Bio::Blogs 19 - A look at Bioengineering

Duncan is hosting the 19th Bio::Blogs issue and wrote down some thoughts about bioengineering.

Pedro will take care of the next one that might cover data integration.

Good physics phun

Phun - A fun 2D physics sandbox by Emil Ernerfeldt - seems to be an awesome program that can be a black hole for planned working hours. You can draw physical objects and switch on gravity and friction etc. Have a look at the video. It reminds me on the video MIT sketching which showed a more natural interface (draw your stuff on a board and make it run) but is less powerful. Phun is not (yet) open source but according to the FAQ the author is planning to make the source code available at some point.

[via Bad Science]

The STRING and STITCH blog

For the bio crowd: If you want to be informed about news regarding the web tools STRING (proteins and their interaction) and/or STITCH (protein-chemicals interactions) you should have a look at the blog that Michael set up recently for that purpose.

Bruce Schneier on security vs. privacy

Here is just a quick link to an article about privacy and security by Bruce Schneier at Wired. He explains the wrong perception regarding the trade-off between these two values.

The debate isn't security versus privacy. It's liberty versus control. [...] If you set up the false dichotomy, of course people will choose security over privacy - especially if you scare them first. But it's still a false dichotomy. There is no security without privacy. And liberty requires both security and privacy.

SPIEGEL archive freely accessible

As announced recently Europes biggest magazine DER SPIEGEL (trans. = "The mirror" - not to confuse with "The Mirror" in UK!) made today articles of SPIEGEL (including sub-magazines and their lexicon) and Manager Magazin at wissen.spiegel.de online available for the public. The material is still copyrighted but it is a huge knowledge dump as the archive contains articles since 1947. The keyword search results not only in a list of articles from SPIEGEL and/or Manager Magazin but also includes entries of the German Wikipedia. There are also dossiers like "Die Sprache des Lebens" (= "the language of life) that combine some articles about selected topics. You can get an overview about the content at the statistics page.

How about some biological treasure hunting?

Lars Juhl Jensen, another member of the Bork group, started his new blog Buried Treasure some days ago. As said in his first posting the main intension is to make some of his scientific loose ends public:

My primary goal with this blog is to make my never-to-be-published observations openly available. As I don’t plan on continuing these projects, anyone is welcome to pick up a project and continue where I left off.

I wish a happy treasure hunting.

Calais - get sematic into your content

It looks like the predictions come true and semantic web takes off in 2008. After Google another big player (one you wouldn't expect in the game at the first first glance), Reuters, made a nifty tool for semantic processing called Calais available.

The Calais web service automatically attaches rich semantic metadata to the content you submit – in well under a second. Using natural language processing, machine learning and other methods, Calais categorizes and links your document with entities (people, places, organizations, etc.), facts (person ‘x’ works for company ‘y’), and events (person ‘z’ was appointed chairman of company ‘y’ on date ‘x’). The metadata results are stored centrally and returned to you as industry-standard RDF constructs accompanied by a Globally Unique Identifier (GUID).

It seems to have quite some power under the hood.

Bio::Blogs#18 out now

Issue #18 of Bio::Blogs is available at Bioinformatics Zen and has some hot links regarding Open Notebook Science and other topics for the bio crowd.

Googles's Social Graph API

The Google Code Blog introduced today the Social Graph API which is meant to make the information of a social graph to be reused easily. It's based on the open standards XFN and FOAF data that is embedded into websites. You can find some simple toys to get the idea at the project page. It is real fun to play around with this! Tim O'Reilly asks for mechanism that enforce privacy about selected connections what I also really would like to see. I am not sure but I think it (actually not the Social API itself but XFN/FOAF/etc. in general) also offers new ways of spamming: An advertisement site could like to random profiles pages as friends and if the linked person checks their graphs (asking for people who linked to them) they see the link. Not sure if I got that wrong. Anyhow, this stuff looks really interesting and promising!

Wikia and GoPubMed - New kids on the search engine block

Wikia search, the search engine of Jimmy Wales' company Wikia, is now online as an alpha version. Everything is very basic so far - no much functionality, content or eye-candy. It relies on user contributions and is supposed to be open and transparent.

Life scientists have a (new) tool to search for literature: GoPubMed. Many others have already reported about and I just found it via this posting (sometime I am quite resistant :)). The press release tells us:

This, the first semantic search engine, reduces search time by up to 90%. By sorting search results it enables scientists to answer biomedical questions in completely new way.

I played around a little bit and think it is really functional and fancy. Funnily "shot gun sequencing" in one of my papers leads to the key word "Firearms". Recently Folksonomy 4 Science was included which "allows users to identify experts in the biomedical field and gain important information on recent research topics by viewing their networks."