Nascent

In the Science in Brisbane forum, William Burns brings up a recent report that states Australia has fewer PhDs in the workforce than other countries. The report recommends that Australia seek to increase the number of doctorate level employees in the workforce. Burns wonders whether that recommendation is worthwhile, "Aren’t we (us lot with PhDs) an impractical, overly-analytical bunch?" While the response to the posting is split, Jon Moulton suggests that, "Without Ph.D.s in the workforce, who will design those new tools the academic Ph.D.s like to use in their research?"

Ever wonder how reviewers for journal articles are chosen? In the Ask the Nature Editor group, Ravi K wonders how one can become a reviewer for a Nature Journal: "Is it purely on invitation basis, or can one volunteer their services in their area of research?" A number of Nature editors respond.

On the heels of an article in Wired, which suggests that scientific modeling may soon be an outdated approach, David Basanta asks, "Does any one else think that traditional science is a thing of the past and that cloud computing will drive us modelers to the employment office?" The ensuing discussion covers issues ranging from open data to the potential for a "cultural shift in the way we look science." Bob O'Hara continues the discussion on his blog.

Tai-Chung Huang is in the process of deciding whether UK or US-based graduate programs are the best fit for his goals. He asks, "…for admission to UK’s school, what matters most? The past publications? recommendation letters? or the hard-selling of introducing oneself via email?"

Nature Network users test their knowledge of scientific legends by attempting to identify the scientists pictured on a mural at the Royal Institution of Great Britain (Ri). Guesses range from George Clooney to the more probable Ludwig Mond. The plot thickens when Matt Brown clarifies that, "…these [persons] are not scientists, but architects and benefactors connected with the Ri." A number of them remain clouded in mystery. Take a crack at identifying these historic individuals yourself.

If you’d like to nominate a conversation you’ve read or taken part in on Nature Network for next week’s roundup, please email us at network [at] nature.com.

Posted by Anna Kushnir at 03:02 PM | Permalink | Comments (0)

Nature Network is an online meeting place for scientists all around the world, designed to facilitate discussion, form connections, and keep in touch. The following is the first in a weekly series of articles highlighting the best conversations on Nature Network. Check back here every Monday for a round-up of the previous week’s activity on Nature Network.

Euan Adie, a Nature Network blogger, brings to Nature Network the science blog buzz surrounding California’s recent cease and desist order targeting direct-to-consumer genotyping companies. Euan elaborates that two issues California legislators have with the genotyping companies are that “…that the labs they [genetic companies] outsource to aren’t always licensed and secondly that they’re breaking a Californian law that requires all genetic tests to be ordered by a physician.” The resulting discussion addresses whether physicians are good resources for interpreting genotyping results and whether the government should have the authority to legislate whether individuals can seek to sequence their own DNA.

Pub nights are expanding beyond the London and Boston hubs. New York Nature Network users came together for their third meet-up while Toronto hosted its first. The New York meet up brought together scientists from disciplines as disparate as neuroscience, computer science, and glaciology.

The organizers of The Source Event, a science career fair taking place in London on September 26, 2008 (organized by NatureJobs), have organized a question and answer forum in which attendees can ask speakers about their background and for advice on their own career direction. In one such exchange, Daniel Weekes, a cell biology post-doc, asks Jim Loftus, a research recruitment manager at Pfizer, how an academic researcher, “…how important is previous industrial experience when applying for a job in industry?”

The recent publication of a Nature commentary on research integrity and the prevalence of academic misconduct, prompted an in-depth discussion of the current framework of regulating scientific fraud and how it may be bettered. In a forum, Brendan Maher, a news editor with Nature, asks, “How could better policies push back against this seeming flood of misconduct?” The conversation continues on Richard Grant’s blog, The Scientist.

The pros and cons of maintaining blogrolls, or lists of links to other blogs, are discussed in the Nature Networks Bloggers Unite forum. Neil Saunders suggests that, “All I get from a blogroll is a very long list of blogs, with obscure titles telling me nothing about their content. Furthermore, a lot of them are likely to be inactive or dead, since the blogroll creator will have realised that maintenance is a complete pain.” Neil suggests that FriendFeed is a better option, while Heather Etchevers and Maxine Clarke volunteer wikis and Connotea as tools for maintaining a community NN group blogroll.

If you’d like to nominate a conversation you’ve read or taken part in on Nature Network for next week’s roundup, please email us at network [at] nature.com.

Posted by Anna Kushnir at 03:17 PM | Permalink | Comments (0)

Nature Precedings launched back in June 2007 with the support of several partner organizations, including the British Library, the EBI, Science Commons, and the Wellcome Trust. Since then it's been an exhilarating year. Wired described Nature Precedings as an island of innovation and several editorials in Nature journals throughout the past year have discussed how Nature Precedings can enhance scientific communication (see Community service, Virtual networking for microbiologists, Free market science, and Shared genomes).

Over the past year, researchers in a variety of disciplines, including genetics, neuroscience, bioinfomatics, and ecology have posted 475 documents and 180+ comments. Thousands of readers have signed up to comment, vote, and submit documents on the site, and we’ve seen steady growth in site traffic and posted documents. The Nature Precedings group on Nature Network has become a lively place with discussions on many topics including “findability” , posting negative results on Precedings and academic search engines.

In response to suggestions from you, our users and contributors, we’ve rolled out a number of new features, including comment notifications, an OAI-PMH interface, and many usability enhancements.

To all of our visitors and supporters: Thank you! for helping turn the past year into a strong start for the project. The site relies upon your contributions for its success.

As we celebrate one year of Nature Precedings, we'll be releasing new features on the site in the upcoming weeks and making some additional announcements. We look forward to the year ahead!

-The Nature Precedings Team

Posted by at 03:24 PM | Permalink | Comments (0)

Over the last year, Microsoft has really engaged with the STM publishing community and has been maintaining a steady dialog on how they can help publishers start to use OOML and the OpenXML (DOCX) format.

I had the honor of moderating a seminar session at the SSP Annual Meeting on 28 May titled The View from the New Office: Opportunities and Issues Incorporating Office 2007 into Scholarly Publishing. Microsoft staff Pablo Fernicola, Murray Sargent, and Alex Wade all did a wonderful job of presenting many of the new features of Office 2007 and the value of OOML and OpenXML/DOCX formats. Cyndy Wessling also of Microsoft also chimed in from the front row on the latest release dates. Paul Topping of Design Science presented the amazing progress he has made on MathType. Tim Ingoldsby and Bruce Rosenblum presented the issues surrounding the new format that are still causing problems for publishers. Presentations can be found at inera.com/word2007directory.shtml. Here are my observations.

Microsoft has Created a New XSLT to Fix MathML Support in OOML
Great news! Unfortunately, they are currently planning on shipping this when Service Pack 2 is ready for Office 2007. That would mean that it is not likely to happen until early 2009. This would be a real shame. Apparently the XSLT transform has been tested and really would make a significant difference. Without this XSLT it is not really advisable for publishers that need MathML in their workflows to start supporting the OOML/DOCX format. If anyone from Microsoft is listening out there, I highly recommend you simply publish this XSLT as a beta out on your developer forum or even better please post it to your scholarly website at microsoft.com/mscorp/tc/scholarly_communication.mspx . The XSLT is not technically part of the Office 2007 offering. It is a transform that publishers and their partners (as well as others) can readily start inserting into our automation routines. You have come so far! Give us the tools so we can start the migration. You want, we want it, let’s get moving together.

ODF Support!
Back in February, Microsoft announced support for ODF coming in Office 2007 Service Pack 2 (SP). This SP is planned for release in early 2009. This is huge news. It means that authors now have much more freedom of choice. A beta may be ready as June/July 2008. Keep an eye out for this one.

Macintosh Office 2008
The new Office 2007 Math Editor is not shipped in Mac Office 2008. It turns out the Mac Office group is completely separate from the Windows team. There is no shared code base.
In order to do math in Mac Office you will need the MathType/Design Science toolset.

VBA is due back soon for Mac Office.

Simple Demo of DOCX Containers
To demo the power and components held within a DOCX file
Change the .DOCX extension to .ZIP and then open within a ZIP program to see the various containers (folders).

Plugins
Microsoft is always releasing new experimental improvements that further the usefulness of their product line. One such improvement is a plug in that allows the user to quickly
Search Commands in Office. It is a vast improvement over using the Help function.
See this at: www.officelabs.com

Microsoft have created a free plugin that allows OpenXML (DOCX) files to be translated to the Daisy format for accessability. See this at http://www.openxmlcommunity.org/daisy/

Microsoft Research Projects
• Ontology Markup of Scholarly Papers – prototype with PLOS
• Are interested in chemical markup via Office
• Storing datasets inside DOCX files – prototype with Broad Institute
• Autodeposit into Gene databank
• Data Archive project – prototype with Johns Hopkins

See information about these at Microsoft.com/science

Posted by Howard Ratner at 04:57 PM | Permalink | Comments (2)

Barend Mons left a comment on last week's critique of WikiProteins which deserves a new post, really, to help balance out the critical one. I think that for the most part Barend's points are helpful and reasoned, and you can read the full thing under the fold.

I should address one part, though: the suggestion that as Nature is a commercial company it's somehow disingenuous to complain about the overtly commercial aspects of Knewco and WikiProteins on this blog. It's not.

When it comes this kind of stuff - open access data, working collaboratively, science 2.0 - we're deeply conscious within Web Publishing of the need to back up what we say with APIs (Connotea), mirrors and / or data downloads (the Pathway Interaction Database). You can't just slap an 'Open Access' sticker on the box and expect to ride a wave of goodwill, no matter who your CEO or partners are!

Although the rather sour blog by Euan is quite an exception in the overall positive reactions we receive on the beta site of WikiProteins, I feel that a matter-of-fact reaction from the lead author of the article in Genome Biology that announced it is warranted. It goes hereby.

First of all on Authorship: Jimmy was instrumental in making the initial contacts between me and Gerard Meijssen who was then working on WiktionaryZ, now Omegawiki. He also gave invaluable advice on several aspects of the system and he therefore deserves as much of an authorship acknowledgement as the average senior author/professor who ‘conceived of the study’.
See also Gerard Meijssens’ Blog about that

On the interface etc., we all know this is beta and we struggled for a long time to make it as ‘good’ as it is. Obviously a flat file is easier than managing a relational database and therefore the interface can never be ‘really easy’. I agree with Peter Jan that constructive criticism would have been more useful.

Criticism on the commercial nature (as it were) of a company on a blog made available by another commercial company – one that makes money on others’ scientific contributions for as long as we have been studying nature – is a bit peculiar as well. With the involvement of Amos Bairoch, Michael Ashburner , Mark Musen, Abel Packer, Roberto Pacheco, Matt Cockerill and many others in this process, not to mention Jan Velterop’s reputation, it seems to me that the OA nature of the projects is sufficiently safeguarded.
With my personal background in malaria, working for 15 years with colleagues in developing countries, I also built a public track record in pushing free access to information for developing countries.

The content in WikiProfessional applications is completely freely available under the Creative Commons Attribution license (we are working on making author credits more clearly visible). The Knowlets are indeed proprietary as we create added value and apply algorithms that by themselves now have taken several million dollars to develop. It has proven exceedingly difficult to get sufficient public funding for this project, which has been carefully internationally discussed and prepared for several years. Bill Melton and Al Berkeley are to be highly commended for taking the risk to fund the vision.
Also the Knowlet space is in Open Access for non-commercial use. I sincerely hope that seasoned investors like Bill and Al would be more imaginative than trying to monetize this site and the others to come by ads only.

On potential fear of competition: let me tell everyone up-front that the authors on the paper have every intention to connect all information on important concepts via WikiProfessional, not trying to put it behind any barrier or to compete with anyone. Some may see us as a competitor to IHOP or Wikipedia pages on biomedical concepts for instance, which is not true, as you will soon see.
We are planning to add locally maintained databases on genes such as www.dmd.nl to the appropriate concept page in WikiProteins much more prominently placed than today (now an indirect link via SwissProt data), but also locally-maintained databases on single gene mutations such as the growing number of Leiden Open Variation Databases (LOVD’s). We have a project starting to map all concepts in WikiProfessional, including all biomedical concept pages, to the corresponding pages in Wikipedia and other emerging wiki’s. People who find the WikiProfessional interface too difficult will be soon able to contribute to their own wiki of choice and their contributions will be seen in Wikiprofessional anyway.

We collectively ‘own’ that basic data and anyone is free to ‘add value’ to these and make that ‘added value’ freely available to all or just for public not-for-profit use. Knewco is just one of the companies that derives value from the data and has decided to make the added value available to the scientific community for free.
I cannot wait until Nature will be Open Access as well, at least as far as the scientific articles are concerned. Then it will be easier to make full use of Nature content for the benefit of the scientific community.

One more point on equity and access: The collaboration with our Brazilian colleagues, with whom I co-developed and signed the Salvador Declaration on Open Access, referred to in the supplementary data of the Genome Biology paper, will soon result in crossing the language barrier to Spanish and Portuguese.
The record for my beloved ‘malaria’ in Omegawiki will show you our ambition on in how many languages we would like to support in the indexing on-the-fly. For Free.

I hope these further explanations take away at least the worst of Euans fears. I see in today’s version of the blog that he did not only change the original title of the contribution [Ed note: I edited the title to be a bit less provocative], but I also saw a more balanced reaction to Peter-jan Roes.

However Euan, if you still feel that some of your comments were justified and not yet properly addressed, please substantiate your claims and in the process it is highly appreciated if you give some constructive criticism. You would really help the community – and us – by doing that. Let’s keep discussing this project to make it better.

Posted by Euan Adie at 09:20 AM | Permalink | Comments (0)

Yahoo! SearchMonkey lets anyone create "applications" that enhance the Yahoo! search results of users that have chosen to add them.

Following last.fm's lead today, I created an example application for Nature Reviews Immunology - if you have a Yahoo account, you can add it to your customisations and then see an enhanced search result. [note: it seems to be intermittently not showing up, hopefully it'll settle down soon]

It makes use of the article metadata that was recently added in meta tags to Nature.com journal articles (and could equally easily make use of any metadata embedded as RDFa - the information is extracted from the pages using PHP and XPath).

Posted by Alf Eaton at 03:21 PM | Permalink | Comments (0)

I've added a feed of the latest activity from the Life Scientists room on FriendFeed (now nudging sixty - seventy users) to the Nascent sidebar.

'nuff said.

Posted by Euan Adie at 11:53 AM | Permalink | Comments (1)

WookieProfessional

Jimmy Wales is also on the author list. That's pretty cool although I have to admit that after reading the actual paper I wondered briefly how strictly the ICMJE guidelines for author attribution had been adhered to (Matt Hodgkinson has a good post about this). It's not because I've any reason to doubt Knewco - in any case Genome Biology is very good about listing author contributions - it's just that the temptation to give honorary authorship on celebrity researchers must be pretty strong, especially when it's such a good hook for a press release. I know that sounds cynical, blame Merck.

Anyway, here's the idea in a nutshell: WikiProteins has sucked in content from a bunch of existing scientific databases and identified the unique concepts (proteins, GO terms etc.) across all of that data. For each concept there's something called a Knowlet, which records the relationships between that concept and all the other concepts in different ways. Using the data from the Knowlets they've linked different concepts together into a 'concept web'. Each concept also has an associated wiki page on the system which is publicly editable. By default each wiki page contains relevant information from the existing scientific databases mentioned previously.

As concepts I like both the semantic web and community annotation of databases. Both ideas have been around for years and it's great that we're finally reaching the point where we can start putting them into practice.

Unfortunately WikiProteins is a bit rubbish.

It seems almost churlish to say that about a site that only launched two weeks ago and there's been some debate about this within Web Publishing (you can take the above as individual rather than collective opinion) so I'm willing to stand corrected but as it is the site just doesn't do it for me.

My objection is primarily to the implementation, not the vision. Having said that I probably wouldn't have written this post if I hadn't been irked by all the 'we call on a million minds' rhetoric and associated hype coming from Knewco. If you talk the talk...

.... make sure that your site is at least fit for purpose, which WikiProteins isn't. Considering that scientists have only just gotten to grips with Wikipedia wouldn't it have been better to spend a little bit more time on the user interface, which is cluttered and confusing?

Speaking of Wikipedia and without singling out any Knewco executives - dudes, there are notability criteria to meet before you can create a page for yourself there (edit histories are public, remember). No biggie but considering the 'wikipedia for professionals' tag you probably want to read the help pages more.

There's a very high crap to content ratio and the actual information about concepts is condensed into a tiny sidebar. I consider myself fairly au-fait with scientific databases and the web yet it still took me a couple of hours to properly grok how the site works. I find it
hard to believe that a thousand bench scientists - never mind a million - are going to get past the initial barrier to entry, browse, register and then actively contribute.

Once you do start using the site it becomes pretty obvious that for all of the cleverness of the RDF backend the actual content is nothing special. I guess that's why there's a call for community annotations but there's not much of a lure in sub-GeneCard level stats on proteins.

I'm concerned that the site has no mirrors, no export facility for the wiki data and a one way data suck - content from public databases and wiki users goes in, nothing comes out. That well respected OA proponent Jan Velterop is CEO of Knewco is some reassurance on this front but also makes it doubly disappointing that they're currently all talk and no trousers. "Eventually we may have [the community annotations] available in a suitable form for downloading"? Seriously? For proper community collaboration that's really not good enough. What if Knewco goes bust? What if they can't support themselves through advertising (dozen staff, ads on sparse wiki content, you do the math) and decide to switch to a subscription model?

What do you get out of participating, in any case? A system like this needs to keep track of provenance and provide recognition for good contributors. There's nothing like this in WikiProteins which strikes me as a missed opportunity.

I'm disappointed by other aspects of Knewco's corporate approach to science on the web: firstly Knowlets is a stupid name, secondly the trademark sign makes it more so, thirdly the actual technology is patent pending. I have great difficulty reconciling software patents with the spirit of open scientific progress - which is what I feel Knewco is implying that you'll be working towards if you contribute to WikiProteins. Very uncool, Knewco.

The vision underlying WikiProteins is a worthy one and the fact that Knewco has actually implemented something while everybody else just talks about it deserves credit. If this was an academic project I'd chalk my criticisms up to the site's beta status and be cheerleading with BoingBoing, but the fact is that Knewco is a venture funded, for-profit company whose business is trafficking the work of scientists. There's nothing wrong with that - Nature is also profit making, after all - but it means we need to hold them to higher standards.

Posted by Euan Adie at 05:09 AM | Permalink | Comments (9)