OpenSci Info

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

currently works with plaintext DOIs like http://www.plosone.org/article... and with DOI class spans like http://www.nature.com/nature... - Mike Chelen

RegExp missing some chars, e.g., % if URL-encoded. We tend to use 10\.(?:\d{4})/(?:[^ "'<&]+) but that can break too - it's annoying that the DOI spec doesn't limit the chars allowed! This is for searching the whole text (incl. within href), not element-wise so might not suit your code exactly. - 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

from biotorrents, there should be several fast seeds: http://www.biotorrents.net/details... - 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

CCK node types available at http://github.com/mchelen... and CSV format data at http://github.com/mchelen... . - Mike Chelen from Bookmarklet

Mike - in the next couple of weeks we will add all the 'missing' usage data (pre-July 05 and 1st 200 PLoS ONE articles). I will ping you when we have it in an excel sheet. - Peter Binfield

"SL is a Linux release put together by Fermilab, CERN, and various other labs and universities around the world. Its primary purpose is to reduce duplicated effort of the labs, and to have a common install base for the various experimenters. The base SL distribution is basically Enterprise Linux, recompiled from source. Our main goal for the base distribution is to have everything compatible with Enterprise, with only a few minor additions or changes. An example of of items that were added are Pine, and OpenAFS. Our secondary goal is to allow easy customization for a site, without disturbing the Scientific Linux base. The various labs are able to add their own modifications to their own site areas. By the magic of scripts, and the anaconda installer, each site is to be able to create their own distributions with minimal effort. Or, if a users wishes, they can simply install the base SL release." - OpenSci Info from Bookmarklet

"A dedicated bioinformatics workstation - install it or run it live. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base." - Mike Chelen from Bookmarklet

Deepak: that's good, been trying to find a way to get the bio-linux packages installed on 64bit instance. desktop could be handy for learning and testing - Mike Chelen

it looks like semantic mediawiki? - Mike Chelen

We didnt work with them on this (other than to have some early meetings). I suspect they just copied and pasted... However, it can be extracted from our XML file of course. - Peter Binfield

"This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 20, 2008. An introduction to Open Notebook Science is presented followed by an illustration of how ONS can be used in drug discovery. New data relating to the anti-malarial activity of Ugi products on 2 falcipain-2 docking sites is detailed. The docking calculations were provided by Rajarshi Guha and the enzyme and in vitro assays on Plasmodium falciparum were provided by Phil Rosenthal and Jiri Gut. Most of the syntheses were carried out by Khalid Mirza in the Bradley group." - Mike Chelen from Bookmarklet