Another move

Despite the fact that nobody should follow this feed anymore: The blog moved again. Now you can find it at http://thedaoofflow.fluxionary.net/

Konrad's considerations moved - update your RSS readers

I finally moved my blog so please update your bookmarks and RSS readers: The new URL is http://konrad.foerstner.org/blog/

The design is not yet set up properly and there will be a change of the categories, but I am very busy these days and want to avoid to post here and in the new blog.

DiSo - the distributed social network

The DiSo project is a promising attempt to create a distributed social network - so is not following the "silo" approach as other social networks do. The blog of the project offers a short (4 min) introductionary video in which Chris Messina explains the vision and ideas behind this solution. The project will make use of open standards like OpenID, XMPP and different microformats. Code is available as open source. Really looking forward to see this stuff in action soon.

The WWW is not the Internet

Yes, maybe I am little bit too nitpicky, but this bugs me: April 30th 1993 the World Wide Web became officially accessible for the general public and libwww became open source. Some media saw this as a reason to celebrate yesterday the 15th birthday of the WWW. Due to this "birthday" I stumbled across a common mistake more often then usually: Mixing up WWW with the Internet.

The WWW is not the Internet!

As an analogy - a car is not a highway. The WWW is one of many internet-based services like email, IRC or p2p networks. The Internet is the underlying network that is using the Internet Protocol (IP). I personally would like to see a little bit more awareness of this issue.

OpenBSD 4.3 released

After 6 months of hard work the OpenBSD project released version 4.3 of the great, (non-)fishy operating system. As usually there is a collection of micro-interviews with some of the developers about new features at the O'Reilly's BSD DevCenter.

Ready to register - The 10th International EMBL PhD Symposium

This year the well known EMBL PhD Symposium will cover fields belonging to the topic "Decision Making in Biology - Nature at the Crossroads" and you can already register. It is still some time until October (23rd - 25th) so the program is not yet available but the list of speakers looks very promising.

Blossum62 error - Never stop questioning

Outch! Styczynski et al. [1] found an error in the BLOSSUM62 - THE substitution matrix used since 16 years in bioinformatics for protein database searches.

Lessons learned:

• Don't stop questioning even fundamental laws/tools/assumptions/etc.
• Transparency - in bioinformatics the access to the source code and the data - is essential for proper science

[Via Suicyte Notes]

[1] BLOSUM62 miscalculations improve search performance. Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G Nat Biotechnol. 2008 Mar ; 26(3): 274-5

Petition - Open the GCG and SeqLab code

Steven M. Thompson has initiated a petition to make Accelrys' GCG and SeqLab available under an open source software. He wants to prevent the loss of these bioinformatics tool sets after Accelrys' recent decision to stop the support and development of them.

Synthetic biology against global warming and energy crisis

Craig Venter gave a talk at the TED conference this year in which he presented a synthetic biology approach to create an organism that might solve two major problems of mankind: The increasing CO₂ concentration in the atmosphere and limited fuel resources. Venter claimed that the project will take further 18 month. The video of the talk is now available.

The iTOL toolbar for Firefox

Ivica just created a Firefox toolbar for iTOL which might be handy if you manage your phylogenetic trees with this cool web tool.

(Yes, looks like I became the unofficial announcer of new tools etc. from the Bork group) ... that wasn't planned.)

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."