For discussion of cyberinfrastructure, e-Science, eResearch, data curation, and similar questions. Librarians, IT folks, researchers, and scholars welcome!
"OSCAR3 (Open Source Chemistry Analysis Routines) is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries."
- Mike Chelen
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"17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology The talk specific feeds will be created each day shortly before the start of the first presentation. Find talk specific blogs by searching here for the authors, the title of the talk or the talk identifier as given in the program (like HL03 for the 3rd Highlight paper) The feeds can also be accessed on the conference pages in the according sections: SIGs, Keynotes, Proceedings Track, Technology Track and Highlights and the last few blogs are shown on our web-portal page."
- Mike Chelen
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There are quite a lot of cell phone sensor network projects out there - I've been following the Urban Sensing project at UCLA for a while... http://urban.cens.ucla.edu/
- Hilary
Wonder if there are discussions between the different groups, either for direct collaboration, or to plan for interoperability of software and data.
- Mike Chelen
I think Nokia is trying to address some of the interoperability questions through their SensorPlanet project: http://www.sensorplanet.org/
- Hilary
"InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. Parsers are provided for integrating data from several common biological formats and there is a framework for adding your own data. InterMine includes an attractive, user-friendly web interface that works 'out of the box' and can be easily customised for your specific needs."
- Mike Chelen
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"The dANN project is a library to help facilitate artificial neural networks within other applications. It is currently written in Java, C++, and C#. However only the java version is currently in active development."
- Mike Chelen
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"Should there be a universal standard, like RSS, that enables people to rate (and otherwise describe) websites — and to syndicate that data? If there were such a standard and such syndicated data, search engines could seed their results in creative ways using the data."
- Daniel Mietchen
The answer's in your question, I think: no, as RSS / Atom are already syndication standards. You can put hReview markup on web pages and in your feeds right now and a whole bunch of services will understand it (not least Yahoo! and Google).
- Euan
@Ruchira - in general yes, but less so in environments with consistent ID schemes based on real names, e.g. Researcher ID. @Euan - thanks for the hint at hReview, I was not aware of it.
- Daniel Mietchen
A similar idea is "Vote Links" at http://bit.ly/N5mnp : "We propose a set of three new values for the rev attribute of the <a> (hyperlink) tag in HTML. The new values are "vote-for" "vote-abstain" or "vote-against", which are mutually exclusive".
- Daniel Mietchen
"BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis."
- Mike Chelen
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"Cellular automaton consist of an infinite number of cells, which have a finite number of states. These states change depending on the state of their neighbours. Each cell has the same rule for updating. In this program, the cells can have two states: 0 or 1. This state depends on the state of their neighbours and the place where the cell is."
- Mike Chelen
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Thanks Mike, Im the author of the SINK, but is open and free like the same LIFE.
- Jorge G. Casanovas
Here is a copy loaded on GitHub, it makes collaboration very convenient using an Eclipse plugin. That's one of the good things about open source, and the .NET framework should be compatible with Linux by using Mono.
- Mike Chelen
Hi Abhishek, the sink is based in Conway's "Game of Life". There is more information in wikipedia. The difference is that in SINK there are patches of good quality environment, and is possible to change the number of this patches. I'm inspired in the classic paper of Van Horne "Density as a misleading indicator of habitat quality. J. Wildlife. Management". I program the first version of...
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- Jorge G. Casanovas
"This package provides a simple GUI, based on the GNU interface to Tcl/Tk, that is suitable for teaching introductory statistics."
- Mike Chelen
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to run, start R and then enter: library(Rcmdr)
- Mike Chelen
interface is pretty accessible for new users, even more so than RKWard
- Mike Chelen
"This study attempts to trace the evolution of scholarly communication from the days of publication of Journal-des-Scavans to the era of web 2.0, explaining the Open Access (OA) movement in brief. The views of Harnad on OA are highlighted. The emergence of Open Access 2.0 is put in context. This study also explains science 2.0 as the emerging practice in scientific knowledge sharing and scholarly communication. The positives and drawbacks of science 2.0 are discussed. Some of the science 2.0 concepts like OpenWetware, PLoS and other science 2.0 systems used in scientific research for communication as put forth by Hooker and Surridge are cited to indicate that science 2.0 is the future for scholarly communication."
- Daniel Mietchen
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"...3 Quarks Daily (www.3quarksdaily.com), where a group of bogglers write about science and culture..." Bwahahahaha! The mind blogs, I guess. Also, some of that stuff is pretty close to word-for-word lifted from Mitch's article.
- Bill Hooker
I like the fact of the article, but the writers didn't seem to plunge into the 2.0 world much in terms of tapping discussions that have already taken place on OA, sci comm, etc. Still, it's appropriate as an intro read for young scientists (or other audiences) looking to get a handle on the basics, so is deserving of a place on the bibliography of sci communication. The snarky applied...
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- Mickey Schafer
I don't think it really is an appropriate introduction -- it's poorly written where it isn't more-or-less plagiarised. I really wouldn't want that to be anyone's introduction to the idea of Open Science. I'd much rather point people to Mitch's SciAm article (http://www.scientificamerican.com/article...) and Michael Nielsen's essay (http://michaelnielsen.org/blog...).
- Bill Hooker
Bill, thanks for the SciAm link -- I've used Michael Neilson's essay, and it's my current fave, but can be a bit long for time-pressed undergrads -- I agree with the poorly written critique. Maybe I'm being too easy on my students:-).
- Mickey Schafer
Interesting to see where this discussion goes - it seems that we'd need something like Education 2.0 to explain what Science 2.0 is all about. I have thus started http://en.citizendium.org/wiki... (registration required, may take a day) and put up a freely editable semi-mirror at http://en.wikiversity.org/wiki... for those who prefer to edit right away.
- Daniel Mietchen