Posts Tagged Access

Free Ivy-League Education

 After I mentioned theScienceNetwork in the previous post and you might already be aware of sites such as, and iTunes U it’s time to share some recent links in the area of online-courses:

First, with a biological focus, there is iBioSeminars accompanied by iBioMagazine – let me just highlight this talk by David Baltimore.

On the computational side, there is udacity which was started by former Stanford professor and Google fellow Sebastian Thrun. He developed a vision for “University 2.0” under the motto of “democratizing higher education”. After having experienced that he could reach out to more people in a better way by a single online course than he could have by traditional teaching (even in huuuge overcrowded lecture halls) during the next couple of years he just couldn’t go back to the olden ways. He really has a point in dumping his professorship I heartily agree with, and that’s an understatement. I highly recommend to check out his talk at DLD (hosted by the gorgeous Maria Furtwängler), here is a teaser-trailer for the CS101-class “Building a Search Engine”:

(You might want to check out this previous post on the online courses at Stanford)

To round things up, at the moment there is a free introductory course on Machine Learning “Learning from Data” ongoing at Caltech by Professor Yaser Abu-Mostafa covering basic theory, algorithms, and applications. Registration is still possible, the previous lectures are available here.

Video et studio, ergo sum.

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Molecular Interaction Exchange

The International Molecular Exchange Consortium IMEx is the latest effort of data-providers to integrate Protein-Interaction Data –

IMEx provides

  • A non-redundant set of protein-protein interaction data from a broad taxonomic range of organisms
  • the data in standards compliant download formats (MITAB or PSI-MI XML 2.5)
  • Expertly curated from direct submissions or peer-reviewed journals to a consistent high standard.
[ … aiming to … ]
  • Develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals
  • Make these interaction available in a single search interface on a common website
  • Make all IMEx records freely accessible under the Creative Commons Attribution License

If you’ve been looking for that one-stop shop for getting a representative dataset of Protein-Protein Interactions, this just looks like it. There is an overview available on youtube (see below)

… and a training course on “Networks and Pathways Bioinformatics for Biologists” will take place at EMBL-EBI in May.

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Dear Elsevier Employees, With Love, From @FakeElsevier.

Came across this via the satirical twitter-stream!/FakeElsevier – in part the argument is very much along the lines on CargoCult Science I wrote last year (i.e.

Admittedly, this is my first attempt at reblogging … let’s see how this works out.

P.S.: See the comments for additional info …

The Real Fake Elsevier

An Open Letter.

A little background

As anyone who is reading this probably already knows, the publishing giant Elsevier has recently placed itself at the center of a shitstorm of animosity from the research community, thanks in part to its vocal (and financial) support of the Research Works Act (RWA). Currently, the National Institutes of Health mandate that the research products they fund with tax dollars must be made freely available to the public; the RWA would make such mandates illegal, enabling Elsevier to keep research papers resulting from taxpayer-funded research behind paywalls for as long as they like. There’s some douchey attempted subterfuge in the language of the bill about not locking up the research results themselves, but make no mistake: research papers are our output as researchers, and they are what makes up the scientific literature. While manipulating the legislative process for financial gain would be galling by itself…

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Science: 2011 Visualization Challenge

Separation of a Cell, Andrew Noske et al. (Illustration - People's Choice)

An article describing the 2011 International Science and Engineering Visualization Challenge just appeared in Science 3 February 2012 (Vol. 335 no. 6068 p. 525, DOI: 10.1126/science.335.6068.525). Access to all materials in this section is FREE (like in free beer), especially the web-gallery of the corresponding special issue available as a slideshow is definitely worth a visit.

Each year, Science Magazine and the National Science Foundation host the International Science and Engineering Visualization Challenge. The 2011 Challenge received over 200 submissions in five categories, which were evaluated based on visual impact, effective communication of a scientific idea, and overall originality. Visualizations with the most votes from the public received the People’s Choice award.

Among the Informational Posters & Graphics I like “The Cosmic Web“, and all the videos are just awesome.
Congrats to FoldIT for making 1st Place in the “Interactive Games”-Category and thanks to Sathyapriya Rajagopal for the link!

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A bitter taste of things to come?

On January 18, 2012, sites all over the internet will be blacking out to protest and try to mobilize more people to speak out against this bill coming up in the Senate next week — S. 968: the Protect IP Act (PIPA) — in an attempt to let U.S. lawmakers know how much opposition there is. [ News]

Unfortunately, this is really no hype – just recently I heard highly-paid, no-nonsense corporate lawyers on the topic saying they’d recommend their clients to basically shut down most of their internet-presence immediately in case this bill passes, just to be sure not to be sued to the bones. Ruling by fear, that is….

A video on the topic is on

Please see this post from last year on how the story developed.

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The Science of Insecurity

From last week’s 28th Chaos Communication Congress (28C3) – an annual four-day conference on technology, society and utopia – there are a couple of really interesting talks. Of course, these are freely available (the logo on the right directs to their youtube-channel, the link in the blockquote takes you to the wiki) under a creative commons (BY-NC-ND) license.

As practised with 26C3 and 27C3 we want you to come together. no nerd left behind: Allow those unable to attend the Congress in Berlin to celebrate their own Hack Center Experience, watch the streams, participate via twitter or chats, drink Tschunk, cook and have a good time.

Read the rest of this entry »

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a database of biological databases

MetaBase is a user-contributed list of all the biological databases available on the internet.


Nucleic Acids Research Advance Access published December 1, 2011
Nucleic Acids Research, 2011, 1–5, doi:10.1093/nar/gkr109

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