OpenSci Info

"matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (ala matlab or mathematica), web application servers, and six graphical user interface toolkits. matplotlib tries to make easy things easy and hard things possible. You can generate plots, histograms, power spectra, bar charts, errorcharts, scatterplots, etc, with just a few lines of code. For a sampling, see the screenshots, thumbnail gallery, and examples directory" - Mike Chelen from Bookmarklet

thanks to this post for mentioning the library: http://biostumblematic.wordpress.com/2009... - Mike Chelen

I've found matplotlib to be one of the more mature plotting libraries out there. It's also a great reason to use tools like f2py to bring data into Python. - Christopher Granade

"I’ve gone back to using another wonderful visualization package, PyMol. I find that it hits the sweet spot between easy setup of the scene I’d like and generating nice figures. The specific feature that I’ve come to rely on quite heavily is the built-in ray tracer. There are three available ray tracing modes in addition to the default, each of which has its uses. Mode 1 will place a black outline around your structure, which can help make the secondary structure elements visually distinct. Mode 2 is really interesting, in that it only renders the outline. I find this especially helpful if I want to show something in an overlay without obscuring what is behind it. Mode 3 produces “quantized” color in addition to the outline, giving your figure a very cartoonish appearance. I find that this one has to be used with care :) " - Mike Chelen from Bookmarklet

it looks like semantic mediawiki? - Mike Chelen

here is a guide to import data (TSV, tab separated values) to Semantic MediaWiki with a script: http://semantic-mediawiki.org/wiki... and some extensions for XML import: http://semantic-mediawiki.org/wiki... - Mike Chelen

"collected resources for the Boston Open Source Science Lab (http://bosslab.org)" - Mike Chelen from Bookmarklet

Some of them were - classic moment of confusion, when I ask myself why I hadn't seen it before, then look at the source, realize it is me, and get really confused :-) Then I remember to check the date... - Cameron Neylon

"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

nearly everything to automatically download & seed new releases from http://www.biotorrents.net/browse... is working, rssdler still has to be run manually though it is easy to do once per week or so - Mike Chelen

"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

D0r0th34: thrilled to see existing and ongoing exploration of the topic, which is a natural extension for scholarly repositories and a crucial goal for ongoing curation. now reading one of the linked papers, "Open Access Statistics: an examination how to generate interoperable usage information from distributed open access services" (Herb, Ulrich '09) http://www.dini.de/fileadm... - Mike Chelen

usage of open source software, and application of its principles, advances science research & publishing by allowing faster and more efficient replication and modification of new ideas - Mike Chelen

Interested in the contrast between open science and distributed science - can you have "closed" distributed science? Or is that just collaboration? - Richard Badge from Nambu

"The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data." - Mike Chelen from Bookmarklet

sourceforge project page: https://sourceforge.net/project... - Mike Chelen

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