OpenSci Info

"Scientific Publications cover a wide variety of publishers, hosts, business models, usage models, publication stages, logical and technical presentation. Therefore it is important to learn which portions of the publication space can be and which agents want to be included in the sampling. For those willing to participate only two aspects are relevant: 1. What data needs to be gathered? 2. How can it be transferred to the statistics provider? Open-Access-Statistics (OA-S) is a joint project adressing these questions. Starting in July 2008 an infrastructure for the standardised accumulation of heterogenous web log data with an emphasis on institutional repositories will be built. In tight cooperation with the Network of Open Access Repositories (OA-N) various added value services will be made available to users." - Mike Chelen from Bookmarklet

"download all files on the biotorrents rss (see http://www.biotorrents.net/links...) - on server using only command line interface server os: debian etch 4.0 and lenny 5.0 bittorrent programs: rtorrent http://libtorrent.rakshasa.no/wiki http://packages.debian.org/search... deluge http://packages.debian.org/search... rss programs: rssdler http://code.google.com/p... podget http://packages.debian.org/search... rss sources: http://www.biotorrents.net/rss... http://www.biotorrents.net/rssdd... http://www.biotorrents.net/rss_per..." - Mike Chelen from Bookmarklet

rssdler works nicely, podget might be easier to install though since there are packages for distros like debian - Mike Chelen

it looks like semantic mediawiki? - Mike Chelen

Yes, it's copy and paste at present. A better workflow would be a good enhancement to Semantic MediaWiki if anybody's looking for a project! - Jodi Schneider

Biomed Central's policy on publishing open science defined: "Articles may be submitted to BioMed Central’s journals when data have been previously discussed or posted in such venues as blogs, wikis, social networking websites or lab electronic online notebooks. However, given the rapidly evolving nature of these resources, where discussion of data or manuscripts posted to these venues has subsequently been incorporated into the manuscript, the BioMed Central journal Editors may make their own assessment as to whether there may be duplication in the submitted manuscript." It's excellent that we are gaining some clarity here. To my mind the idea of open science is precisely to have "discussion of data or manuscripts posted to these venues" being subsequently "incorporated into the manuscript". In these cases the Biomed Central manuscript editor decides. We really need some test cases, and we need explicit policies from other publishers. - Matthew Todd from Bookmarklet

Good example Daniel - if we are looking more broadly than BMC I think most fully OA publications would accept pre-prints. I also suspect hybrids would not - for example AuthorChoice at ACS - but I don't know for sure. - Jean-Claude Bradley

"used as source for Amazon EC2 EBS snapshot: snap-7044d219" - Mike Chelen from Bookmarklet

convenient way to query some NCBI services, allowing some server-side processing with results available in XML or JSON - Mike Chelen

"Links any Document Object Identifiers for resolution with http://dx.doi.org" - Mike Chelen from Bookmarklet

One special case worth looking for is "COiNS" OpenURL. Our (jQuery) code is var z = jQuery(".Z3988:eq(0)"); if (z.length) { var r = z.attr("title").split("&"); for (var i=0; i<r.length; i++) { var x = decodeURIComponent(r[i]); if (/^rft_id=info:doi\/.*?(10\.\d\d\d\d\/.*)/.exec(x)) { var doi = RegExp.$1; doSomething(doi); return; } } } - Fergus Gallagher

"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 from Bookmarklet

access PLoS article level metrics by DOI for use in Javascript and more - Mike Chelen

I'd really like to see that refactored as a collaborative Google Wave gadget. - Dan Hagon

@Neil: WikiPathways is intended exactly for that type of collaborative pathway creation. WikiPathways pathway format is based on, and developed in cooperation with, http://www.genmapp.org. So admittedly it's not a widely supported standard, but at least it wasn't a complete new invention. SBML / SBGN support is on its way. Re Google Wave: unfortunately, all this work predated Google Wave by several years... - Martijn van Iersel

"Discussion of issues relating to the use of Debian for science research, including useful packages, particular problems faced by scientists using Debian, how to make Debian more useful to scientists, etc." - Mike Chelen from Bookmarklet

there are a number of useful software packages that have been integrated already, and debian makes a great foundation for science projects since it can run well on servers and desktops. it is also used as the basis for other popular derivatives like ubuntu - Mike Chelen

here are some of the packages currently available: http://blends.alioth.debian.org/science... - Mike Chelen

"The Global Earth Observation System of Systems (GEOSS) 10-Year Implementation Plan explicitly acknowledges the importance of data sharing in achieving the GEOSS vision and anticipated societal benefits. The Plan, endorsed by nearly 60 governments and the European Commission at the Third Earth Observation Summit in Brussels in 2004, highlights the following GEOSS Data Sharing Principles: 1. There will be full and open exchange of data, metadata, and products shared within GEOSS, recognizing relevant international instruments and national policies and legislation. 2. All shared data, metadata, and products will be made available with minimum time delay and at minimum cost. 3. All shared data, metadata, and products being free of charge or no more than cost of reproduction will be encouraged for research and education." - Mike Chelen from Bookmarklet

good to see a specific focus on "open exchange of data" and it will be interesting to hear the plans to achieve this - Mike Chelen

"The student Right to Research Coalition, a group of national, international, and local student associations that advocate for governments, universities, and researchers to adopt Open Access practices, has now grown to include some of the most prominent student organizations from the United States and across the world. The recent addition of 8 new organizations brings the number of students represented by the coalition to over 5 million, demonstrating the broad, passionate support Open Access enjoys from the student community." - Mike Chelen from Bookmarklet

helps to appreciate the global reach and scale of these scientific concepts - Mike Chelen

wonder which existing published statements from CC science commons and other groups might discuss some of the topics raised? - Mike Chelen

"Dear all, last year, Michael opened a discussion to have bibliographic information displayed in package summaries: http://lists.debian.org/msgid-s... In the discussion that followed, we talked about where to store this information, and in which format, since adding more content to the debian/control file is not an easy thing (it ‘costs’ a lot because it goes to pivotal files like the Packages.gz files on our mirrors). A four line summary is available here: http://wiki.debian.org/DebianS... This year, some progresses are being made. For the display, Andreas has modified the ‘Web sentinels’ so that they can display bibliographic informations. See http://debian-med.alioth.debian.org/tasks... for instance. But currently the limitation of the system is that the bibliographic information is in a quite remote location, in the Blends ‘tasks’ files. I am currently working on a new workflow which would help the... more... - Mike Chelen from Bookmarklet

"Any object in Amazon S3 that can be read anonymously can also be downloaded via BitTorrent. Simply add a "?torrent" query string parameter at the end of the REST GET request for the object." - Mike Chelen

This is a great feature of S3. Perl gurus might also want to see: http://search.cpan.org/~qantin... or http://code.google.com/p... - Todd Harris

see which journals received each type of citation (scopus, crossref, and pubmed) and compare among the most recent years - Mike Chelen

Shows that PLoS One has an overall equal rate of citation to PLoS Biology, and that more of One's articles have been published in a recent year. - Mike Chelen

Peter & Cameron: ah yes, there is history data is in the other sheets, hadn't even started looking past the first one =) - Mike Chelen

"fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently only available as command line driven program. A GUI is in development. fpocket includes two other programs (dpocket & tpocket) that allow you to extract pocket descriptors and test own scoring functions respectively. As the algorithm is very fast it can be used on a large scale level (PDB size for instance)." - Mike Chelen from Bookmarklet

"Speaker: Stefan van der Walt" - Mike Chelen from Bookmarklet

"One of the major developments in the human rights field over the past decade has been the increased application of new technologies, such as satellite imaging, database and data analysis tools, medical forensics, mobile phones, and social networking software to situations in which human rights are under threat. The convergence of scientific innovation and human rights advocacy may well represent a major breakthrough in the struggle for human dignity. Full realization of that promise will require far greater collaboration between government, business, the scientific community, and human rights NGOs than we have seen to this point. Our panel will describe ways in which new technologies are revolutionizing human rights work and make recommendations for how the U. S. government can play a leadership role in promoting the nexus between technology and human rights." - Mike Chelen from Bookmarklet

panelists include members of PHR and AAAS - Mike Chelen