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Science Commons

Science Commons

A room for people interested in Science Commons and open science in general.
Mike Chelen
rt @kirtan A 36-year-old spacecraft just told us that it's left our solar system over a 23-watt transmitter from over 11 billion miles away. Science.
Mike Chelen
Science Commons
World Opera, Collaborative Science, and Getting On The One -
Shadows on the wall: "Truth never triumphs, but its opponents eventually die" -
Mike Chelen
"The Open Citations Project is global in scope, designed to change the face of scientific publishing. It aims to make bibliographic citation links as easy to use as Web links. Its goals are three-fold: To establish, a public RDF triplestore for biomedical literature citations. (Note: In this context, a bibliographic citation is a reference within a particular citing work to another publication termed the cited work. This use of the word ‘citation’ should be clearly distinguished from the common related use of this word to indicate the cited work itself. Within this application, ‘cite’ and ‘citation’ denote the performative act of citation itself, not the target document of that citation.) To harvest the reference lists from many current and recent open access journal articles, and to convert these datasets into RDF, starting with those in UK Pubmed Central, those published by the Public Library of Science and Biomed Central, those from other publishers willing for... more... - Mike Chelen from Bookmarklet
As the next step in our ever continuing mission to provide all the software needed to push online science forward in one place, we are proud to announce the launch of the Science 3.0 Etherpad! The etherpad can be found here: - The pad is open to members and non members alike. The reason we ask users to...
[Special bookmark] Open Access and Open Data links only And get ready: the very first Science 3.0 Blogging contest is on Open Access!
Chocolate… Miam! The cocoa genome in the public domain? Not really...
In a Letter to Science, Donald Siegel and Philippe Baveye discuss what they call « the paper glut » we face and address suggestions to improve the reviewing system.
Science Commons
Lisa Green
Tomorrow Prof Tania Bubela is giving a talk at the Creative Commons office! ""Building a Robust Research Commons: Institutional Impediments to Enhancing the Precompetitive Environment" You can watch live at noon pacific
If you were off to kiwi foo camp tomorrow, what issues around Open Data/ Open Science/Open Access /Open Education would you take with you? (or any other topics for that matter)
That there are still almost no tools (data entry/collection & management, database import) to support the various kinds of standards developed within various kinds of communities (especially the multi/cross-domain ones) to support data sharing as many funders and journals now require. Why oh why can there not be a coalescence of all the bits of effort in this direction around the world... more... - Chris from twhirl
+1 D0r0th34 - Bill Hooker
@Chris, that is brilliant. The kind of stuff I think will be great to stalk the FLOSS developers with! I came back from the Linux Conference Australia with a bunch of business cards as well, so it may be worth trying to brainstorm around that. - Kubke
I actually think its still a bit early to build such a thing - we need both the technology, UIs, and vocabularies to mature a bit more yet. ISA for instance is really no good for my specific research work, but that doesn't mean it can't be effectively applied in some areas. But I think we haven't yet got our heads around how to talk sensibly about real interchange standards in science.... more... - Cameron Neylon
@D0r0th34 and Bill Great points too, and one that which occupies my mind too often. Do you have any suggestions as to what *pitches* have been successful or failed in the past? - Kubke
@D0r0th34, thanks for the link. @Cameron, I think you raise a good point. Any idea where/how this could happen? (decide on a unified standard). Also, what do you think (from the UK point of view perhaps) are the social probles that prevent this kind of thing? - Kubke
Funnily enough I was in a meeting today about a project that was asking a question "can we generate a data model that covers these two specific projects". Not the whole world, not science, just two very specific projects, that are not even that different. Answer...maybe. Its tough and we're really just starting out and I think it needs a lot more careful thought yet. I saw something... more... - Cameron Neylon
For me the answer is that you can never have something unified that actually describes the science. What we might be able to achieve is a sufficiently generally framework that people can hang locally agreed vocabulary systems off it to enable some level of flexible interoperability. Need to do some writing on this to work it out in my head though! - Cameron Neylon
Hah, interesting, I don't know anything about the innards at all...something else to put on my reading list? - Cameron Neylon
Will take a look at that tutorial this pm (browsed through it and I think I know a few people that might be really interested in it, if they dont already know about it). - Kubke
Mmmm...interesting - quite different in technical details but coming from a similar place I think... - Cameron Neylon
Thank you all... great food for thougth... Will get back to this if I learn anything interesting - Kubke
I had a quick look at islandora but man do I need some more headspace to think these things through. No time! - Cameron Neylon
islandora certainly looks good. A start --> productive use story would help evaluate whether it's worth the effort! - Chris Rusbridge
I'd want to raise awareness amongst data consumers that passing credit back to data generators is vital to encouraging further sharing. Mechanisms are coming to do this (for example, & - Chris from twhirl
Carl Boettiger
I'm looking for a good solution to upload figures into my open lab notebook. Need fast, many photo, automated / scriptable uploading, permanent hosting, with searching/tags/comments. Trying photobucket: Thoughts?
I think ideally I would run a script which would run some code which generates a png figure, pushes the photo to the host site under a given album/tags and a link to the version of the code that created the figure on the project's github site. Since the codes take a long time to run, simply having the code version is no longer sufficient for me. - Carl Boettiger
Have you considered the possibility of using Flickr to host the photos? They have an API, are quite inexpensive and I know that there is/was a plugin to add Flickr images easily into OWW (mediawiki). - Ricardo Vidal
Yup, Flickr seems very promising since there's lots of development around it. Do I need to buy a subscription to make sure the uploads are permanent? Think I'll give it a try... - Carl Boettiger
No, all uploads are permanent and I believe you can "display" up to 200 images for free. The last 200 are always visible and nothing is lost. If you pay the $24 USD/year, all images become public/visible again. - Ricardo Vidal
Flickr seems to be a nice solution. With one command-line call I can have a full slideshow of results embedded into the notebook! Each image can collect comments and other tags and be organized into groups. the command-line upload also doesn't seem to spam my FF/twitter feed even though I added flickr to FF. guess that's a good thing. - Carl Boettiger
Science Commons
University Public Access Policy Whitepaper Part 2 -
Ali Numan
Science Commons
Mike Chelen
"CONNECTION DETAILS: * IRC: #okfn on (easy connect via ) * Skype: Send your Skype username to Greg (greg.grossmeier) * Phone (backup option - only if there are more than 8 or so participants): * Dial: +44 (0) 844 84 84 84 0 (UK) or +44 (0) 844 873 60 60 * Code: 366697" - Mike Chelen from Bookmarklet
Panton Discussions - podcast / interviews about PP - Mike Chelen
Other speakers outside publishing? - Mike Chelen
Maybe health data - Mike Chelen
Start with people in Cambridge - Mike Chelen
Email science list to contact if in town - Mike Chelen
Host on and post on PP site - Mike Chelen
PP logo is good, Greg working on SVG version - Mike Chelen
Multiple sizes to pick from - Mike Chelen
PP logo to show support, Open Data to show compliance - Mike Chelen
Several PP translations finished, put on separate pages - Mike Chelen
When published, ask for more to be done - Mike Chelen
How to find more people who would be interested in PP - Mike Chelen
Highlight inst. supporters on site - Mike Chelen
Produce poster / 1 page for noticeboards - Mike Chelen
Powerpoint / slideshare presentation - Mike Chelen
Panton Papers: short outlines of critical issues - Mike Chelen
Focus on open data - Mike Chelen
Meeting or session - Mike Chelen
Several authors to help with each subject - Mike Chelen
Open science pledge, an overview to collect resources & standards - Mike Chelen
CKAN and DataPkg - Mike Chelen
Registration and download of open data sets - Mike Chelen
Training session for CKAN and science data - Mike Chelen
Package maintainer drive - Mike Chelen
Upcoming OKF conference needs organizers for open science section - Mike Chelen
Mike Chelen
Fwd: For those you you who can't make the Open Science Summit this w/e RT @soulcatalyst
Carl Boettiger
Anyone know good sources of data/graphs to highlight information explosion in science (partic. bioinformatics) # of published papers, scientific software on cran/sourceforge/github, entries in genbank, etc, over time?
Nucleic Acid Research - Database issue 2010 - joergkurtwegner
Paragraph 2 here ( might be some use. - Bill Hooker
science in an exponential world - joergkurtwegner
Finally, naming scientific information overload is easy, preventing a scientific filter failure is more difficult - joergkurtwegner
@jkw, I don't know how I missed it -- perhaps you are only in my RSS feeds since after Jan 2009 -- but that is a very nice blog post! - Bill Hooker
you can ask data from sourceforge here: - Pierre Lindenbaum
PPI networks in DIP and Metabolic pathways in KEGG over the last decade : - Khader Shameer
Yearly growth of protein structures in PDB : - Khader Shameer
What about figures 1 and 2 in ? Also (similar to what Joe pointed out in the first comment). - Daniel Mietchen
See growth of biological databases via - joergkurtwegner
Science Commons
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