a lot of last week fixing initial-only names in the repo. - D0r0th34

+1 Björn, except I'm not so eager to sign up if it means letting people know that I'm an orc. :-) - Ruchira S. Datta

Maxine

Consortium to address author ambiguity - http://blogs.nature.com/nautilu...

December 11 from Nautilus - Blog Posts - Comment - Like - Share

Daniel Mietchen, Thomas Brox Røst, Martin Fenner and 8 other people liked this

That's great - a bit worried about the lack of funders on the list though...NSF/NIH, RCUK, MPG, DFG etc? - Cameron Neylon

I'll post any more information as I find it out, Cameron. Seems rather preliminary just now but I hope there will be some more news soon. I guess it takes time to put these initiatives together. Of course, with all these investigators on Friend feed, you'll probably find out more before I do! - Maxine

Absolutely - and it's very definitely good news - but as you know I think this needs to go far beyond publishers. - Cameron Neylon

Ricardo Vidal

Feeling boxed in? | Mendeley Blog - http://www.mendeley.com/blog...

December 10 from Bookmarklet - Comment - Like - Share

Martin Fenner, Kubke, Mr. Gunn and Björn Brembs liked this

Interesting to watch how this evolves. will scientists buy the classic freemium model. My guess is yes for storage and no for shared collections. Although a play for department or institutions subscriptions could well work here - Cameron Neylon from Android

Like a "collaboration service provider", Cameron? - Mr. Gunn

Mr. Gunn

crossref.org joins orcid initiative - http://www.crossref.org/01compa...

December 11 from Bookmarklet - Comment - Like - Share

Steve Koch, suelibrarian, 'Mummi' Thorisson and 5 other people liked this

Pierre Lindenbaum

Add CrossRef metadata to PDFs using XMP - http://www.crossref.org/CrossTe...

December 9 from Google Reader - Comment - Like - Share

Martin Fenner, Duncan Hull and Egon Willighagen liked this

Mr. Gunn

Thinking big for a moment: What would have to happen for citation styles to cease to exist?

December 7 - Comment - Like - Share

Ana Ivkovic, Michael Habib, Pete and 15 other people liked this

If everything had a DOI... - Jiahao Chen

33 more comments

What I don't get is why there are so many different ones for the same disciplines. Is it really superior to have a semicolon here instead of over there? Really? There should be two styles: numbered and alpha. That's it. We really don't need more than two. OK, maybe law gets their own. - Jenny Reiswig

Lots of things that have DOIs still have citation styles, though. Just wondering why we can't just pick one format and stick to it. - Mr. Gunn

I understand that different fields have various types of things they need to reference (like law referencing case numbers and such or art history referencing folios or repository pieces, but here's what I was thinking - Have a format that contains fields for all the information that might be needed for anything, then let the tool that generates the bib output what's needed (for the... more... - Mr. Gunn

On paper I find alpha style much easier to follow than numeric. But online doesn't matter as all info should be available by just hovering over ref in body of text. Good question! Part of scoialisation to being an academic? - Anne Marie Cunningham

I have wondered this for a long time. This is a constant source of stress, vexation, and wasted time (especially for undergraduates). I especially dislike it when faculty ask their students to use the citation style of a particularly esoteric journal in their sub specialty. I also dislike citation styles that call for abbreviated journal titles (like ACS style, a classic holdover from the print world). - Bonnie Swoger

EndNote lists over 3,000 citation styles, would be interesting to see how this number has risen over the years! - aarontay

The world would be a better place. I'm holding onto http://friendfeed.com/karenja... in the hopes that it might someday come about. - Peter Murray

Theoretically, if some of the big journal editors and publishers could agree on some kind of streamlined style (or two styles maybe - one for footnotes and one for in-text citation) this would save everyone a lot of time. How much time (and therefore money) is wasted making sure that the date goes after the authors name or at the end of the citation? - Bonnie Swoger

Wonders are reference management software like EndNote actually benefiting from the proliferation of styles? But on second thought no, I go crazy trying to see if it's possible to duplicate some obscure feature in a obscure citation style that reference management software don't quite do yet. If there are say only a dozen styles, it would be possible for reference manager software to perfectly duplicate all of them. - aarontay

aarontay - I'm thinking that there probably are parallels between the obscure holdings many academic libraries have and the proliferation of citation styles Endnote has developed. In other words, it's a user-driven accumulation of things over the years, badly in need of a pruning. - Mr. Gunn

There's http://citationstyles.org that Zotero and Mendeley are working with which should at least reduce the effort required to support the variety of styles available, (and for someone technically inclined, you can submit your own format) but we really don't need them all. My question is: What would be the first item on a todo list written today if the goal was eliminating all but a few styles? - Mr. Gunn

I think the first item on your list would be what was mentioned first in this thread: a unique identifier for anything potentially citable. - Daniel Mietchen

I agree that having DOIs for things is the next thing that needs to happen for citation infrastructure, but I'm thinking more near term. Is there any reason that cell, nature, science, and the antarctic journal of snow biology need different citation formats? Couldn't this change almost overnight if the will to change existed? - Mr. Gunn

I don't think the unique identifier would be enough on its own (though I agree it's needed). If I'm reading through the reference list, I want the titles not a list of DOI's -- so we still need some way to turn the unique ID into a human-readable citation, and then we're back to citation styles and how do we kill off most of them? Bottom-up approaches seem likely to fail since everyone is going to want their own favourite style or element. - Bill Hooker

To do list: 1. design Universal Citation Style that will satisfy most requirements for most people; 2. start campaign to have all journals accept submissions in their own style, or in UCS. Once authors had a single style that they could use for most submissions, they'd want it for all submissions -- and journals could either just use it or reformat the ref lists if they really wanted their own style. - Bill Hooker

They will "go away" when the document is configurable by the end user, to whatever style they want, for whatever purpose they're using it for, in whatever medium is convenient. - Cameron Neylon

Print probably has to become near-marginalized before this happens, right? But seriously, couldn't they just agree to accept one of the formats in use today and it would work for pretty much all life science papers? I guess, Bill, that leaves Step 2, but why should it be necessary to even campaign. Do academic publishers NOT want to save on manuscript preparation costs? - Mr. Gunn

Bill - I do not think of a reference list, rather some direct linking from the article to a page hosting the metadata (and possibly more for OA stuff) of the reference, as at http://en.citizendium.org/wiki... . Ideally, these metadata pages (example:... more... - Daniel Mietchen

I'm guessing that change is resisted by the old guys with a million hard-coded references in their chosen style. If you use EndNote, Zotero etc then changing from one style to another is pretty much trivial, isn't it? - Chris Rusbridge

The bibo group are working on an ontology of bibliographic information. The depressing thing is to see it get more & more rococo as it tries to take in more and more attributes from different groups, especially Law. - Chris Rusbridge

I guess I ought also to mention David Shotton's cito ontology, which (in part) looks at the "flavour" of the citation, eg supportive, background, refute etc. But perhaps I'm straying off the point here! - Chris Rusbridge

Well, Chris, it isn't trivial, even with a citation manager. "Why doesn't my reference manager support my favorite citation style?" is a question I hear with some frequency. Now, because they work with http://citationstyles.org, Mendeley and Zotero support more styles than any other product, but the whole thing just strikes me as, well, just damn silly. It's one of those things that hasn't been given much thought and over the years has evolved into a monster. It's time for that to change. - Mr. Gunn

Changing the reference style is often trivial if you use BibTeX. However, even then adaptation to the post-rejection journal's style still often requires changes in the format of the abstract, figures, figure legends and so on, and these have usually stolen more of my time than the references. - Daniel Mietchen

My understanding is that even "supported" styles in citation managers aren't 100% supported if you look closely at the obscure rules, causing a lot of hair pulling. I've being at the end of this, where people come and tell me.. they want EndNote to do this thing that is actually supposed to be in, but the default style can't duplicate. Multiple that 3000x and you go crazy - aarontay

well, yeah, so that could easily be handled by journals giving authors a BibTeX template and telling them submissions will only be accepted using the template. - Mr. Gunn

Except we, ahem, can't currently accept LaTeX and hence presumably BibTeX for our journal... (#shame!) - Chris Rusbridge

The "Uniform Requirements" style is pretty good and I don't understand why more journals don't sign on to it. It's got a lot of use in clinical medical journals, less in basic science. I agree with dumping journal abbreviations - useless holdover. - Jenny Reiswig

Citation styles are ridiculous. We should all just use Chicago. Or Harvard. No wait, Chicago. Then again... - Neil Saunders

But seriously, +1 Cameron. - Neil Saunders

@Cameron way up there: I like that idea: user decides on reference format. - Steve Koch

@Peter way up there: Thanks for that link! Very interesting, I'll relink it again here: http://friendfeed.com/karenja... - Steve Koch

I just had this conversation with my 8th graders - we use NoodleBib and they wanted to know the difference between MLA, APA and Chicago. I did my best and they asked "why are there three different styles". For the life of me, I couldn't tell them why we're still at that stage. - Lazygal

There really shouldn't be any need for this discussion... - Björn Brembs

Citation styles - stupidest things on earth! (sorry, I had to say it, I feel better now) - Cesar Sanchez

Cameron Neylon to Cameron's feed, scienceapps, The Life Scientists

I'm going to do a round of looking at some of the Science Social Networking sites again. Is anyone active on ResearchGate, Epernicus etc. and interested in testing functionality?

November 20 - Comment - Like - Share

John Delacruz, Jack H. Pincus, Dan Hagon and 24 other people liked this

I'm interested in joining the testing. Need to agree on criteria for comparison before starting, though. - Daniel Mietchen

63 more comments

I'm willing to keep an open mind but so far FF surpasses these in terms of networking and ease of use. But if you want to experiment I have accounts in many of these and I would be willing to try. - Jean-Claude Bradley

I'm really just looking to make sure that things haven't moved on and improved significantly, particularly in the light of the NIH projects. - Cameron Neylon

I tend to migrate to social networking sites based on "pull" - virtually the only time I go on LinkedIn or Facebook is when I get an email alert to something relevant to my interests. I would assume that if there was anything really cool going on in these new sites I would get these alerts generated by actions by you and my other friends. - Jean-Claude Bradley

BTW Cameron - that is one of the issues I'm finding with Wave - I tend not to check it because I don't get alerts that there are updates - is there a way to get an email alert for Wave updates? - Jean-Claude Bradley

Yes, there is an email alerter. I'll add you and it to Wave... - Cameron Neylon

Agreed to the general point though - if there isn't a pull, I'm not going there really. And I think that is a big issue with Wave - people just aren't checking in. - Cameron Neylon

@Jean-Claude I don't think there's currently a way of doing this with the current interface without adding a robot but I saw there's a robot on the Haskell public wave which has similar support http://wave-xmpp.appspot.com/public... - Dan Hagon

I'd be interested in testing (I recently started looking over Epernicus for an article on NGS). Where is the email alerter for Google Wave? Currently, I'm using Waveboard (Mac), which alerts you when there's activity. However, it needs to be running in order to do so. - Walter Jessen

Just added you to a Wave with the email notifier Walter... - Cameron Neylon

New SNS from American Institute of Physics, got email invite today: http://www.aipuniphy.org/ - Andrew Lang

I have accounts on Epernicus, SciLink, Laboratree, and maybe could consider BenchFly a social networking site too, but like JC, I don't go to any sites besides FF and Twitter (and those are typically through 3rd-party apps), not even Facebook or LinkedIn, unless I get some alert. But I would be happy to see if anything's changed in those science-oriented sites I mentioned - Shirley Wu from twhirl

I do get alerts that new people have joined the organic chemistry group in Research Gate but there is no discussion and my questions have not been answered there by anyone so not much motivation to check in. - Jean-Claude Bradley

I have accounts at NN, Epernicus, BioCrowd and SciLink. I have begged for account deletion at the latter for months, to no avail and have not visited most of the others for as long as I can recall. So: active - no, interested - no. It's all FF/Twitter for me. - Neil Saunders

It's alright - this is a benefit of the doubt exercise - making sure that things haven't changed or that we've missed something. My brief look around yesterday suggested that nothing much has but I wanted to make sure I'm not missing something. - Cameron Neylon

What about the criteria for comparison other than some "pull" functionality (which they all seem to have, to different extents)? Does usability boil down to feed import/ export and (hierarchically) threaded conversations ordered by novelty and importance, as at FF? - Daniel Mietchen

When considering the usefulness of the individual platforms, perhaps discipline-specific ones should also be on the list? Besides http://polymathprojects.org/ (maths), these would include, for instance, http://openanthcoop.ning.com/ (anthropology), http://www.apecs.is/ (polar research), or this very life science group at http://friendfeed.com/the-lif.... - Daniel Mietchen

It would be worth doing a compare and contrast - also things like Math Overflow and even some of the chemistry blogs act more like community sites. Seems particularly apposite with respect to Pawel's blog post yesterday about the idea to set up a next generation sequencing community site. - Cameron Neylon

I have a ResearchGate account but don't actively use it. I currently do some FriendFeed, Nature Network (where my blog is hosted) and Google Wave, but mostly Twitter. - Martin Fenner

The last issue (November 23) of the German computer magazine c't has an article on social networking for scientists. They like ResearchGate and Mendeley, but also include ResearcherID, Scholarz (a German network), Nature Network, SciLink and Scientist Solutions: http://www.heise.de/ct... - Martin Fenner

That c't article (which shall come out in some OA fashion soon) may serve as guidance but I found the choice of networks therein rather arbitrary, and the comparison between sites was done on a more general level rather than on the basis of specific criteria. - Daniel Mietchen

The article makes two obvious omissions: a) no mention of CiteULike (or Connotea), b) no mention of the recent $12 Mio social networking NIH grant to U of Florida/Cornell University. There are some more things in it I don't like, so I wrote a letter to c't magazine. - Martin Fenner

Cameron, what criteria were you thinking of using? - Mr. Gunn

Key questions: a) What is the immediate impression on signing up? Is there a pull for people to come back? b) What functionality is being offered? Is it immediately available? How dependent is it on having a network in place? c) Funding model and stability d) User numbers, ideally active users and accounts, but whether we can get those is another question. Those aren't very objective criteria and they are built on my biases but nonetheless - Cameron Neylon

Sorry if this is slightly tangential to the discussion, but I was imagining a new kind of social network for publication of research results here: http://virtualchrisleonard.co.uk/blog... - Chris Leonard

Chris - when you talk about "credit" are you expecting tenure and promotion committees to count it or do you have some other system in mind? If you set something up I have content that might be suitable to play with. As for citability - in our last few papers we have used blog posts and wiki pages as references and have not had any problems with that - so I think the system is quite flexible and can accommodate the types of activities you are proposing. - Jean-Claude Bradley

I think Chris means system credit or karma. The idea as I understand it is somewhere between Friendfeed and Stack Overflow - Cameron Neylon

Thanks Cameron, yes, that's what I meant by 'credit' - however, by quantifying and metricising that credit, there is a possibility that one day tenure and promotion committees may want to use it as another measure of a scientists influence in a field. Apologies to Cameron for hijacking his thread. There is another discussion on this blog post here: http://friendfeed.com/chrisle... - Chris Leonard

That's fine, it's not my thread, it the communities thread :-) Pointers are good, they link up the information. - Cameron Neylon

Blog postings to replace (journal) papers and (in-depth) peer review a luxury that can only be acquired if paid for and to be replaced by blog comments instead? Weakening both readability and certification? That does not sound like a healthy idea. - Wobbler

Wobbler: why should blogs lack any aspect of peer review? the standard of any publication depends on how editorial powers are used - Mike Chelen

...and we already pay for peer review. It just isn't a cost transferred as actual cash. - Cameron Neylon

But blogs do not have any editorial powers? What advantage do blog postings have over (journal) papers? They lack format = lack of consistency = lack of efficiency = lack of scalability. Are you seriously suggesting that blogging/blog posts have the potential to replace journal publishing/ (journal) papers as the primary scholarly communication model/channel? Upgrading the traditional... more... - Wobbler

@Cameron: that's true, but now peer review is at least mandatory for the primary scholarly communication model i.e. scholarly publishing. Replacing that with something else and having peer review only on request/payment is a very different story. - Wobbler

Wobbler - there is a difference between requiring the peer review to be performed before making some information public and allowing it to take place after that. I do not see why the latter option would generally fare worse than the former. In fact, we already practice it here at FF, with numbers of likes and comments roughly indicating the popularity of a topic, while the quality has to be sought in the individual comments (and of course the source item that started the thread). - Daniel Mietchen

... it isn't a cost transferred BY YOU as actual cash. Yet. It should be, in my not-terribly-humble opinion, however, because the market disconnect in the current system has proven ridiculously unsustainable. Wobbler, some of my blog posts have had more measurable impact than anything I've ever written. Sure, it's a lightning-strike sort of thing, and most of my blog posts languish in... more... - D0r0th34

@Daniel: I'm not talking about post-"publication" peer review. That's still different from random blog commentary on blog posts. There's no evidence that what we're doing here isn't just a "niche" thing that works well because we're a niche. There's certainly no consistency in quality in our blog postings (well, at least not in mine :p ). Not to mention a lack of consistency in... more... - Wobbler

@D0r0th34: No, we should absolutely not ignore lighting strikes. But we should see them as lightning strikes and consider them to be an exception more than a rule and focus our attention on something that provides that level of quality more as a rule than an exception. Blogs as a complement to (journal) papers is great. But once you start to see it as a primary source, a replacement for... more... - Wobbler

We don't know about our OA bets. As for slow-and-steady, a well-run blog isn't? Lightning strikes aside, building a reputation and a readership is hardly an immediate thing. - D0r0th34

@D0r0th34: That's one more reason why blogging as the primary scholarly communication model is a broken idea. "Popularity" and "building a readership" will be important for blogs (and other post publication peer review models) to be visible/significant. But aren't we going after journals for using their JIF to attract peeps to read their stuff? How is "blog (poster) popularity" to get a... more... - Wobbler

I think the most important property of non peer-reviewed scientific communication is that the content be easily indexed and searchable. Relying on comments and rankings can be very misleading indicators for utility in long tail systems. For example we get over 100 searches a day for our solubility data via Google and Wikipedia but we have never had a comment or any type of feedback from the people who searched for and found information. - Jean-Claude Bradley

Shrug. System-gaming goes on everywhere; there are a number of studies of citation-impact gaming, if you look. Also, why is connectivity a bad thing? We are talking about scholarly *communication* after all, right? Restricting "what counts" only to what goes through the baroque serials-publishing process is IMO an extraordinarily blinkered and limiting view of how knowledge really advances. Sure, it's not easy to come up with more inclusive views -- but that doesn't mean it's not worthwhile. - D0r0th34

The problem is that I'm not sure we can talk about "gaming the system" rather than "an intrinsic part of the system that everybody will be forced to play or greatly risk invisibility" when it comes to blogs and other models relying on postpublication "peer review". PLoS ONE is, intentionally or not, already trying to stake their claim on an as large a readership/community as possible.... more... - Wobbler

@D0r0th34: And connectivity can be unfair if your serious/scientific works are getting more attention than others simply because you've managed to draw a bigger crowd through non serious/scientific stuff. On a slightly more personal note: for someone who occasionally complains about the (lack of) readability of (journal) articles, I had expected that you, of all people, would appreciate... more... - Wobbler

I have to say reading down this I am unsure of whether the complaints apply to blogs or journal articles. Consistent structure and copy editing would be nice but it is rare for both blogs and journal articles. Quality is an issue across the board. Going back to peer review - it's only mandatory for the author, refusal rates for reviewers are going through the roof and unless we acknowledge that cost the system will collapse sometime soon. - Cameron Neylon

@Cameron: Consistent structure and copy editing are rare for journal articles? They are? Not entirely sure about copyediting, but surely most, if not all, journal papers have a recognizable structure? And I don't think they're as rare or rarer than for blog postings. I also think the issue is with peer review, and not with the (journal) paper (format). As such, we should find ways to... more... - Wobbler

Of my recent papers, only one received close copy editing by anyone but me. And that was the Nature piece for which to be honest I would have been happier if the editor had got a co-credit. And formats are all over the place - maybe consistent for a single journal but that's not use to me. The costs of both peer review and publication are so high we need to find a way to lower them -... more... - Cameron Neylon

@Cameron: I'm not sure that's a convincing enough argument for me. Maybe your other papers were written clearly enough already? You're a prolific blogger/writer, Cameron. It's not weird to assume that your ability to communicate concepts clearly is higher than the average scholar. Maybe high enough to not warrant copyediting (in a lot of journals)? My impression of journals is that... more... - Wobbler

Well others can pitch in but perhaps a different anecdote. Until I started getting into arguments with Maxine Clarke I didn't even realise that journals might do copy editing. Nature and similar are very different beasts to the average of course. - Cameron Neylon

So, generally speaking, only the high profile/impact journals provide copyediting services? Hmm, that is definitely not what I expected. If you had to estimate the % of journals that provide copyediting services, what % would that be? The (top) 10% of all journals? - Wobbler

I have the same experience as Cameron - the only time my manuscript was copyedited was when I published in Nature - Jean-Claude Bradley

So far as I'm aware, no-one here wants to replace peer-reviewed journals entirely by blogs. Yet that seems to be what you're arguing against, Wobbler. For some functions, journals are a lot better than blogs. But for other functions, blogs are a lot better than journals. At the least, I really can't imagine how, say, DHJ Polymath or Galaxy Zoo or the Open Dinosaur Project or [fill in... more... - Michael Nielsen

Most of this is as a response to an FF comment by Chris Leonard on the 23th of November in this thread, who is arguing for exactly that. - Wobbler

Cameron, any progress on the roundup? Is there any information I can provide from Mendeley? - Mr. Gunn

Right - getting there slowly! Have set up a wiki page (ignore the state of the rest of the site I am working on it!) at http://wiki.cameronneylon.net/index... You should be able to login with openids, any problem give me a yell. I would suggest a week by week schedule to dive into and try and use a specific site, give it a good shot and then report as we go. I... more... - Cameron Neylon

Cameron, what do you mean by "stability" - things like a service being bought/shut down vs. server outages? What about one week to agree on parameters and sites to check? I added data portability. - Daniel Mietchen

I was thinking more of medium to long term financial stability - but technical stability is a good criterion in terms of functionality. Data portability is a good point! - Cameron Neylon

Cameron, I spoke with Drew Endy, Bill Flanagan, and a couple other PIs that use OpenWetWare (Maureen, Pam) last week about the future of OWW. There are two major issues (a) funding and (b) overhauling the platform. I think funding will work out, if we can figure out what is the best way to do (b). Bill and Drew have some good ideas at this point, but in my gut I think we're still not... more... - Steve Koch

I guess my easy question for everyone who's familiar with OWW: Do you think with the resources we have (one full-time excellent lead developer) we can transform OWW into a killer openscience resource for many more people going forward? One thought that keeps coming to me is that something could be (needs to be) done to tap into the energy of the user base. I.e., obsessed students who... more... - Steve Koch

Another thing that keeps coming into my head since the conference call last week: FriendFeed is quite possibly very similar to what many people need for OpenScience. As far as science goes, we generate information from all kinds of different sources (Machine-specific data; gel photos; microsoft word; evernote; scratch paper; blogging; etc.). This needs to be aggregated and shared in a... more... - Steve Koch

Oh, and to clarify a bit: I don't want to replace FriendFeed with OWW. I want to use the FriendFeed model as a starting point for the new OWW. As an OpenScienceAggregator / Networking tool. As others have pointed out, much of the value of friendfeed is that it's not limited to scientists generating data. - Steve Koch

Steve, that's a great way of asking the question. I'd go one step further and say how can we make it the framework in which we can integrate all the other things we do on other services. It's never going to be a no-brainer to move from what you use to something else - there is always the simple problem of the activation barrier to change - its a question of the balance. But my guess is... more... - Cameron Neylon

Cameron, I agree with you exactly: I don't want people to switch, and indeed I want to think "one level above." Do you think there's a real possibility for doing that? - Steve Koch

If we could coordinate a series of activities and get proper funding then yes. Quite a lot of interest in the pieces of this (including the grant I'm currently rushing to finish), Chris's ideas further up this thread, OWW obviously, Mendeley/Citeulike/Zotero. But coordination is the hard bit - and getting agreement that its what enough of us want. Do I think we have a clear idea of what... more... - Cameron Neylon

Should we include some discipline-specific ones or are we going for general-purpose only? - Daniel Mietchen

Heather to Science Online, Science 2.0, The Life Scientists, ScienceOnline09, science21

Reminder: anyone in the world can now attend Science Online 2009 London without leaving the comfort of their pyjamas or computer on August 22nd: http://network.nature.com/people.... Please pass the word!

August 9 - Comment - Like - Share

Michael Habib, Bora Zivkovic, Lisa Green and 10 other people liked this

But the best part of conferences is the social hours -- those don't seem so fun sitting in front of a computer screen. - Donnie Berkholz

sure they are, you are all quite enjoyable to talk with even online, though attendance is always a great aspiration :) - Mike Chelen

Cameron Neylon

Article-Level Metrics and the Evolution of Scientific Impact - http://www.citeulike.org/user...

November 17 from CiteULike: CameronNeylon's... - Comment - Like - Share

Bill Anderson, Bill Hooker, Anders Norgaard and 37 other people liked this

Article on ALMs by myself and Shirley Wu - Cameron Neylon

27 more comments

Terrific. Are we still maintaining that list of "outputs resulting from FriendFeed"? - Neil Saunders

I was planning on doing a demo of annotation at PLoS before the end of the year - perhaps this article would be a good candidate. As always, anyone willing to join is welcome. - Daniel Mietchen

@ Neil: It's at http://spreadsheets.google.com/ccc... , and I have added the article as #25 (details missing). - Daniel Mietchen

i added a note once, but now it won't let me add any other notes :( I don't see a rule about one note per person. I should have held off for a good one. - Christina Pikas

I also just noticed that my "annotation" - provided the link to StackOverflow - shows up in the general discussion, where the title "Link" certainly is not helpful, and there is no way I can edit it. - Daniel Mietchen

maybe something is broken, my note appears in general comments but also in that portion of the text as a comment. maybe that's why I couldn't add other notes? - Christina Pikas

Not sure why you can't add more notes. Certainly been able to in the past. I see both notes where they are supposed to be I think. But they will also appear in the general comments as well I think. - Cameron Neylon

Great article! I really need to add some comments or notes, just to prove the authors' point :-) - Björn Brembs

BTW, when does PLoS finally get karma? I've been asking for proper 'show off' userprofiles for like ever :-) - Björn Brembs

As in PLoS Overflow? - Cameron Neylon

Cameron, et al. - What's the most useful thing I could do to nurture and support this renewed interest in article level metrics? (not from a competing data product point of view, but a let's get some good technologies out there with good visibility) - Mr. Gunn

@Cameron: Exactly! I even think having a profile where you can post a pic and see how many papers and comments were published, papers edited, etc.was the very first thing I asked for when I signed up :-) - Björn Brembs

But it needs to be federated across publishers... :-) - Cameron Neylon

if authors put in their 'customer' weight, this will go faster, so why not go syndicate :-) - Claudia Koltzenburg

I think I'll use this paper in my spring thesis class -- this is the main one where I discuss publishing models -- and maybe I'll demo Diigo with this as a class project next to an article that discusses IF. - Mickey Schafer

While we're on the subject of functionality wish lists, I would also like an embed functionality for PLoS papers. Collecting my publications together but don't want to duplicate copies and reduce googlejuice for the journal - at least not for the OA papers anyway... - Cameron Neylon

Whilst not a darts-player http://www.flickr.com/photos... , I think Cameron has hit the "triple-twenty" there :) - Graham Steel

BTW, why isn't there a way to register this thread with the article? Why are we posting here and not on the article? There's got to be a lesson to be learned from this :-) - Björn Brembs from iPhone

http://bullseyevaluation.com/yahoo_s... - Graham Steel

Done. See comment #4. - Graham Steel

Search results: http://topsy.com/s... from Topsy http://labs.topsy.com/about/ - Jim Till

I've included a link to this thread in a blog post: Article-level metrics getting attention http://ff.im/bGuNY - Jim Till

+1 Bjoern :-) another question along these lines would be: why does Cameron's intial FF message link to CiteULike and not to http://www.plosbiology.org/article..., or plainly doi:10.1371/journal.pbio.1000242 ? - Claudia Koltzenburg

Because that was the way I brought the link in. I think that that pointer is appropriate. It is a pointer to the fact that I bookmarked it. Other people linked to the paper directly. Perhaps the issue is that we accidentally aggregated around the "wrong" item to talk about the paper. I'm not sure this is a problem as long as the referral works - its a UI irritation not a problem with... more... - Cameron Neylon

well, not directly, maybe in this ff-thread we're just providing some material for what you say in your paragraph "Technical Solutions to Social Problems", namely: "approaches that gather information from processes that are already part of the typical research workflow are also much more likely to succeed." - even though ff may not be part of 'the typical research workflow' (yet?) - and... more... - Claudia Koltzenburg

That's true, and certainly conversation sparked by the paper. But how to capture that in a way that is useful further down the line might be tough... - Cameron Neylon

I am still wondering if we would not need at least one metric for each 'scientist type' as described in http://dx.doi.org/10... - joergkurtwegner

joergkurtwegner -I'm interested to see what tenurometer comes up with re: h-index correction factors for disciplines. - Mr. Gunn

The Life Scientists: Pierre Lindenbaum

There will be a new element <NameID> in the NCBI/DTD for 2010 http://www.nlm.nih.gov/bsd...

November 24 - Comment - Like - Share

Matthew Llewellin, Dave Bridges, Daniel Mietchen and 9 other people liked this

NameID data will not be present in the baseline files. There is no target date for the implementation of this field. If implementation occurs during the 2010 production year, records for which NameID data become known will be redistributed as revised records in update files after the baseline distribution. NameID data may be associated with the Author (personal and collective) and Investigator elements. - Pierre Lindenbaum

2 more comments

To support ContributorID and related projects? - Mr. Gunn

@MrGunn. As far as I understand, you'll find anything that can be used as an identifier under this element:. The type of id will be described by the @source attribute. Source="Publisher" , Source="e-mail", Source="openid", etc... - Pierre Lindenbaum

Cool, Pierre, that's what I was hoping. May the best identifier win! - Mr. Gunn

Euan

Cool new nature.com project has made it onto staging for final testing. May the QA gods be with us.

November 23 from Twitter - Comment - Like - Share

Martin Fenner, Noah Gray and Pierre Lindenbaum liked this

What sacrifices do the QA gods like? I too will need to appease them over the next few months. - Bill Hooker

Biscuits, mostly. - Euan

Surely you need to burn an offering of ISO9000 documentation (in a fully documented manner of course...) - Cameron Neylon

Shirley Wu

A brief analysis of commenting at BMC, PLoS, and BMJ - http://shirleywho.wordpress.com/2009...

November 18 from I was lost but now I live here - Comment - Like - Share

Mike Chelen, Michael Nielsen, Deepak Singh and 11 other people liked this

Pretty plots. - Neil Saunders

6 more comments

I like the BMJ numbers. There is hope for more uptake of comments on papers. - Martin Fenner

I should note that the data for each publisher are not exactly comparable. For PLoS, I looked at articles with the all-time most comments (data courtesy of Pete Binfield). For BMC, I looked at the most highly accessed articles in the last 30 days (with a brief glance at the all-time list for a sanity check), though I also had a short list of all-time most commented articles (data... more... - Shirley Wu

What can BMJ and PLoS do to get audience for the comments? Seems like there's no shortage of opinions on papers, rather it's a questions of where those comments are left. People tend to speak to where they have an audience, so maybe there's a way to indicate what level of audience the comments have? - Mr. Gunn

@MrGunn, that touches on a good point - that leaving comments at journal websites is rather cumbersome, requires a login, etc, and so many people don't bother (see RPG's post:http://blog.f1000.com/2009..., more commenting might be happening on FF, Twitter, on other blogs, because it's more convenient. - Shirley Wu from twhirl

Yep. which brings us right back to where we were earlier this year with author identifiers needed to be able to aggregate things left all over the web. My take is that we can bootstrap an audience by aggregating content through whatever imperfect means we have at our disposal now, and when we have sufficient content, and it's discoverable, the ball will start rolling on this. I try to... more... - Mr. Gunn

It's kinda like the situation with Genbank accession numbers.People didn't start providing them until journals started demanding them, which they didn't start doing until the proliferation of sequences scattered around everywhere became a problem. - Mr. Gunn

It's not just author IDs though. If we want this taken seriously we probably ought to include dois in these conversations as well. Need to uniquely identify both author and paper. - Cameron Neylon

Victor / Mendeley Team

Some great Mendeley news featured on TechCrunch: Mendeley On Course To Be World’s Largest Research Database http://eu.techcrunch.com/2009....

November 18 from Facebook - Comment - Like - Share

Martin Fenner, Björn Brembs and Graham Steel liked this

Cameron Neylon

Wave as a scholarly document editor: not promising at this stage - http://ptsefton.com/2009...

November 17 from Google Reader - Comment - Like - Share

Martin Fenner, Egon Willighagen, Mr. Gunn and 9 other people liked this

Pete Sefton has some significant criticisms of the Wave document model - Cameron Neylon

I hope the #Google #Wave developers are listening... - Egon Willighagen

Aim to feed some of this in - or at least get some answers - we also have some other significant issues that need to be solved so will try to make a list soon. - Cameron Neylon

AJCann

How Meaningful Are User Ratings? (This Article = 4.5 Stars!) - http://scholarlykitchen.sspnet.org/2009...

November 16 from Bookmarklet - Comment - Like - Share

Michael Habib, Christina Pikas, Cameron Neylon and 7 other people liked this

Article on The Scholarly Kitchen knocking PLoS article level metrics. Makes sense, if you're trying to sell overpriced journal subscriptions. - AJCann from Bookmarklet

4 more comments

LOL @ AJCann The author there is going through every publishing innovation that people are trying out and blogging about why it sucks. That's a big part of what the web is for, and he's right on many points, less so on others. Also, any criticism he gets from people who are using these technologies he immediately discredits as part of the choir, so better to say "People I talk to say X is great" as opposed to "I think X is great" if you're writing a response to him. - Mr. Gunn

Mr/Dr Gunn -- liked your comment at the post! - Mickey Schafer

Also interesting comeback from David - a reverse advertising open access model - Cameron Neylon

Crotty loves to blog about how scientists don' blog or read blogs - oh, the irony! - Christina Pikas

Yes, it's just a little silly, Christina, but hey, it got Nicholas Carr a book deal, so maybe this shtick will work for him, too. It's not like he's solely contrarian, either. It's actually nice seeing comments from him contain ideas from my side of the argument from discussions he and I have had on previous posts. It shows he's thinking about this in not entirely dismissive terms. - Mr. Gunn

Maxine

Presubmission enquiry or entire manuscript? - http://blogs.nature.com/nautilu...

November 16 from Nautilus - Blog Posts - Comment - Like - Share

Yaroslav Nikolaev, Neil Saunders, Mr. Gunn and 5 other people liked this

That's actually quite good to know. - Mr. Gunn

Cameron Neylon

Nature Communications Q&A - http://blog.openwetware.org/science...

November 16 from Science in the open - Comment - Like - Share

Kubke, Jim Till, Mr. Gunn and 7 other people liked this

NPG responds to a series of questions about the new journal Nature Communications. Some interesting responses but nothing terribly earth shattering. - Cameron Neylon

Michael Nielsen

MEDLINE in the UK: Pioneering the past, present and future - http://www3.interscience.wiley.com/journal...

November 14 from delicious - Comment - Like - Share

Martin Fenner and Duncan Hull liked this

"This article provides a brief history of the development of the medline database and its huge impact within the UK, from its inception to the present time. The origins of medline can be traced back to a collection of books in the US Surgeon General's Office during the American Civil War and John Shaw Billings' decision, during 1867, to make this Library as complete as possible. From these beginnings, Index Medicus was developed in the early years of the 20th century, and electronic versions of the database began with the computerized on-demand search service MEDLARS in 1964 and then via CD-ROM and Internet Grateful Med to the web-based and free-to-all service, PubMed, in 1997. The response to PubMed was immediate and startling with usage increasing from 7 million searches per annum in 1996 to 400 million searches per annum in 2001 and the service continues to improve..." - Michael Nielsen

The Life Scientists: Wladimir Labeikovsky

News Releases » Elsevier announces new ‘Reflect’ tool with Cell - http://www.kaizo.net/release...

November 13 from Bookmarklet - Comment - Like - Share

Hope Leman, Deepak Singh, Martin Fenner and Abhishek Tiwari liked this

Mickey Kosloff to Mickey's feed, The Life Scientists

Byte Size Biology » Open Access: what’s in it for me? - http://bytesizebio.net/index...

November 3 from Bookmarklet - Comment - Like - Share

Martin Fenner, Cesar Sanchez, Mickey Schafer and 2 other people liked this

"One problem that I am facing is convincing colleagues of the utility of an Open Access publication. ... Not everyone operates on large grants. Many lab budgets leave very little room to buy a new laptop, let alone pay for an OA publication (typically the price of two of said laptops)." - Mickey Kosloff from Bookmarklet

Good points here. Proving a rival to current closed-access or setting a precedent to get grant-givers to make line-items for OA publication are good in an abstract/aggregate level, but the individual lab decision-maker is thinking on a lot more concrete terms. Perhaps, some sort of Impact Factor or "open access journal news" to add credence/credibility can substitute? - Benjamin Tseng

I'm glad you've made the point -- I talk about it with students who will have to make these kinds of decisions in the coming years -- and it's a tough one: ideological belief against practical action. Maybe we need a kind of OA investment account where interest can be accrued over the life of a grant. Okay, not realistic...government subsidies, maybe;-)? - Mickey Schafer

Kevin Emamy to Kevin's feed, Science 2.0, The Life Scientists

Early data from citeulike's automated article recommender http://blog.citeulike.org/...

November 4 - Comment - Like - Share

Yann Abraham, Martin Fenner, Mr. Gunn and 16 other people liked this

"It’s really gratifying to see the social discovery of science generated by the simple act of keeping your references public on a Web page." - Duncan Hull

Jan Aerts to Jan's feed, The Life Scientists

If anyone has a #google #wave invite to spare: think of me... Thanks.

September 29 - Comment - Like - Share

Mike Chelen, Abhishek Tiwari, Daniel MacArthur and 10 other people liked this

i'll also join the line, if somebody has an invite to spare :) - Endre Sebestyen

38 more comments

Perhaps we need to make a combined list? :-) - Cameron Neylon from twhirl

I know @dgmacarthur hopes to get lucky as well. - Jan Aerts from Android

Drat. Me too! Nominate me! And I'd nominate you too if I get one XD - RK

Setting the barrier low: firstname.lastname google email address :-) - Jan Aerts from Android

Me too! - Benjamin Tseng

I'd actually do something with it if I had an account :P I guess I do have a thesis defense coming up in 2 months though... - Brian Krueger - LabSpaces

I want one too!! - Alejandro Montenegro

maybe we should collect the existing science related wave plugins/robots or how do you call it, and some new ideas. and start to develop them after receiving our invites :) - Endre Sebestyen

Just a reminder there is a Google Group for aggregating ideas and code for Wave in Research: http://groups.google.com/group... and a Doodle Poll for a date for a UK meetup: http://www.doodle.com/partici... - Cameron Neylon

@Jan... I get a Mail Delivery reply on firstname.lastname@gmail.com ... :) - Egon Willighagen

@egon I was afraid the address would already be taken :-) - Jan Aerts

Anybody here got an invite already? Still no invite for me :( - RK

Nope... Website says "Google account not yet activated for Google Wave" - Jan Aerts

As of 8am GMT not seeing any further information in my inbox - will update as soon as I know anything - Cameron Neylon

Not spotted anything here either... - Egon Willighagen

Looks like we'll just have to be patient... It'll come when it'll come. - Jan Aerts

How do I invite? - Björn Brembs

Just read somewhere that invites will be available at 4pm BST. Didn't check sources, though. - Jan Aerts

100,000 invites sounds like a lot but worldwide soon thins out :( - Anthony Underwood

@Jan if you get the invite and you happen to have some invites as well, consider me please - george

Word on the street is that only existing wave users will get invites. The new invitees won't get any. - Chris Miller

Chris: But they did post that about the three groups of people that'll receive invites. *sigh* - RK

Me, too! I'll offer a drawing in return! - Kamilah Gill

Cameron: Where did you read that? If it's true then there's hope after all :D - RK

Various things going around on Twitter and in wave suggesting that the release will be at 9am PST which would be 4pm UK time I guess but I would give that the status of rumour rather than fact. Haven't seen any convincing info that anyone has a new invite yet. - Cameron Neylon from twhirl

Cameron: Yea. Saw it on Brizzly too. Anybody got an invite? Should be out now :) - RK

FWIW - sounds like invites won't be out until this evening, so that the Sydney-based googlers will be awake to troubleshoot. http://twitter.com/twephan... - Chris Miller

Yep - all information I have suggests tomorrow morning Sydney time. Even if we assume they are in at 6am thats still some hours away yet. I'm off to bed me-self. - Cameron Neylon from twhirl

Wave invites starting to roll out over the next few hours: http://twitter.com/twephan... - Chris Miller

The "request invitation" link has reappeared at wave.google.com. I wonder if I should fill it in again? - Neil Saunders

yes please - Thomas Power

I'm told that once you even get an invite it can take a couple days for the activation email to arrive. I wonder what email would be like now if they had required invites back in the day... - Paul J. Davis

So you people have invites now? - RK

I don't have one yet. - Carl Fulp

Got 4 more wave invites, pls send me your email. - Khader Shameer

Thats all my invites just got over. - Khader Shameer

No invites yet either.:( - RK

RK, can I have your email ID please ? - Khader Shameer

I had 12 invites on Friday: http://friendfeed.com/the-lif... - Björn Brembs

Shirley Wu

Is peer review necessary? - http://jopm.org/index... (via http://twitter.com/DoctorZ...)

October 22 - Comment - Like - Share

Bill Strathearn, Marie likes mistletoe, Dimitrios Diamantaras and 7 other people liked this

"Summary: After 30 years of practicing peer review and 15 years of studying it experimentally, I’m unconvinced of its value. Its downside is much more obvious to me than its upside, and the evidence we have on peer review tends to support that jaundiced view. Yet peer review remains sacred, worshipped by scientists and central to the processes of science -- awarding grants, publishing, and dishing out prizes. It would be a bold funding body or journal that abandoned peer review, but could we at least do better? I want here to explore peer review -- from a rather personal point of view -- and ask questions about what would be the best system..." - Shirley Wu

6 more comments

This is disturbing but perhaps not surprising: "One way that we studied peer review at the BMJ was by inserting deliberate errors into short papers and then asking reviewers to review the papers without telling the that they contained the inserted errors.[10] These studies consistently showed that reviewers spotted only a minority of errors and that many reviewers spotted none." - Shirley Wu

Also very interesting: "The plan at that stage at the BMJ was to proceed to open up the whole process -- placing submitted papers online, asking reviewers to comment, and allow anybody, but particularly authors, to comment as the process proceeded. Peer review would thus be transformed from a black box to an open scientific discourse. This development hasn’t happened, and it seems to... more... - Shirley Wu

This kind of public peer review is already being practiced at a small number of journals - example at http://www.cosis.net/members... . A good description of this system is at http://www.nature.com/nature... . - Daniel Mietchen

Further quote from Smith: "I think that it would make much more sense simply to publish the paper -- on a university website or in an electronic journal with a low threshold -- with my comments and those of the other reviewer and let the world decide what it thinks." Yes. - Daniel Mietchen

thanks Shirley - I adapted your question for my cheminfo retrieval class to answer: http://getcheminfo.wikispaces.com/FAQ #17 - Jean-Claude Bradley

Very cool - your students will be way ahead of the curve in their knowledge of publishing, peer review, copyright, etc after that class! whew - Shirley Wu from twhirl

This is a class where the content will change significantly every year - Jean-Claude Bradley

Michael Nielsen

Stitching science together : Nature - http://www.nature.com/nature...

October 14 from delicious - Comment - Like - Share

Andrew Perry, John Hogenesch, Dan Hagon and 15 other people liked this

Cameron Neylon on Google Wave. - Michael Nielsen

4 more comments

nice Cameron! Indeed we'll only know the impact of Wave when everyone can participate - Jean-Claude Bradley

are there any actual robots (that is, Wave-enabled machines) on Wave? it would be interesting (at some level) to see a Wave that was just software robots talking to hardware robots. - Richard Akerman

Great question, Richard. I'd like to know, too. Cameron? Anyone? - Michael Nielsen

Me too - Deepak Singh

@richard copied from http://www.slate.com/id... : The core feature of Wave is that it is a real time communication PROTOCOL. Right now that manifests itself as live time chatting, but Wave is not meant to be just a fancy new IM client like you seem to have been using it. It is extendable by developers and the real time nature of the protocol allows it to be potentially... more... - Pierre Lindenbaum

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