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Pierre added an event on Upcoming

Nov 28, 2008: International Workshop on Semantic Web Applications and Tools for Life Sciences at e-Science Institute NESC

16 hours ago - Link

Egon Willighagen, Richard Akerman and Duncan Hull liked this

@Pierre, you going to SWAT4LS? - Duncan Hull

no :-( sometimes I just found it's a too bad that such workshops are not registered on upcoming.com. Semantic Web is just a leisure for me and I would attend this meeting if it was closer to me. - Pierre

Jan Aerts posted a message on Twitter

“Has there been progress on an open alternative to ResearcherID?”

Monday at 4:12 am - Link

Timothy Driscoll, Richard Akerman, Egon Willighagen and Pierre liked this

RDF? Seriously... using BIBO or so, every author is identified by a unique ID... it's not only an open alternative, distributed too! - Egon Willighagen

2 more comments

The problem would be to give a unique ID to any author... - Pierre

If there is anything that's easy to use and understand (including by non-tech-savvy scientists): what can we do to get that train rolling? What actions can we take? - Jan Aerts

@Jan ask the NCBI to give a unique ID to the authors in pubmed (dream... dream...), create a FOAF/BIBO central server where you could register your foaf profile, create tool building foaf profiles (I already started something like this here http://plindenbaum.blogspot.co... ), .... - Pierre

My gut is telling me that having this distributed is going to be very important, based on the way ISI(and tangentially Fair Isaac, for Americans) can jerk people around. How dangerous would it be to have something essential and worldwide managed by a central authority, no matter how (currently) benevolent? - Mr. Gunn

Pierre posted a message on Twitter

“transformed EndNode/xml to Zotero/Ris for a Friend.”

Friday at 8:27 am - Link

Pedro Beltrao, Cameron Neylon, Egon Willighagen and Neil Saunders liked this

Paulo Nuin posted an entry on Blind.Scientist

Why Open Science/Research won’t work (at least for now), first part of a long series

November 13 at 11:14 am - Link

Bill Hooker, Richard Akerman, Egon Willighagen and 5 other people liked this

good point - Pedro Beltrao

The point about a lack of good highly ranked web presence(s) is a really good one. Talked about it a lot but never actually got something off the ground. - Cameron Neylon

Left my comment in the blog. - Egon Willighagen

Jonathan Eisen favorited a video on YouTube

the muppet show - the best of swedish chef

November 13 at 7:17 pm - Link

Mr. Gunn, Pierre, Daniel Swan and 2 other people liked this

Der chocolate moose is my favorite! Well, maybe "Der chickie in der basket" is. - Mr. Gunn

Neil Saunders posted a message on Twitter

“us linux-only types are tired of hearing about chrome; now we have listen to gmail video chat too...”

November 14 at 12:03 am - Link

jerobins, i80and, Pierre and 4 other people liked this

gmail video chat doesn't work on Linux? I'm so unthusiastic about it that I didn't bothered to try... - ☂Marcos Marado

OK, it's just going to http://mail.google.com/videoch... and we get the finger there. Way to go Google, one more step to break the web. - ☂Marcos Marado

Chemistry Development Kit: an entry from cdk

Changed from java.awt.genom.Point2D to javax.vecmath.Point2d

November 13 at 4:48 am - Link

Egon Willighagen liked this

Benjamin Good posted an entry on Connotea: bgood's bookmarks

myExperiment SPARQL Endpoint

November 12 at 2:09 pm - Link

Duncan Hull, Deepak, Pierre and Egon Willighagen liked this

Nice! - Egon Willighagen

Works fine ! (Learned SPARQL Yesterday :-) ) PREFIX myexp: <http://rdf.myexperiment.org/on...> PREFIX dc: <http://purl.org/dc/elements/1....> select ?x ?title { ?x a myexp:Workflow . ?x dc:title ?title } - Pierre

Noel O'Boyle shared an item on Google Reader

I571- Userscripts for the Life Sciences (IU Chemical Informatics Journal Club)

November 12 at 9:58 am - Link

Egon Willighagen liked this

A fantastic paper. I'm sure Rajarshi and Egon will agree. - Noel O'Boyle

:) - Rajarshi Guha

Bioclipse: an entry from Delicious/tag/bioclipse gist

gist: 23900 — GitHub

November 11 at 11:28 pm - Link

Egon Willighagen liked this

Molecule DB support in Bioclipse. - Egon Willighagen

Björn Brembs posted a link

JoVE: Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling (Video Protocol)

November 12 at 6:28 am - via Bookmarklet - Link

Graham Steel, Jean-Claude Bradley, Ricardo Vidal and 3 other people liked this

"Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling" First author: Jean-Claude Bradley. Cool! - Björn Brembs via Bookmarklet

Thanks Bjorn! This is our first peer-reviewed paper with links to lab notebook - Jean-Claude Bradley

Pierre posted a message on Twitter

“Need to re-write a clean RDF document of the ONS solubility data to test with SPARQL”

November 11 at 6:09 am - Link

Jean-Claude Bradley, Egon Willighagen and Cameron Neylon liked this

Noel O'Boyle shared an item on Google Reader

Open source != peer review

November 11 at 6:06 am - Link

Egon Willighagen and Rajarshi Guha liked this

Left my comment... from the Andrew's essay I'd say the CHARMm license is pretty OpenSource... at least it allows partial redistribution of the code. - Egon Willighagen

Lars Juhl Jensen shared an item on Google Reader

4th German Conference on Chemoinformatics: ChEMBL

November 10 at 5:42 pm - Link

Rajarshi Guha, joergkurtwegner, Egon Willighagen and Duncan Hull liked this

Ha, coverage of the GCC! Thanx Lars! - Egon Willighagen

"Thanks Michael" would be more accurate - all I did was to press "share" in Google Reader ;) - Lars Juhl Jensen

Thanx Michael! - Egon Willighagen

Deepak bookmarked a page on delicious

chem-bla-ics: Finding the commit that causes the regressions...

November 10 at 11:42 pm - Link

Egon Willighagen liked this

Cameron Neylon posted an entry on Science in the open

More on “theft” and the problem of identity

November 10 at 2:21 pm - Link

joergkurtwegner, Michael J. Cohen (mjc), Mr. Gunn and 8 other people liked this

Each post in this "series" makes me cringe even more. - Paulo Nuin

35 more comments

Just a question Cameron, do you have tenure (or whatever-they-call-it-in-UK)? - Paulo Nuin

I'm happy to be argued with. I'm interested in where the argument breaks down. Two obvious arguments. I have a salary so I can play a long game with this. I don't need to put food on the table tomorrow, so I don't need an immediate monetary return. For people who do the choice has to be to protect the ability to make a return on each item. Second one: many of these are not purely digital objects, they have a real world connection, that does make copying damaging. - Cameron Neylon

Paulo - I have a permanent position yes. I appreciate that makes it mcuh much easier for me. - Cameron Neylon

You haven't answered my question. - Paulo Nuin

Well there's not really such a thing as tenure in the US sense in the UK. You go into an academic position and get past probation to get a permanent position. But probation doesn't take as long as a US tenure track and the few people fail to get confirmed as permanent. So I have done that. But I now have a permanent position at a government research lab, which is not really an academic position at all in the sense of a US university department but more like a job at e.g. ORNL or NIST - Cameron Neylon

So if you mean do I have reasonable job security then the answer is yes, and if you mean, have I been through the fire of a US-style tenure process then really the answer is no, some similarities but not the same sudden death experience that it seems to be in the US - Cameron Neylon

Thanks for you answer, a yes or no would suffice. But the fact that you have job security tells a lot of what you support, why you support it and the naivety of some of your ideas. People that have a protection bubble around them, tend to have the same discourse that you have. It's like listening (reading) to what a public servant says in comparison to a person that works in the private sector. - Paulo Nuin

I think this is the first time I've ever agreed with David Crotty. :-) - Bill Hooker

I think Cameron is making a good point. Sure, principled arguments often seem naive because we live in a grey world, not a black and white one, but if I understand correctly, he's just cautioning against advocating "extreme openness" and then being quick to apply a different standard when openness comes back to bite you. - Shirley Wu

Not to bring up the election again, but there are many examples of this - republicans demanding less government regulation, and then when the economy self-destructs (impacting them negatively) they blame the government for not regulating enough. Prop 8 too, maybe, in a different way - either we subscribe to "equal rights for all" under the constitution or we marginalize certain groups because some people claim it takes value away from marriage - Shirley Wu

I commented as well. I also agree with Crotty :). To cut a long story short, openness cannot exist in a vacuum. You always need some guidelines. The very existence of CC and people using CC licenses, for example, is a finger in the eye of existing big media, just as the GPL and the Apache license is a finger in the eye of close source software. There is the public data commons, and again, it's a matter of choice. If we want to change the system, we need to stay within some boundaries. - Deepak

i almost always agree with david. Usually a question of degree rather than absolutes - Cameron Neylon via fftogo

So basically Cameron you still agree with the statement you wrote with no caffeine? Or you just bringing the discussion to a place that you guess you have control over? That's what it seems. - Paulo Nuin

Not entirely. Specifically I withdraw the use of the term hypocritical. What I still maintain is that it is not helpful <emp>for those people who beleive in and advocate encouraging re-use of digital material</emp> to use language of property rights when what they are complaining about is a lack of attribution. I also still maintain that <emp>if you believe and advocate encouraging the re-use of digital material</emp> then you can't then pick and choose as to what types of re-use you think are acceptable. - Cameron Neylon

Cameron, we'll have to agree to disagree on that one. I think in a culture where re-use was part and parcel of the process, you won't have these problems. It's why those of us who release under CC always re-use appropriately as well. It's a mindset - Deepak

Actually - Shirley put it better than I did. - Cameron Neylon

Deepak, I think I am trying to say exactly the same thing as you are. I do my best to respect copyright, licences, and any other requests the authors make. I am absolutely not advocating a free for all - but social and technical systems that encourage respect and attribution, rather than rules based systems. - Cameron Neylon

Actually I think I've crossed the wires here - what I meant by 'what types of re-use above' was that you can't choose between 'nice' people and 'bad' people re-using your stuff. I won't argue that people shouldn't be allowed to use CC-BY-NC or copyrights. I will argue that I think they are counterproductive but they have every right to use them and expect them to be respected. - Cameron Neylon

I agree your comment immediately above is a concern for some people,, Cameron. Without taking a personal view either way, at Nature we have for a year or so "imposed" creative commons licences on our genomics publications, by negotiation with the various community representatives and conferences etc. It always takes a while for these things to filter through, and this is no exception. We, the journal office, inform authors of this licence when their papers are accepted - and quite a few of them have expressed concerns to us about "bad" re-use as you put it, as opposed to "good". I think these authors are people who havenot particularly thought about it before (in common with almost all of the scientific community), and I hasten to add that nobody has objected to the CC licence - I just think it is a natural concern if it isn't a topic you've thought about much if at all before. - Maxine

I think that you (Cameron) are making a point similar to the one made by Michael Heller in The Gridlock Economy. Heller points out that it is easier to talk about (and point to examples of) the tragedy of the commons (e.g. abuse and overuse of the common resources) than about what he calls the "tragedy of the anticommons" (TAC). TAC can result when there are too many restrictive property rights governing use of a resource and the problems arising from underuse are more difficult to spot. His book is, in part, an attempt to demonstrate that more property rights are not always the answer to abuse of the commons, and also to create a new language for talking about this problem. - Hilary

Yes, when I was trying to come up with examples (both pro and anti my argument) many of them turn into tragedy of commons versus tragedy of the anticommons, and fundamentally that the application of property rights _does_ make some people richer, but that it reduces the overall value. For the argument to work, the pie needs to grow enough overall that most people do a bit better. And there will be (possibly many) cases where that doesn't work in practice. Really must read the Heller book. - Cameron Neylon

This isn't the kind of argument that you can entirely destroy by taking to its logical extreme. Of course things need some bounds around them, because as Shirley reminds us, we live in a grey world. Unfortunately, it's easier to think in black and white, especially where laws and regulations are involved. I agree that the problems resulting from underuse are harder to see than overuse, simply by nature, but I would also argue that the overuse problems tend to be more trivial. - Mr. Gunn

One other minor point - I think trademark appropriation is different than other types of IP infringement as it undermines the trust between the two parties (this was David Crotty's point). TMs are intended to identify the source of a good, and I think there is less of a case to be made here for encouraging open reuse of your trademarks. (Although resuse of Ricardo's image was technically copyright infringement) - Hilary

In other words, I have no sympathy for the people on Flickr that get pissed when someone uses one of their pictures on their site. Copy an original design and make it the logo for your company, now, that's being a douchebag, but if you're posting pictures to a photo sharing site, it's fair game to repost that picture, with attribution of course. - Mr. Gunn

Hilary ... great points, esp the Heller reference. I think if Ricardo's imagine had been used say as a graphic on a blog post, the discomfort would be much less visible. That it's being used to sell a commercial service, especially a dodgy one, speaks to this grey area that we talk about. - Deepak

Deepak, that is right. I've had folks ask me to use the logo for various other things and I've rarely said no. Someone even used it on the cover of their phd thesis. I have no problem with that. It's the simple hijacking and no-questions-asked that I don't like much :-) - Ricardo Vidal

I agree with Hillary's distinction. David made a trademark/identity-focused comment to Camerons mostly copyright focused post. Cameron then made a very nice post about the trademark/identity perspective. So I am unsure what agreeing with David means. Does it mean that the identity perspective is the interesting view of this discussion? Or that it is not important to distinguish between the properties and features of how current law works? Or that community norms will not work, no matter the domain? Or? - Anders Norgaard

After some more thought: I find the post confusing in that it starts with what seems like a discussion of trademark infringement ("The name is just a pointer", "misrepresentation") and then shifts to a discussion about plagiarism and attribution. What he (Cameron) seems to be asking is that if one promotes liberal licensing of one type of IP, ought one to support the same principle for all types of IP? In supporting liberal licensing for copyright, do you think one ought to necessarily support liberal licensing of patents? Or should we not be using the language of IP to talk about this issue at all? - Hilary

I was definitely talking about copyright, just to be clear :) - Deepak

And a related question: can the tragedy of the anticommons (if we want to call it that) occur for all types of IP? Heller makes a case for biotechnology patents, and I think there is a case to be made for copyright, but is there a case for trademarks? - Hilary

The point I think I was trying to make was that what is bad about this trademark infringement is that it is essentially either misattribution or lack of attribution. The infringer is both failing to acknowledge your work (the trademark) and also effectively attaching your name to work that is not yours. So that the bad thing here is the failure to attribute correctly because it breaks down trust between the trademark holder and its customers. Essentially my argument is that the thing which reduces value in these cases, and is therefore objectively bad, rather than just breaking the rules, is not the process of copying but the incorrect attribution. - Cameron Neylon

Unfortunately I haven't read "The Gridlock Economy" - so I will try to watch this talk http://www.youtube.com/watch?v... and see I can have an opinion from that. - Anders Norgaard

My view would be that the same arguments should hold for copyright as for patents, but I'm interested in whether that breaks down. I am appreciating the strength of the argument that it may not hold for trademarks - but the question then becomes what is the best response to dealing with that? And is intention important? - Cameron Neylon

One unified perspective that I have of IP law is that copyright and patent law is made for regulating businesses. And the reason that so much of IP law gets negative attention is that the world has changed so much that normal behavior (copying, sharing, reusing) now falls under what some of these laws regulate. Therefore I also think that Camerons perspective on community norms is very interesting. - Anders Norgaard

Anders, would you feel that we can use norms within our community but we need law for regulating our interaction with business (or other communities with perhaps different norms)? - Cameron Neylon

Good question. I am not sure. I think that community norms are not strong enough to deal with companies. But I think they may be good for communities. I will keep an eye out for examples. - Anders Norgaard

Tragegy of of the Anticommons has a Wikipedia page (http://en.wikipedia.org/wiki/T...) - Deepak

Pierre bookmarked a page on delicious

HugeURL

November 10 at 12:37 pm - Link

Richard Akerman, Egon Willighagen and Daniel Swan liked this

reverse tinyurl :-) - Pierre

Allyson Lister posted an entry on Systems Biology & Bioinformatics

Two Journal Special Issues: Big Data, and Semantic Mashups for Bioinformatics

October 7 at 5:55 am - Link

Rajarshi Guha, Egon Willighagen and Deepak liked this

Deepak bookmarked a page on delicious

EMBRACE Registry

November 10 at 9:04 am - Link

Egon Willighagen liked this

The EMBRACE Service Registry is a collection of life-science web services with built-in service testing. - Deepak

Noel O'Boyle shared an item on Google Reader

Journal of Cheminformatics - a new open access journal from BioMed Central

November 10 at 7:56 am - Link

Egon Willighagen and Rajarshi Guha liked this

Jocinf open for business... - Noel O'Boyle

Paulo Nuin favorited a video on YouTube

One in a million chance

November 9 at 6:52 am - Link

Anita Brojnas, joergkurtwegner, Chris Lasher and 2 other people liked this

Hahaha! My goodness, chance can bring some delightful, beautiful moments. Nice find. - Chris Lasher

Tire folding ;-) - joergkurtwegner

Science Online: Maxine posted a link

“Announcement for the first speaker of our new GBCB guest lecture series. (I think some of you might recognize this guy.)”

November 9 at 6:32 am - via Reshare - Link

Richard Akerman, Egon Willighagen and Jill O'Neill liked this

Pierre bookmarked a page on delicious

IO Data

November 9 at 8:04 am - Link

Egon Willighagen liked this

Pierre, just let me know if you have questions... or want to set up something locally! - Egon Willighagen

Thank you Egon. I might soon have to implement a web service. I'm not an expert in this field so WSDL was my only option. But since your post, I might consider some new choices. - Pierre

Chemistry Development Kit: an entry from cdk

Revised: 'Hueckel' to 'Hückle' as Egon suggested.

November 9 at 7:33 am - Link

Egon Willighagen liked this

Pierre posted an entry on Connotea: lindenb's bookmarks

Sindice - The semantic web index

November 9 at 12:56 am - Link

Egon Willighagen, Richard Akerman, Garret McMahon and Deepak liked this

Thanks Pierre, was wondering what the DERI chaps were up to of late. - Garret McMahon

from Chris Lascher's bookmarks on delicious - Pierre

Noel O'Boyle shared an item on Google Reader

Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language

November 8 at 5:32 am - Link

Egon Willighagen liked this

Pedro Beltrao shared an item on Google Reader

Open{Data|Source|Standards} is not enough: we need Open Projects

November 7 at 9:27 pm - Link

Egon Willighagen, Cameron Neylon, Colin Ashe and Deepak liked this

Duncan Hull bookmarked a page on delicious

myGrid » Taverna 2

November 7 at 10:00 am - Link

Simon Cockell, Deepak, Pierre and Egon Willighagen liked this

Taverna 2 beta 1 is now available for download. Please read the release notes for details of its new functionality. Taverna 2 is a redesign of the Taverna Workbench from the ground up. It has a greater emphasis on scalability to enable the manipulation of larger and more diverse data. The new enactor is more robust with a range of new design features and improvements, including a reduced memory footprint and new data streaming functionality to greatly improve speed and efficiency. In addition to the improvements to the enactor, Taverna 2 beta 1 provides more support for workflow design with a new graphical workflow editor for direct manipulation of the workflow diagram, context-specific views over Web Services and other resources (activities), and a configurable service discovery panel. This release is a Beta, so there are still some bugs and known issues to resolve, but we would very much like your feedback and opinions before the full release, which is scheduled for December 2008. - Duncan Hull

... but watch out for the "issues" http://www.mygrid.org.uk/tools... they might just bite you in the ass - Duncan Hull

Simon Cockell shared an item on Google Reader

How Do I Get Open Source Programs Written For Me?

November 7 at 9:10 am - Link

Egon Willighagen and Pierre liked this

Like the comments on ./ say: beer and a pizza normally does the job :) - Egon Willighagen

Duncan Hull posted an entry on CiteULike: dullhunk's library [1713 articles]

OWL 2: The next step for OWL

November 7 at 4:59 am - Link

Pierre and Egon Willighagen liked this

XML syntax.... Yay. Wave goodbye to RDF (sorta)! - Duncan Hull

4 more comments

Only scanned the paper... looks interesting... but do they actually propose OWL2 as XML only? - Egon Willighagen

...still compatible with RDF for backwards compatibility, but the option of using XML is now there, which opens up a new toolset (XPath, XQuery, XSLT etc) - Duncan Hull

Duncan, I don't get it... OWL1 has the option of using XML too, not?? - Egon Willighagen

@Egon, I (still) didn't read the paper, but I know you cannot safely use xslt with rdf because there is too many ways of depicting a set of triples. - Pierre

Not quite, because most OWL 1 ontologies used RDF for its syntax, which causes problems (see paper). You can't reliably use XML tools with OWL 1. OWL 2 uses XML for its syntax, which means you can now. - Duncan Hull

Oh... never was aware of that. I only used XML-based OWL... even more reasons to read this paper :) - Egon Willighagen