'Mummi' Thorisson - Likes

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

Mickey Schafer, Hope Leman, joergkurtwegner and 19 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

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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

Mark A Jensen to Mark's feed, The Life Scientists

RT - Fwd: Sanger FASTQ format and the Solexa/Illumina variants: I’m delighted to announce an open access publication in Nuc... http://news.open-bio.org/news... (via http://friendfeed.com/c03db34...)

December 17 - Comment - Like - Share

Mike Chelen, Oliver Hofmann, Brad Chapman and 'Mummi' Thorisson liked this

Itachi to Itachi's feed, The Life Scientists, Science 2.0, Highfalutin

Science: The looming crisis in human genetics | The Economist - http://www.economist.com/display...

December 5 from Bookmarklet - Comment - Like - Share

Alexey, Pavlo Zahozhenko, Björn Brembs and 25 other people liked this

"Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races." - Itachi from Bookmarklet

6 more comments

we'll know more than before - surely a good thing....... - winckel

For a different perspective, see the Nature article "Let's celebrate human genetic diversity" http://ff.im/9PbOx - Ruchira S. Datta

Uh-Oh... - Christopher Harley

See rebuttal by Luke Jostins at The Sanger Institute "The Economist has a rather distressingly bad article by the evolutionary psychologist Geoffrey Miller, about the supposed general failure in human disease genetics over the last 5 years...." http://www.genetic-inference.co.uk/blog... - Duncan Hull

Thanks Duncan. - Itachi

my opinion sides heavily towards nurture (upbringing, environment) versus nature (heritable traits) in human behavior - Mike Chelen

Certainly, one could never use knowledge of how drugs work differently in different genetic backgrounds to help cure disease, right? - Mr. Gunn

Allyson Lister

CTAN: directory: /tex-archive/macros/latex/contrib/glossaries - http://tug.ctan.org/tex-arc...

December 15 from delicious - Comment - Like - Share

'Mummi' Thorisson liked this

The glossaries package for Latex. This obsoletes the glossary package. What's great about glossaries is that you can combine your acronyms and your glossary together in one file, and reference acronyms inside your glossary entries. Unfortunately not in texlive-latex-extra on ubuntu :( , which only has the old glossary package. - Allyson Lister

Allyson Lister

Modelling data across labs, genomes, space and time - http://www.citeulike.org/user...

December 14 from CiteULike: allysonlister's... - Comment - Like - Share

Deepak Singh and 'Mummi' Thorisson liked this

Nature Cell Biology, Vol. 8, No. 11. (01 November 2006), pp. 1190-1194. Logical models and physical specifications provide the foundation for storage, management and analysis of complex sets of data, and describe the relationships between measured data elements and metadata — the contextual descriptors that define the primary data. Here, we use imaging applications to illustrate the purpose of the various implementations of data specifications and the requirement for open, standardized, data formats to facilitate the sharing of critical digital data and metadata. Jason Swedlow, Suzanna Lewis, Ilya Goldberg - Allyson Lister

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

"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." - Mr. Gunn from Bookmarklet

Mr. Gunn

An anonymous source has informed me that the ASCB has banned “replication of data” by visitors, but has presented Twitter as the poster child of conference data... - http://synthesis.williamgunn.org/2009...

December 6 from Synthesis - Comment - Like - Share

Mike Chelen, Daniel Mietchen, Benjamin Tseng and 5 other people liked this

Sad, just sad - Deepak Singh

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"forms of communication involving replication of data" - pretty much invalidates the entire conference? - Neil Saunders

I wonder if people are allowed to talk - Deepak Singh from IM

Natural selection in action. Either another set of organizers, or another conference, will take over as this one dies off. - Bill Hooker

What is the point of scientific conferences again? - 'Mummi' Thorisson

What was the point in science again? - Cameron Neylon

What was the point of life again? [descending into pessimism...and trip to the pub] - 'Mummi' Thorisson

Bill, another source reports that attendance seems way off this year from what it has been in the past. - Mr. Gunn

As I see it, the problem is one of copyright. All the biologists I know (and to a degree, myself included) are alright with presenting pre-publication data at a conference as long as it isn't digitally recorded or disseminated. If there were a way to enforce "first presentation rights", less people would worry about getting scooped and be more willing to share unpublished data. - Walter Jessen

It'd be nice if the talk were publicly available, either during or very soon after the talk. Then, this public record, combined with the tweets, blogs, etc. would provide pretty good evidence of who did the work and presented it first. At least for me it would. Even as it stands now, though, if scooping is a worry, it seems to me that allowing the audience to tweet & blog will make it... more... - Steve Koch

Walter, you might be right, but surely it has been disseminated in the form of conference abstract prior to someone tweeting about it. If they have copyright concerns, they're simply not understanding things. - Mr. Gunn

I disagree - abstracts are much different than data. I like Steve's idea .. let's get the status quo to swing in the opposite direction and make everything publicly available following conferences and meetings. - Walter Jessen

what is so harmful about having your research referenced by another? if it is cited, it can bring attention and acclaim to the original. if it is not properly cited, then that is itself the problem - Mike Chelen

Cameron Neylon

Nearly final version of collaborative proposal for a lightweight data management framework for submission in next few days.

BBSRC-CN-v2.0-public.doc 331 KB

December 7 - Comment - Like - Share

Allyson Lister, Claudia Koltzenburg, Steve Koch and 5 other people liked this

Crud - sorry for the re-post folks, there was something in that version that shouldn't have been (and if anyone's downloaded the file and figured out what it is I'd appreciate it if you didn't spread it around - some details to be ironed out yet) - Cameron Neylon

16 more comments

darn. now I wish I'd downloaded it! *curious* - D0r0th34

Object lesson in not trying to bowdlerize documents too late at night. And that it is so much easier when _everything_ is public. But its not my thing to make public as yet...and no, I'm not moving jobs :-) - Cameron Neylon

We're thinking along similar lines to this (without Wave as yet) and trying to generate interest in Aus for a linkup with Jeremy Frey/PMR. Cameron if you wanted a remote experimental Chemistry partner let me know - our open science project officially starts tomorrow (!) for 3 years, so we'll start to generate data in Sydney we want to share. - Matthew Todd

Cool, JGF mentioned he'd been talking to you and I meant to follow up. If you're up for writing a letter of support that your interested in the project that would be very cool. I can do the same obviously for anything going in on your side. The more (diversity) the merrier, although we can't stump up for endless disk space for everyone so we might need to find a re-charging mechanism if... more... - Cameron Neylon

Sure, OK. Could you email me an address for the letter? m.todd@chem.usyd.edu.au. Data would be small size but lots of little files - mainly NMR/IR/MS. I'm guessing what you're proposing though would need installation of a little software on local computers attached to spectrometers. The institutional inertia is the problem there. - Matthew Todd

Yes, there has to be a widget installed on the computer from which the file gets copied one way or another and this could clearly be a problem in many cases. But one problem at a time. - Cameron Neylon

Side musing: How long does it take a researcher using method X to generate 1Tb of data? In microimaging, this may easily be a day, and some particle or astrophysics may be even faster. - Daniel Mietchen

Not long in many cases - images stack up pretty quickly. - Cameron Neylon

Looking good, Cameron, albeit judging from a really quick skim-through. Makes me want to work on this, in fact. - 'Mummi' Thorisson

I don't get out of bed for less than 1TB per day. An impending deluge of >1 PB that I'll have to manage does give me sleepless nights though :) - Dan Hagon

By the way - is AtomPub (http://en.wikipedia.org/wiki...) being considered for publishing & editing web resources via a Atom store back end? I don't know much about the Amazon cloud storage and apparently can't be asked to find out (!). RSS/Atom is a nobrainer for monitoring for updates obviously. But is content create/update perhaps all supposed to be done via Wave / XMPP? - 'Mummi' Thorisson

One practical issue which might be important to clarify is whether or not you'll be able to develop the Wave components on a local Wave federation server and/or robot server (I forget the exact terms used in the draft spec.). If you're looking at wave for rapid prototyping, especially of robots, having these in place from the start could be crucial to how far and how fast the you can get with the tools you intend to develop. - Dan Hagon

@Matthew interested to see how you get on; We've put our undergrad OS lab on hold, but my projects(equivalent to honours)/postgrads are waving whether they like it or not (and actually most of them seem to like it so far :>) - Anna Croft

@Mummi, AtomPub is an obvious approach but we don't want to tie ourselves down in advance. Certainly most likely contender so I should put it in though. @Dan, almost certainly on the central Wave server, which does mean we may end up with a performance hit I admit. Assuming that increases in performance combined with these being small waves in most cases will mean things are ok.... more... - Cameron Neylon

And I think this is the final version: Form here http://dl.dropbox.com/u... Case for support: http://dl.dropbox.com/u... Impact statement: http://dl.dropbox.com/u... - Cameron Neylon

That's had various bits taken out of it, specifically support from commercial partners and the financial details, as well as the names of suggested referees. - Cameron Neylon

....and its gone! - Cameron Neylon

François Dongier

Drupal, the semantic web and search | Dries Buytaert - http://www.twine.com/item...

December 8 from Twine - Comment - Like - Share

'Mummi' Thorisson liked this

Allyson Lister

MIREOT: the Minimum Information to Reference an External Ontology Term - http://www.citeulike.org/user...

December 8 from CiteULike: allysonlister's... - Comment - Like - Share

Duncan Hull and 'Mummi' Thorisson liked this

In International Conference on Biomedical Ontology (July 2009), pp. 87-90. While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions. Mélanie Courtot, Frank Gibson, Allyson Lister, James Malone, Daniel Schober, Ryan Brinkman, Alan Ruttenberg - Allyson Lister

Cameron Neylon

It wasn’t supposed to be this way… - http://blog.openwetware.org/science...

December 5 from Science in the open - Comment - Like - Share

Bill Anderson, Jan Wessnitzer, Duncan Hull and 12 other people liked this

Ah - found a clearer statement from Met Office on data release: http://www.metoffice.gov.uk/corpora... - Cameron Neylon

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I must admit that until 48 hours ago, I never realized the Met Office data was secret. I'd always assumed it would be in the public domain. Silly me. - AJCann

You basically have to send them an email saying what you want and what you're using it for. If you are an appropriate accedited researcher you can get access to the thing you want, but not distribute it I think. Its a classic demonstration of public domain benefits in some ways. - Cameron Neylon

blimey - I never knew that met office data wasn't public record. Is the idea that Ordinance Survey introduced deliberate small mistakes into their map to protect their copyright? Or is that an urban myth. Depressing is about right. - Jo Badge

Brilliant post Cameron. - Andrew Lang

*applause* - Bill Hooker

I've heard from people who do mapping type stuff that the OS errors are real. Can't say I've ever checked myself though. - Cameron Neylon

in the US NOAA NWS data is open, but there's a cost recovery model for some of the historic data sets. I think the art around these parts is to combine NWS stuff with Navy stuff and stuff from the literature, but that's just my impression. - Christina Pikas

My understanding was that most of it was provided at cost - but a lot is in formats that are not terribly useable or useful so they charge for transfer to media and some reformatting. Bottom line is that most of it is government data and therefore in the public domain by definition. - Cameron Neylon

Some interesting comments on the blog itself - first time I've had that many comments in ages! - Cameron Neylon

AJCann

Prohibition - http://scienceoftheinvisible.b...

December 3 from Science of the Invisible - Comment - Like - Share

'Mummi' Thorisson, Andrew Perry and Cameron Neylon liked this

Sadly, not all of my fellow #altc2010 Web Editors seem to agree with this point of view :-( - AJCann

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Whether they agree or not they're not going to be able to stop a back channel going on. Which was your point surely? Read a clueless article yesterday about brands having to make a choice about whether going online because they might encounter negative content about their brand. Well duh - the content is going to be out there anyway - engage or don't those are the choices. - Cameron Neylon

Yes, but since I've assumed a sort of responsibility for guiding the process, it would be nice to avoid a car crash rather than picking up the pieces. - AJCann

Ah, I see your dilemma... - Cameron Neylon

For me the issue is whether or not to have the/a back-channel visible on screen next to or behind a speaker. If the speaker wants it, then fine. If they do not, then that is their choice. The fact that a proportion of the audience may be watching and contributing to the back-channel on their own device seems to me to be a different issue, where I think that it's a free country. - Seb Schmoller

@Seb And conference organizers who have tried to block the backchannel have also felt the wrath. Of course the easy way to do it is not to have wifi and a building which blocks the 3G signal :-) As a compromise, how about letting speakers choose whether they want the backchannel (which in the context of #altc2010 means Twitter, I guess) visible or not? - AJCann

@ Alan. Exactly. That's the point I was trying to make. No pressure on speakers to have it visible. No pressure not to. A bit of "caveat" info to help them decide. (Practically speaking we'll have to think through where Elluminate's back channel might fit in.) - Seb Schmoller

Might I suggest no screen, but a moderator who can pass on info to the speaker as an alternative. I have used this in my classroom and in presentations. - Terry Elliott

I couldn't understand why there was a permitted back channel via elluminate at ALTC2009 but not via twitter, I assume because elluminate was moderated? - Jo Badge

There was a Twitter backchannel, because ALT promoted the #altc2009 hashtag, but it just didn't receive any official love. - AJCann

I think the speaker should be able to see the backchannel but not the audience unless they have their own kit (backchannel of limited use if you can't contribute). I've seen talks in SL (where backchannel is in chat) derailed by inexperienced speakers becoming overly engaged with a minority using the backchannel. Using a moderator is good if there is an inexperienced speaker or very noisy backchannel. Of course, in SL the audience also chooses when to change your slides unless you're careful. ;) - Peter Miller

seen this? http://scienceblogs.com/terrasi... - Jo Badge

Yes, I saw that. Sigh. Twitter banned. But not facebook, Posterous, Wordpress, Friendfeed. etc. FAIL. - AJCann

The Dark Side of Digital Backchannels in Shared Physical Spaces - nice summary http://gumption.typepad.com/blog... - AJCann

Cameron Neylon

Distributed Science, Part 2 - http://scienceblogs.com/commonk...

November 5 from Google Reader - Comment - Like - Share

Mike Chelen, 'Mummi' Thorisson and Graham Steel liked this

John Wilbanks nails it - no surprises there then :-) - Cameron Neylon

open source as a metaphor applies through application and perhaps adaption to aspects of science - Mike Chelen

Cameron Neylon

The Climate Modeling Leak: Code and Data Generating Published Results Must be Open and Facilitate Reproducibility - http://blog.stodden.net/2009...

December 1 from Google Reader - Comment - Like - Share

Benjamin Tseng, Steve Koch, suze and 2 other people liked this

I've avoided writing about this because a) I find the whole thing profoundly depressing and b) I have no time to look through the original documents (the raw data as it were) but Victoria does a good job of teasing apart one of the central issues here. - Cameron Neylon

Duncan Hull

Drop and Compute | e-Research, DropBox - http://blog.openwetware.org/deroure...

November 30 from delicious - Comment - Like - Share

Andrew Spong, Neil Saunders, Anna Croft and 4 other people liked this

Did you know you can run remote computations from your Windows/Mac/Linux box without any special client software installed, just by dragging and dropping? And it even doesn’t matter if it’s not online all the time… The trick uses Dropbox, which is software that syncs your files across your computers. This is incredibly handy – as time goes on we all use more PCs, laptops (and indeed iPhones!) and Dropbox synchronises the contents of your Dropbox folder across all these for you. Note this is quite different from having some centralised filestore (or WebDAV drive) mounted on everything – it doesn’t need you to be online at time of use and it doesn’t need a sysadmin to set it up. Dropbox is very easy to install and incredibly easy to use – there really is no need to read a manual and the benefits are immediate. (Other synchronising software exists, but Ian prefers the simpliciity and ease of Dropbox.) - Duncan Hull

Anyone tried this? - Duncan Hull

We've not tried the compute side, but have been using dropbox to move stuff between our compute machines. Looking forward to trying this - thanks for flagging it up ... - Anna Croft

Christopher Comella

JanRain Offers Distributed Social Options Galore, Interscope Geffen A&M Bites - http://www.readwriteweb.com/archive...

June 23 from Bookmarklet - Comment - Like - Share

'Mummi' Thorisson liked this

"Interscope Geffen A&M, a division Universal Music Group, likes what they've seen from JanRain - no doubt thanks to the names "MySpace," "Facebook," and "Google." So they have chosen to deploy RPX across 200 artist sites, enabling fans to login to the sites with the credentials they prefer. In so doing, Interscope Geffen A&M stands to connect a number of artists to their fans - and their fans' existing social networks. Currently, artists like OneRepublic, Robin Thicke, Keri Hilson, The Game, and Lady Gaga all offer access via RPX." - Christopher Comella from Bookmarklet

Ade Lack

Taking a look at RPX Social login and sharing widget for a new site. Looks to have all the functionality I need,... https://rpxnow.com/

November 8 from Twitter - Comment - Like - Share

'Mummi' Thorisson liked this

Pierre Lindenbaum

EMBRACE Ontology for Data and Methods (EDAM) - http://www.ebi.ac.uk/~jison...

November 27 from delicious - Comment - Like - Share

'Mummi' Thorisson, Deepak Singh and io2a liked this

EDAM (EMBRACE Data and Methods) is an ontology for bioinformatics tools and data. It consists of a set of defined terms, relationships between terms and rules that govern the terms and relations. It provides a controlled vocabulary for description in semantic terms of: * Web service (WS) WSDL files * XSD data schema, e.g. associated with a WSDL file * Standalone tools, web servers etc * Databases * etc. - Pierre Lindenbaum

Jonathan Eisen

Open Source Science: A Revolution From Within featuring #PLOS, @wjjessen, Jeff Bizarro, Google Research, Priyan Weerappuli, John Wilbanks, Science Commons and more. - http://www.linuxinsider.com/story...

November 21 from Bookmarklet - Comment - Like - Share

Richard Akerman, Neil Saunders, Mackenzie Cowell and 6 other people liked this

I am still confused by claims that Open Science and Intellectual Property protection are not incompatible. The patent system requires non disclosure prior to submission. - Jean-Claude Bradley

9 more comments

Jean-Claude, my understanding is that you can retain US patent rights up to one year after disclosure. However, you lose almost all international patent rights. So, there is some compatibility, as far as US patent rights go. I've been told this by university IP people who seem to indicate that they'd be interested in doing that. I think you said previously that this wasn't true at your... more... - Steve Koch

The other approach is to file the patent before you do the experiment, which was what was recommended to me by our tech transfer people if there was anything that looked commercial. The patent process is so slow, and so subject to changes anyway, that by the time the patent is awarded the project will be over, and if necessary you can insert extra claims in as you go (as long as your original claims are worded generally enough - which they generally are in an initial filing) - Cameron Neylon

Cameron, that's what we did. It was a pain in the ass, though. - Mr. Gunn

More of a pain in the arse than the normal patent process? My personal view is that it simply isn't worth the hassle anyway but maybe I've just had bad experiences. - Cameron Neylon

Steve - yes we have discussed this but I haven't heard about other researcher experiences. At my institution, international rights were important. Filing provisional patents every few months is doable but not every day or week if you really want to discuss your research openly. - Jean-Claude Bradley

Cameron filing the patent without doing the key experiments is what caused the failure of one university to collect royalties from a patent related to Vioxx - Mel Reichman gave a great talk about that: http://usefulchem.blogspot.com/2009... - Jean-Claude Bradley

Coincidentally, I had discussion with university tech transfer office and a patent attorney this morning. The university innovation manager (person in charge of our IP) confirmed that US patent rights are valuable for UNM. And they're probably going to go this route for IP we have disclosed. They remain supportive of our dual open science / IP route (which as noted above will usually... more... - Steve Koch

Steve - you are lucky to have that type of support from your institution. We can use you as a poster child for IP compatible OS, which will only work in the US as far as I know. However, usually when people discuss making OS compatible with IP they are not referring to your approach - they typically mean creating a password protected site, enabling the sharing of their work only with a... more... - Jean-Claude Bradley

@J-C I think I am lucky that the IP people are willing to work with me. But I don't know whether it will actually work out very well. Also, not sure we can be poster children for IP-compatible OS, but we're at least one kind of weird data point :) - Steve Koch

Steve - nobody else has come out of the FF woodwork to say they have a similar approach to yours. I would think this is a terrific area for a business/law student to study and write a report for a class assignment. The other side of the coin here is that doing science openly is a pretty low cost way preventing competitors from filing patents for similar work. - Jean-Claude Bradley

Iddo Friedberg to Iddo's feed, The Life Scientists

Photosynthesis, phages and structures: there’s treasure everywhere! - http://bytesizebio.net/index...

November 24 from Bookmarklet - Comment - Like - Share

Mickey Kosloff, 'Mummi' Thorisson, Wladimir Labeikovsky and 2 other people liked this

Very cool work, thanks for blogging it! - Ruchira S. Datta

Good to see that bioinformatic studies can make it into Nature. Probably helps if your surname is Koonin or Church ;-) - Neil Saunders

Heather Piwowar

Promoting Open Source Science - http://www.walterjessen.com/promoti...

November 21 from Google Reader - Comment - Like - Share

Mike Chelen, 'Mummi' Thorisson, Matthew Todd and 3 other people liked this

Chris Rusbridge

Data and the journal article - http://digitalcuration.blogspot.com/2009...

November 18 from Digital Curation Blog - Comment - Like - Share

Jill O'Neill, 'Mummi' Thorisson, Richard Akerman and 4 other people liked this

Chris Rusbridge is sceptical about the state of supplementary information and data - Cameron Neylon

17 more comments

It would have been great if I could easily have found one... one(!)... example of supplementary data in a re-usable format. But time and agin I found PDFs, with the odd Word document! - Chris Rusbridge

The example I quoted was a chemical one (http://www.rsc.org/suppdat...); do any of you have any suggestions on what might have been better ways of coding those supplementary materials? There are some chemical method descriptions; CML? Fitting the data to a mathematical model, not sure how it might be best described. And some NMR spectra and other images I don't personally recognise. - Chris Rusbridge

No criticism of these authors intended, but what would be better nthan PDFs in such a case? - Chris Rusbridge

Almost anything :-( Seriously the problem is that people think of the online space as a dumping ground, not just a place for data. The assumption is that you have to dump everything into one file. What would be helpful would be good upload systems that let you put the raw files in and help you organize and index them. But even then, when you are in the final stages of manuscript preparation are people really going to send around a directory of files? - Cameron Neylon

Someone told me recently that Nature have appointed a staff member to make supplementary data more relevant, which is encouraging if true. - Chris Rusbridge

I suppose it IS "supplementary MATERIALS". But I would hope there is something a little higher than "raw data files" to recommend? - Chris Rusbridge

I think Nature are doing some good work in this space but I don't know the details. The problem is that it has always been seen as the dumping ground for things "not important enough" rather than an opportunity to include more of the important stuff. But it all comes back to attitudes about data sharing. If people thought it was important they'd make the effort. The fact that they don't... more... - Cameron Neylon

There's a structural problem with expecting publishers to deal with usable supplementary (or even primary!) data: publishers enter the research process too late. By the time a publisher sees anything, the data may well have been ruined by a well-meaning researcher. While admitting my own bias -- I still think this is (for now, at least) an institutional problem. - D0r0th34

Even the institution possibly comes in a bit late really - we're back to needing to re-educate scientists again aren't we? - Cameron Neylon

yes, I think we are. so for the new breed, we can start when they're in school. the oldsters? not much left besides their library. if they'll listen to it. which many won't. - D0r0th34

This is, of course, a culture change >> than asking people to put their papers in IRs. So it won't get fixed any time soon. Doesn't mean don't start, however. And there are some beacons of data sharing out there. Now one of them needs to get a big prize & claim that data sharing helped! - Chris Rusbridge

I don't think there is a general solution here - the most convenient data formats vary between fields. As I've said many times for chemistry the JCAMP-DX format is vastly superior to the common way of submitting NMR spectra as PDFs in Supporting Info if the intent is transparency. There is no new technology to invent here - it requires the researcher to take a few seconds to do the... more... - Jean-Claude Bradley

@D0r0th34, not clear that the structural problem is avoidable. If well-meaning researchers are gonna destroy their data, the institution can't do anything about it! "Sheer curation" (just means managing your data well while you're creating & using it, I think) might help, but that's for the good guys anyway. If publishers (or reviewers) start saying no to articles where the data are mangled up in PDFs, then maybe we'd get somewhere? At least an incentive where none exists? - Chris Rusbridge

There is some rays of hope in the work going on for instrumental data standards like AniML. If instruments default to open standards we will get further much faster. Also currently writing a grant that attempts to link a "just save it all somewhere as blobs" approach to helping the user connect things up together to try and provide metadata. Doesn't solve the format problem of course but it could be a start. - Cameron Neylon

Cameron - my understanding is that AniML is not up to speed with storing and rendering NMR spectra using Open Standards and Open Source Software - do you have different info on that? - Jean-Claude Bradley

Chris, it depends on the reasons for the data destruction. If it's apathy, the answer is incentives, as has been noted. If it's just ignorance, though, the answer has to be education and collaboration -- and crucially, as early in the research process as possible. That to me screams "institutional involvement." - D0r0th34

No, I don't think AniML is up to NMR yet but what I have heard is that some instrument manufacturers are getting interested in open formats. Not necessarily NMR but big players in the instrument world who are sick of having to develop their own complete software suites to handle proprietary data formats. - Cameron Neylon

I think the AniML format has been discussed for many years. JCAMP already solves the Open Standard and Open Source issues and it does not require compliance on the part of instrument manufacturers - so far we've been able to find simple ways of converting NMR data from Varian and Brucker, IR, UV, MS, etc. - Jean-Claude Bradley

Neil Swainston

Bioinformatics has made me very angry. I must light a candle.

November 18 from Twitter - Comment - Like - Share

'Mummi' Thorisson, Duncan Hull, Allyson Lister and Ruchira S. Datta liked this

what's it got you angry about? :) - Allyson Lister

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Bit of a private joke, I guess. One of the Profs here throw a right hissy fit in a meeting yesterday, said words to the above effect and then promptly lit a scented candle in the middle of the meeting to calm her nerves. I don't think I'm eccentric enough to get on in academia. (The anger with bioinformatics is just my general day-to-day demeanour.) - Neil Swainston

That is - imaginative. Thanks for relating the story! :) - Allyson Lister

@Neil I'm lighting a candle for you down in Hinxton ;-) - Duncan Hull

how was it lit? via fire-breathing :) - Frank

Albert Vernon Smith

Keith R completely misses the point on ownership of genetic data and privacy w.r.t. deCODE. http://omicsomics.blogspot.com/2009... -(via @dgmacarthur)

November 18 from Twitter - Comment - Like - Share

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Allyson Lister

Annotation and merging of SBML models with semanticSBML - http://www.citeulike.org/user...

November 18 from CiteULike: allysonlister's... - Comment - Like - Share

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Bioinformatics (17 November 2009), btp642. Summary: SBML is the leading exchange format for mathematical models in Systems Biology. Semantic annotations connect model elements with external knowledge via unique database identifiers and ontology terms, enabling software to check and process models by their biochemical meaning. Such information is essential for model merging, one of the key steps toward the construction of large kinetic models. The tool semanticSBML helps users to check and edit MIRIAM annotations and SBO terms in SBML models. Using a large collection of biochemical names and database identifiers, it supports modellers in finding the right annotations and in merging existing models. Initially, an element matching is derived from the MIRIAM annotations and conflicting element attributes are categorised and highlighted. Conflicts can be resolved automatically or manually, allowing the user to control the merging process in detail. Availability: SemanticSBML is free... - Allyson Lister

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I'm, surprisingly, only mildly irked that Falko didn't reference either of the other software tools out there that suggest new SBML model annotation: Neil's libAnnotationSBML (http://dx.doi.org/10...), and my and Morgan's Saint (http://dx.doi.org/10...). (mini "grrr"). :) - Allyson Lister

@Allyson: yeah, some many years ago it was actually publishing practice to cite related work in the introduction... - Egon Willighagen

@Egon - agreed. It's what I try to do. I know Falko, and he's a nice guy, and this isn't going to change anything professionally or socially, it's just a little bit - irksome :) - Allyson Lister

Peer-review fails again. The software contained in the paper was not set in the context of the domain or in relation to alternatives. Ultimately the shame lies with the authors in the first place - Frank

Allyson, that's at least worth a letter to the editor, to me. It's a serious failure of basic scholarship not only on the author's part, but on the part of the reviewers, and the editors. It's not like you're making an obscure point, either. You're talking about stuff a basic literature review would have caught. - Mr. Gunn

The Life Scientists: Rob Hardwick

deCODE to file for bankruptcy http://scienceblogs.com/genetic...

November 17 - Comment - Like - Share

'Mummi' Thorisson and Nils Reinton liked this

Very sad. - Nils Reinton