konrad's considerations

Another move

2010-07-04T19:11:00.000+02:00

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

2008-06-23T09:59:00.000+02:00

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

2008-06-03T18:08:00.004+02:00

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

2008-05-01T15:30:00.002+02:00

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

2008-05-01T11:52:00.004+02:00

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

2008-04-23T19:51:00.005+02:00

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

2008-03-28T11:24:00.004+01:00

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

2008-03-25T10:13:00.004+01:00

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.

Free hugs worldwide

2008-03-21T18:58:00.007+01:00

Sometimes a warm hug can make a difference: The CouchSurfing community will carry out a wordwide Free Hugs campaign tomorrow, March 22nd. The the CouchSurfing wiki lists 51 cities in which people will give hugs to strangers to make the world a better place.

Join in, I am pretty sure you have some hugs to give away, too!

(Photo taken by moonwire)

Synthetic biology against global warming and energy crisis

2008-03-10T09:43:00.003+01:00

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

2008-03-08T16:31:00.003+01:00

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

2008-03-08T16:22:00.003+01:00

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

2008-03-04T22:31:00.004+01:00

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

2008-03-02T14:21:00.005+01:00

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

2008-02-16T16:41:00.007+01:00

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

2008-02-13T19:59:00.005+01:00

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?

2008-02-08T09:48:00.000+01:00

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

2008-02-06T23:39:00.000+01:00

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

2008-02-01T23:18:00.000+01:00

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

2008-02-01T22:32:00.000+01:00

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

2008-01-07T13:42:00.000+01:00

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."

Let's try to keep some privacy

2008-01-03T17:30:00.000+01:00

Happy new ~~2008~~ 1984. Germany has now the data retention but this doesn't mean that we cannot fight back. Via Roland's delicious links I stumble across Anonymouse.org. This proxy lets you surf any page anonymously in a very easy solution if you don't want to set up Tor or JAP. Only disadvantage is it's low speed. For easy use have a look at the toolbar and/or Firefox search plug-in. If you want to use a Firefox keyword search (always handy!) enter

http://Anonymouse.org/cgi-bin/anon-redirect.cgi?sourceid=Mozilla-search&what=%s

into the Location field.

An alternative for the data collector Google could be the metasearch enginge Ixquick. According to their private policy they delete user specific information after maximum 48 hours. There are also different Firefox search plug-ins available. For the above mentioned keyword search use

http://ixquick.com/do/metasearch.pl?query=%s

Any other suggestions for keeping privacy when surfing?

24C3 - report part 9 - Security Nightmares 2008

2007-12-30T22:00:00.000+01:00

Frank and Ron filled the "told you so"-karma with the annual Security Nightmares presentation/brainstorming. After a short retrospect they had a look into the crystal ball. Some predictions that were mentioned:

hijacking of industrial robots will increase
people will go to jail due to wrong time zone configuration of log servers
more flash memory problems - e.g. no proper cleaning possible
more VoIP-hacks
hacking of large scale storage/computing backends like Amazon S3
malware for mobile phones especially on iPhone
crowed-sourcing for breaking CAPTCHA

24C3 - report part 8 - Some photo impressions 2

2007-12-30T19:56:00.000+01:00

An some more pics ...

A speech bubble machine

Indymedia searches safe habor

"We hate flash"
The ceiling of conference room 1

Quadrocopter

Smiling light

Monitored

Usual suspect

24C3 - report part 7 - Some photo impressions 1

2007-12-30T15:29:00.000+01:00

Here are some photos I took at the conference. It's not allowed to take photos downstairs in the so called Hackcenter so no documentation of that.

The congress center with the famous CCC rocket and some decoration

Hacker Jeopardy

Regarding politics

LED cube

MAKING with LEGO

Research lab

Another photo of the demonstration yesterday

Club-Mate - should be a platinum sponsor of this event

24C3 - report part 6 - Demonstration against data retention

2007-12-29T20:21:00.000+01:00

I wrote some time ago about the new law for data retention in Germany. It passed all hurdles and will come into effect starting from the 1st January 2008. The connection meta data (phone, cell phone, internet) of all citizen of Germany will be stored for six month then. A law suit against this law will be started soon. The AK Vorratsdatenspeicherung organized a demonstration that took place here in Berlin starting in front of the congress center to protest against this and similar laws. There will be more demonstration in the near future. Check the calender if you want to join.

24C3 - report part 5 - resistence 23, GTD, MI5, rule 34, barcode hacking, and chicks for geeks

2007-12-29T16:56:00.000+01:00

Ah, so much to do here. So just some of the highlights.

Yesterday Markus Beckedahl (netzpolitik.org!) gave some (23?) hints of how to fight for your rights starting from lobbying, creating and influencing media, coding etc.

FX of Phenoelit showed cool barcode hacks. Wanna have an upgrade of you flight ticket? Give it a go ...

Another highlight yesterday was definitely the rule 34 content. For good reason this was not recorded. It was great fun!

The morning today started with a presentation by Annie Machon. She was working for the British intelligence service MI5 but became a whistleblower and had to escape from England. She showed the dark (and unfortunately growing side) side of the spy world.

In a workshop Machtelt tough some single geeks how to get a girl by following some simple advices.

Stephan Schmieder introduced the audience of room 3 to the productivity system Getting Things Done. I am using it since some years and share his experiences. The recommended the program ThinkingRock for implementing it. It looks quite bloated to me and I am very happy with jpilot (which I also can use to sync to my smartphone), but I will give it good.

24C3 - report part 4 - raw videos available

2007-12-28T16:10:00.000+01:00

Niiice ... for people who didn't make it to the conference and missed the live stream of a talk - there some raw dumps online.

HTTP 1: http://server.c-otto.de/mitschnitte/
HTTP 2: http://mirror.engelkotzen.net/
FTP: ftp://88.198.6.181/pub/24c3

[via Marius News Blog]

24C3 - report part 3 - the future of e-books

2007-12-28T12:51:00.000+01:00

There was a talk (German) by Steini (*) about the current status of e-books and the future developments in the morning session today. It covered the few current available e-book readers and the status of displaying technologies (e-ink, bistable LCD displays, visplex, etc.). Although e-books are quite promising the available ones (mainly the Sony libre, Sony Reader, iliad iRex, Amazon Kindle (**)) are too expensive and not mature (slow, bad interfaces, restrictions, lacking features).

Steini thinks that in future due to the low energy consumption and better readability of the e-books they might fill the gaps that the PDAs were suppose to fill. Kids will carry them to school, smaller text books (around 50 pages, less redundancy) will be feasible to be produced, new business models without publisher might come up. Book sharing, automatically transfered manuals of new gadgets and interactive stories are other presented implications.

Some design studies

As I am quite interested in this topic I talked afterwards with Steini. He mentioned that his company is currently working on creating an e-book reader that covers all the important features and lack the teething problems. Well, he is definitely biased but I am curious about the result, that will not only included the reader itself but also the necessary web platform. We will see the result hopefully in a year.

(*) the description of him in the wiki of this year is quite poor so I link to the one of last year
(**) During the later discussion also the OLPC was mentioned as a possible e-book reader. This was proposed also at O'Reilly Radar once.

24C3 - report part 2 - DNA hacking and web security ooopses

2007-12-28T00:03:00.000+01:00

I just listen to two cool talks (actually sitting in a sofa down in the Hackcenter watching the live stream :)):

At first: Drew Endy (MIT - Department of Biological Engineering) introduced the audience to molecular, computational and synthetic biology and showed the connection to Making. He mentioned the possible security issues that come up with decreasing prices of DNA synthesising and the availability of sequences of harmful organisms. The talk ended with the question if there will be soon the "Biological Hacker". I have a stream dump of the talks if anybody is interested.

Second: Dan Kaminsky gave one of his legendary talks ... hilarious! He added more examples to the collection of web security oopses by describing how to exploit really bad design bugs. Starting form DNS rebinding, to an IFrame-Flash-hack to "IP via SPAM" (some live demos included). I am sure I didn't get everything completely but it was great fun!

Dan Kaminsky in action:

Conclusions:

24C3 - report part 1 - intro

2007-12-27T22:52:00.000+01:00

Today the 24 Chaos Communication Congress (24C3) the annually hacker meeting organized by the Chaos Computer Club started in Berlin. Here you can find lots of inspiring talks, cool workshops and interesting people. Hacking (in the broadest sense), making, privacy and politic issues and many other topics are covered. The theme"Volldampf voraus" (German for "full steam ahead") is inspired by the retrofuture steam punk genre and you can see at some place of the conference related accessories.

As usually I am mainly hanging out at the OpenBSD booth and am frequently visiting talks and workshops. I will report about some selected stuff in the next days. There are live streams of the talks if you want to watch them yourself and the videos will be available for download some month after the congress.

Google teaches how to enhance privacy

2007-12-19T23:38:00.000+01:00

The Google Blog informs us that the Google Privacy Channel has started offering advice how to enhance privacy when using Google products. Well, nice try but I hope Nat Torkington is right and we can see soon the Google Privacy Dashboard

... where consumers can view all the information that Google has about them, request the deletion of any of that information, and download privacy-enhancing tools such as cookie cleaners.

Yes, we had the hope already earlier ...

Knowledge Mega Mirror - SPIEGEL opens archive

2007-12-19T19:31:00.000+01:00

DER SPIEGEL ("the mirror" in German), Europe's biggest magazine, will open its archive beginning of 2008. As announced the publisher's subsidiary company SPIEGELnet and the Wissen Media Group will set up SPIEGEL Wissen. There the SPIEGEL articles starting from 1947 will be combined with content from Wikipedia and the Bertelsmann-Lexika. Only the current issue needs a subscription.

It's a great step and a lot of knowledge will be made freely accessible. I am looking forward to see how they will implement the mashup of the different sources.

[via Wikemedia Blog]

OPEN proposal online

2007-12-10T18:12:00.000+01:00

Just saw that the proposal for the Open Practises E-science Network (OPEN) is online at Nature Precedings. Nice job, guys!

Wikipedia license update

2007-12-02T12:54:00.000+01:00

As Lawrence Lessig reports Wikipedia has made a resolution to update it's license and make it compatible with a Creative Commons license:

It is hereby resolved that:

The Foundation requests that the GNU Free Documentation License be modified in the fashion proposed by the FSF to allow migration by mass collaborative projects to the Creative Commons CC-BY-SA license;
Upon the announcement of that relicensing, the Foundation will initiate a process of community discussion and voting before making a final decision on relicensing.

There is a video of the announcement by Jimmy Wales (I found a transcript of it here).

OpenCON 2007

2007-12-01T18:24:00.000+01:00

Since yesterday the OpenCON 2007 - a yearly conference only dedicated to OpenBSD - is taking place in Venice. Around 130 developers and users having a good time here and are socializing (as usually) very well. There were some very helpful tutorials yesterday and now the we have a packed schedule of talks. We expect to celebrate a good OpenSSH birthday party tonight. I hope to finally get started with porting some applications to OpenBSD and Bernd's tutorial (will be online soon) was excellent start for that.

Miro - open internet tv

2007-11-13T11:21:00.000+01:00

I use the upcoming release of version 1.0 of the Miro Media player (previously know as Democracy Player) as an occasion to report about this cool project. There are many video platforms in the web but most of them are silos based on proprietary formats. The Participatory Culture Foundation wants to solve that:

Miro is designed to eliminate gatekeepers. Viewers can connect to any video provider that they want. This frees creators to use the video hosting setup that works best for them - whether they choose to self-publish or use a service. It's the kind of openness that the internet allows and that we should all demand. [...]

Our goal isn't to dominate online video - our goal is to push the industry towards openness.

The project is based on three principles of openness: Open Access (not the meaning of scientific publishing), Open Standards and Open Source.
The Miro Guide contains already a lot of interesting channels!

In short: Rocks!

Concerns regarding OpenSocial

2007-11-01T10:49:00.000+01:00

I guess you didn't miss the big hype about Googles OpenSocial (link doesn't work so far), which is a set of open API standards for social networks. I like Google for using open standards and working with and not against the community. But regarding this opening of social networks (same for FOAF/XFN) I have strong concerns as we lose too much control about the data and our privacy. Ralf Bendrath and others precisely describe the problems.

The Internet is challenging our current understanding of privacy/identity/society. Maybe we just have to accept this change and must adept our attitudes. For me personally it is not a problem that a potential employer can find out that I have fun in my spare time (as long as the information is correct ... which I cannot control) for other it might be different. But the potential abuse of this easy-to-harvest data by governmental agencies makes me refuse to stop questioning the legitimation of these technologies.

Puffy is back - OpenBSD 4.2

2007-11-01T10:17:00.000+01:00

Who needs leopards if you can have fish? The OpenBSD project proudly presents OpenBSD 4.2 - the operating system for the practical paranoid. As usually Federico Biancuzzi has interviewed some of the developers about the current release. The interview ~~will be~~ is online at O'Reilly's ONLamp.

Bio::Blogs #16 - Halloween edition

2007-11-01T10:06:00.000+01:00

Check out the 16th edition of Bio::Blogs hosted by Pawel.

Stop data retention - Stop Vorratsdatenspeicherung

2007-10-25T21:56:00.000+02:00

EN: Hacking-paragraph, biometric passports ... German politicians decided in the last time against the recommendations of IT/security specialists (german). Next law in the pipe: telecommunication data retention. The benefits of this law are very low, the effort of the implementation is quite high and the potential of abuse of the stored data (german) is tremendous. There is still the possibility to stop the law - visit www.vorratsdatenspeicherung.de for more information.

DE: Hacking-Paragraph, biometrischer Reisepass ... in letzter Zeit haben deutsche Poliker entgegen den Empfehlungen von IT-/Sicherheitsspezialisten entschieden. Als nächstes steht die Verabschiedung der Gesetzes für Vorratsdatenspeicherung auf dem Plan. Der Nutzen dieses Gesetzes ist gering, der Aufwand der Umsetzung sehr hoch und das Potential des Missbrauches dieser Daten enorm. Noch kann das Gesetz verhindert werden. Mehr Informationen auf www.vorratsdatenspeicherung.de.

Empfehlung: Chaosradio und Chaosradio Express haben in letzte Zeit viele verwandte Themen behandelt und bieten eine gute Einführung.

Max Planck Society puts pressure on Springer

2007-10-19T08:48:00.000+02:00

The Max Planck Society has not extended it's contract with Springer. Michael summarized the story nicely.

Semantic web logos

2007-10-19T08:19:00.000+02:00

The W3C has created a set of logos to promote semantic web technologies. Nice!

(What this means for microformats can be found here. :))

A talk about openness, freedom and transparency

2007-10-12T15:59:00.000+02:00

Finally I took the time to record and finalize the screencast (Xvid4, mpeg, Google Video (*)) of a talk I gave some weeks ago at the EMBL PhD retreat in Barcelona. It is called "A quick trip through openness, freedom and transparency" (pdf) and covers open source, open formats, Creative Commons, open access, open science/knowledge in a very introductionary way.

Thanks to Nikolay Sturm who helped me to create a port (not perfect but fine for this purpose) of recordmydesktop for OpenBSD.

(*) bad resolutions on Google Video ... any suggestions how to improve that?

GRDDL - bringing more semantic into the WWW and getting it out again

2007-09-12T15:36:00.000+02:00

The W3C published a recommendation for the Gleaning Resource Descriptions from Dialects of Languages (GRDDL). The motivation is to make the extraction of semantic data from XML especially from XTHML easier and stimulate by this the usage of embedded sementic data. It describes for example how to extract RDF data from XHTML files that contain data wrapped in a microformat. If you are interested the primer is a good starting point.

Will ebooks finally take-off?

2007-09-08T09:51:00.000+02:00

As New York Times reports Amazon will soon start selling their own ebook reader called Kindle that can download ebook from Amazon's store (unfortunately in the proprietary Mobipocked format). Google will begin with the fee-based access to full versions of some books in their collection. Having these to big player in the game the likelyhood that ebooks finally take-off is pretty high.

[Via openculture]

Video archive of the Metagenomics 2007 Conference is online

2007-09-01T00:56:00.000+02:00

The title says everything so here is the link to the video archive.

Listen to Wikipedia

2007-08-30T14:36:00.000+02:00

Pediaphon, a project of the University of Hagen (Germany), generates audio files of English and German Wikipedia articles on the fly. It can be used with a web browser but there is also a WAP interface and way of requesting the audio file via SMS and a phone call. Nice example barrier-free access to Wikipedia.

[via Pro-Linux]

Web data mining made easy

2007-08-29T21:48:00.000+02:00

Man, and I just complained about Spock which is nothing in comparison to this: If you need an efficient tool for collecting and connection web data about people, organizations etc. then Paterva's Evolution is the answer for you ... but hey, why do you need such a thing?!?. I stumbled across it via a good article on Linux.com. Evolution offers a (closed-source) java-based GUI and two web interfaces (only the classic works at the moment, the web-wizzard cannot be used currently). It is a little bit slow but considering the amount of sources it harvests and the results you get it is pretty okay. I am fascinated and scared on the same time. That just makes it too easy.

Sun's hardware documentation wiki

2007-08-28T13:05:00.000+02:00

Sun just started the FOSS Open Hardware Documentation wiki and offers to publish specifications of hardware after request. This should make it easier for open source projects to code drivers. Theo de Raadt recently criticized Sun for their lacking hardware documentation which was an inspiration for starting this wiki. I hope more vendors will follow this example.

[via golem.de]

Welcome to Germany, black hats!

2007-08-27T18:00:00.000+02:00

As was reported in the media (e.g. title story of the german Spiegel magazine) computers of the German government were compromised by Chinese black hat hackers. The Chaos Computer Club uses this incident to question the competence of the decision makers regarding IT security. Certain politicians are constantly proposing to use Trojan horses to infiltrate computers of "criminals", but are lacking the necessary knowledge to judge the risk of this approach (another proof of this can be found here on netzpolitik.org). The recently established German anti-hacking-tool-law (§ 202c StGB) makes the necessary tools for preventing these attacks illegal. There is something going really wrong.

Ear bud cable keeper

2007-08-27T13:08:00.000+02:00

Okay, this won't make it into Make Magazine but maybe it helps you to solve the cable chaos of your ear bud headphone. It's my do-it-yourself-version of a TuneTie, a ear bud cable keeper, and can be built with some cardboard, sticky tape, a knife and around 10 minutes of time. Just cut the cardboard into the shape you need and stabilize it with tape. In the end add a little cut that is used to hold the end of the cable. As I use bulky "sport" ear buds the shape differs from the original. In the end it looks like this.

PS: Hmm, maybe I should think about making different blogs as my topics are really quite diverse. But I guess people can filter via the tags.

Micropublications

2007-08-23T14:26:00.000+02:00

Michael Nielsen who is writing a book about the future of science posted a week ago an excerpt with a scenario of micropublications. This is nothing else than Wiki-Science as is e.g. described by Kevin Kelly. But the expression micropublication make it very clear that the smallest unit of scientific publications does not need to be a full article but could be much smaller. By giving the option of small contributions more people might be motivated to participate in the creation of something big.

Spreading the spirit of openness

2007-08-23T14:15:00.000+02:00

I really enjoy the discussions and ideas about Open Science and Open Knowledge etc. in the web. Hopefully it will change the way how we communicate and do science. On the other hand I see the problem that these discussions are mainly done by the 31337 web-addicted scientists while the majority of scientists is not involved. I am still meeting so many scientists that have not heard about Open Access (not to mention Creative Commons or Open Source [the origin of the concept]). I do not expect everybody to be a nerdy IT guy but at least the spirit of openness should be in the minds of scientists. The current system does not encourage this attitude. It is not officially taught at university and the scientific credit system makes people scared of being scooped or not being accepted (including myself).

Due to the success of many Web 2.0 services the technical concepts like blogs, wikis and social networks are known by more and more people (even scientists ;)). The usage of Open Source software is also growing but is often only motivated by its price not the freedom (free as in 'free beer' not 'free speech'). The concept of openness, transparency and freedom is lacking. So before we can change the (scientific) system we need to reach a critical mass and in order to do this we have to spread this concept to others. I think we must make clear that access to data is crucial to speed up science and to improve living standards globally. And this has to be much more prominent in "real life". So I would like to encourage people spread the word by giving talks and speaking with colleges and friends who are not yet aware of these concepts.

I am planing to give such a talk next month in Barcelona (EMBL PhD retreat) and make it later online available. It is intended to be a introduction to the topics mentioned above. Let's see how I manage. Currently I am brainstorming and working on draft.

Some quick links - Brave new web

2007-08-23T10:28:00.000+02:00

Although I have not been out of office for so long (CCCamp and some other stuff) my dear office mates had the felling I am permanently on the road.

During the last time I collected some topics I would like to write about, which I will do today. Here are some links I just want to mention quickly.

Spock seems to be the new privacy killer. It harvests data about people from many different sources and users can add tags and even photos of others. This gives me a quite bad gut feeling. A prevention method that most social networks offer might be to make your profile only accessible by other members (well, or not to use any of them at all). A comment on netzpolitik.org (sorry, in German only) gives a hint how to sabotage this platform.

Scary, scary number two: Polar Rose offers face recognition via a browser plugin. It tells you who is in the photo you are looking at. Don't know if it works properly already but I don't like this.

An analysis on Blog Age (German again) shows that many web services make is hard for users to get rid of their account. I recently had a similar experience where I had to mail the support team to delete my account. That's not good practice!

To be no only pessimistic here are some good news: freebase is now in "public alpha" so everybody can read data while adding data is still only allowed to registered users.

Also nice: I can recommend the current CT Quarterly issue which has the title “The Coming Revolution in Scholarly Communication & Cyberinfrastructure”. [via science commons blog]

After some month of waiting: Wikiproteins is online since beginning of August.

CCCamp 2007 - 8 - Misc hacks

2007-08-13T10:14:00.000+02:00

These events are famous for different kinds of hacks. Here are some of my favorite ones that are not so obvious (many thanks to all the people who uploaded the photos):

CCC => CCCP
OpenBSD-shirt => personalized camp-shirt (as the official ones are sold out)
tent + rain => indoor swimming pool 1, 2, 3
golf cart => garbage truck
pallets + Gulden Draake bottles => bikini contest stage

With this post I finish my report series of the camp. It was great fun! Thanks to everybody who was involved!

Update:

melone + bottle => cocktail glas (thanks to Bernd for this recommendation)
towel => sunshade
geek => bikini model
wristband => arm implant stabilizer
lights => black board (another on from Bernd)
mud hole => football field (and again Bernd)
airplane => skull opener
truck => bottle container

Update 2:

Lenin => Hippie

CCCamp 2007 - 7 - Sputnik

2007-08-13T08:18:00.000+02:00

Last project I want to mention that was represented (and applied) on the camp is Sputnik. The aim is to show people the potentials and threats of tracking technologies by personal experience. Active RFID tags (newest version v0.2) with different ids were sold to participants and three shelters were equipped with reader stations. The system (2.4GHz based) can track the tags in the range of 100 meters and discriminates between three levels of proximity. With enough stations you can give a very precise position of a person (this was not the case on the camp, but on the congress last year). A button on the chips can be used by the owner to send at signal that something interesting is going on at the current position. The collected data will be available for public use soon.

Due to the fact that only the owner knows the id of his/her tag and that the active chip can be switched off the user can choose the level of privacy. But it still makes people think more about the possibility of total surveillance. Many things like customer cards and passports are already equipped with (mostly passive, low ranging) RFID tags and the rank-and-file is not aware of this. The technology itself (as usual) is not evil. We just have to make sure that it is applied the right way for the right things.

CCCamp 2007 - 6 - Misc impressions

2007-08-11T16:50:00.000+02:00

Here just some impressions quickly presented by photos.

Quite an attraction - The Italian embassy opened Little Venice after the rain:

The first aid base:

Flying drone:

Cool light installation:

A multimedia table in the Art & Beauty area:

Regarding dogs:

CCCamp 2007 - 5 - The BSD village

2007-08-11T15:51:00.000+02:00

I am an inhabitant of the BSD village and would like invite all interested camp participants to visit us. You can get information and get cool shirts, caps, sweater, stickers etc. at the OpenBSD shop. The request of rain coats increased heavily after the flood that came down some hours ago so hurry up. OpenBSD developers, users and other nice people (like Mark who did the flash-into-iPod-hack) can be found in our huge white tent close to the airstrip if you need support or good company. We have a bikini contest tonight at 20:00!

CCCamp 2007 - 4 - OpenMoko

2007-08-10T19:07:00.000+02:00

I mentioned OpenMoko, the project to create a phone with open hardware(*) and software, already before. Here on the camp I had the chance to talk to developers and hold a Neo1973 (the first developer model using OpenMoko) in my hand. It is even cooler in reality than it looks
on the pictures. The screen is bigger than I thought and has an excellent resolution (640×480). The device is pretty solid. Booting takes still quite a while as the developers focus at stability at the moment and have not had the time for speed optimization so far. But once it is booted it runs very smoothly.

The next model will be for consumers and should be on the market end of the year. Really looking forward to this. An interesting feature will also be the two 3D accelerometers. You can find more details about all this on the project website and the commercial website.

(*) Unfortunately the GSM part will not be open in the near future.

CCCamp 2007 - 3 - BookCrossing

2007-08-10T13:33:00.000+02:00

How about making the world a library? With books everywhere! This is the the precise plan of the BookCrossing project. The idea is simple: books get an id, are registered on the website of the project and put anywhere you want in the real world. Anybody else who finds the book can read it. Ideally the finder sees that the book belongs to Bookcrossing and reports the book as found.

Although I meanwhile prefer ebooks, I think the idea is great. I had already heard about the project years ago, but never tried it. As it was announced on the camp Wiki that there will be representatives of the project at the camp I took two books with me and donated them to the project. Three books in the set up library of the Bookcrossing village library caught my interest and will come with me to Heidelberg. They will be read and then placed somewhere.

Some of my questions were also answered by project members. For example, how many of the books are reported as found. This depends on different factors like where you place it. On average around 10% but some guys place the books in better places (e.g. in fridges at IKEA) and have report rates of around 30%.

So if you have old books you don't need anymore or books you really want to be read by others: Free them!

CCCamp 2007 - 2 - Streams online

2007-08-09T10:27:00.001+02:00

EN: For people who are interested in the talks but cannot attend the camp (and for the lazy slackers who want to stay in the tents) there are good news: The streams are online now.

CCCamp 2007 - 1 - In fairy dust we trust

2007-08-08T12:26:00.000+02:00

The Chaos Communication Camp 2007 is officially open now for the next 5 days. It is located in an open airplain museum right next to a running airport. Talks (program) are hold in two shelters (foo and bar). Them, the airplains, flying drones and the usual light installations give the area a cool, post-apocalyptic ambiente especially when it is dark (I arrived earlier so saw the stuff at night).

More and more people are coming and camping space is getting rare. So most importantly: Don't panic.

There are so many interesting projects going on. Until now I was mostly hanging out at the BSD-village but I will start exploring other villages and meet some people.

The motivation for sex

2007-08-01T17:09:00.000+02:00

EN: What is our motivation to have sex? This study (full pdf) [1] by Cindy Meston und David Buss gives 237 answers to that question and groups them into four categories. Great fun to read!

[1] Why humans have sex. Meston CM, Buss DM Arch Sex Behav. 2007 Aug ; 36(4): 477-507

[Via Spiegel online]

Business IT - OpenBSD and nothing else

2007-07-19T16:00:00.000+02:00

EN: Just a quick link belonging to my "let's-promote-OpenBSD"-postings: The company Echothrust published recently a series (1, 2 ,3) of short articles in which they describe how they use exclusive OpenBSD-based systems in their daily business. It is an informative introduction which clearly shows that OpenBSD is a reliable alternative on all application fronts.

[Via undeadly.org]

Update: The fourth and last part is online now.

Metagenomics 2007 conference report - part 2

2007-07-16T22:25:00.000+02:00

EN: As Jonathan has written already a nice overview of the Metagenomics 2007 conference (while I was spending my time exploring San Diego ... call me a slacker) and as the videos will be online soon, I will only post my take-home-messages:

The recording and use of additional meta-information might be a key-factor for a better understanding of the sequence data. Fortunately more of this data is collected now.
For me the gut metagenome analyzes are pretty promising projects. Masahira Hattori and Janet Jansson presented very interesting studies.
A lot of tools that are developed for "classical" genomics cannot simply be applied in metagenomics. This has also to be explained to funding sources.
Platforms like Camera, img/m and Megx are under heavy development at the moment to fulfill the needs of the community.

Any other highlights? Your opinion?

iPhone pushes ebooks

2007-07-13T21:24:00.000+02:00

EN: Since quite a while I use plucker to read books on my Treo, but would like to see many more book available in a digital form. Although I personally will not buy a iPhone but prefer an open alternative, I hope its popularity will bring finally a breakthrough of ebooks. This post on O'Reilly radar gives hope.

Metagenomics 2007 conference report - part 1

2007-07-12T17:38:00.000+02:00

EN: At the moment I am attending the Metagenomics 2007 conference in San Diego. Around 190 scientists from 12 countries came together to discuss recent results in metagenomics and related fields.

I will later post some notes I took at the talks (as least some of them). To get an overview what's going on here have a look at the program. The talks are also available as a webcast and (I guess) later downloadable.

Jonathan offered to ask questions if they are posted to him.

Data sharing and citation rate

2007-07-06T19:43:00.000+02:00

EN: A presentation by Heather Piwowar at Nature Precedings directed my attention to a PLoS ONE article about data sharing and its effect on the citation rate by her [1]. Now as we have a proof that publishing data increases the amount of citations, more people are hopefully motivated to do so. Unfortunately I think that some people lock their data as long as they can to avoid competition. A further publication is maybe more worth than some additional citations.

[1] Sharing detailed research data is associated with increased citation rate. Piwowar HA, Day RS, Fridsma DB PLoS ONE. 2007; 2: e308

No support of Nature Precedings by Connotea

2007-06-28T20:11:00.000+02:00

EN: I think I am not the only one who would like see that Connotea makes use Nature Precedings meta-data during the tagging procedure. So far not even the title is fetched automatically.

Nutrition-related research biased by funding

2007-06-20T22:14:00.000+02:00

EN: Well, I think it is nothing completely unexpected but interesting to see research going on about this: Lesser et al. showed that nutrition studies are biased by the sources of their funding.

For interventional studies, the proportion with unfavorable conclusions was 0% for all industry funding versus 37% for no industry funding (p = 0.009). The odds ratio of a favorable versus unfavorable conclusion was 7.61 (95% confidence interval 1.27 to 45.73), comparing articles with all industry funding to no industry funding.

A similar study regarding financial biases in clinical studies was published already some years ago [2].

[1] Relationship between Funding Source and Conclusion among Nutrition-Related Scientific Articles. Lesser LI, Ebbeling CB, Goozner M, Wypij D, Ludwig DS PLoS Med. 2007 Jan 9; 4(1): e5

[2] Association between competing interests and authors' conclusions: epidemiological study of randomised clinical trials published in the BMJ. Kjaergard LL, Als-Nielsen B BMJ. 2002 Aug 3; 325(7358): 249

DRIVER wiki for Open Access in Europe

2007-06-20T21:31:00.000+02:00

EN: DRIVER (Digital Repository Infrastructure Vision for European Research) recently launched a wiki to aggregate knowledge regarding open access with focus on Europe. It intends to offer e.g. country specific information about fundings, events and organizations.

[via open-access.net]

Nature Precedings

2007-06-18T19:55:00.000+02:00

EN: As announced on Nasecent the preprint-server Nature Preceedings is officially launched now:

Nature Precedings is a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents. Submissions are screened by our professional curation team for relevance and quality, but are not subjected to peer review.

Pedro who tested it already for some month as a beta user reported some days ago about it. His earlier post regarding policies of journals regarding preprint-server might take some fears away. Some of the usual suspects have already added documents.

ENCODE - Functional analysis of the human genome

2007-06-13T22:13:00.000+02:00

EN: The ENCODE-project presents the results of the functional analysis of 1% of the human genome [1]. I have not have the time to read it completely so far but listened to a talk by Ewan Birney at EMBL on Tuesday. The approach might be the prototype of how some of the big questions in biology have to be solved - in huge consortia (308 authors contributed to this publication). 30 Mbp (1%) of the human genome were analyzed using different wet-lab techniques and intra- and inter-species sequence comparisons. One result of the integration of all this is that there is much more (10fold) transcription going on than reported before, but not all of the transcripts contain genes. The plan to extent the analysis to the full genome is currently reviewed.

[1] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 447, 799-816 (14 June 2007)

Google privacy again and how to improve privacy communication

2007-06-12T08:56:00.000+02:00

Privacy International published an analysis [1] in which 23 (! ;)) web companies are ranked by their treatment of the users' privacy. As described before (and here again) Google's huge collection of personal data that is havested by the toolbox of services can be seen as a harm for privacy. The authors of the study think that Google's behaviour regarding privacy is the worst one of all companies in the analysis. Although the study is highly criticized e.g. at Search Engine Land I really like to see the topic discussed in the media and getting more awareness.

Part of the privacy problem is the communication of the policies of the web services. The language of the general terms and conditions is in rare cases well understandable by usual people. There was recently a podcast (german) on netzpolitik.org with Matthias Mehldau. Matthias developed similar to Creative Commons an icon set for data privacy (PDF but SVG should be available soon). It is created to communicate in an easy way the privacy policies of a web service. So far is it in an early development phase and Matthias invited everbody to contribute with ideas and improved icons.

[1] "A Race to the Bottom - Privacy Ranking of Internet Service Companies", 09/06/2007

You cannot publish with the MS Word 2007 format

2007-06-04T21:59:00.000+02:00

... at least not in Science or Nature (also other journal from the Nature family e.g. EMBO journal) as Undernews reported. These publisher cannot handle the new format (docx). Hopefully this issue stimulates to rethink the current pipelines. Having a work flow based on a proprietary format (and despite its name Microsofts new Office Open XML format is also not really open) is in my opinion a bad idea as it forces possible authors to use a distinct software to create the publication. Not everybody can effort the Microsoft products or wants to use them. Sure, LaTeX would be a cool solution (and is used e.g. by some mathematical journals) but for many people it is just too nerdy. But how about ODF? It is a file format that is open, ISO-accepted, XML-based, and used by many (mostly open source) office suits like OpenOffice.

[via O'Reilly Radar]

Bio::Blogs 11 - Tips for bioinformatics practice

2007-06-02T10:47:00.000+02:00

EN: It is again the beginning of a month so time for a new issue of Bio::Blogs. The 11th edition is hosted on nodalpoint (pdf-version) and has the usual best-of-bioinformatics-blogs of the previous month (thanks Pedro!). Additionally a collection of tips with focus on best practice in bioinformatics can be found on Bioinformatics Zen (pdf). Michael Barton did a great job as an editor of this nicely designed collection. I contributed some recommendations, too and post below my raw version as it contain the links. Michael did some modification/cleaning to fit it into the style of the collection so there might be some small differences.

Here are some of my lifehack tips for computational biologists based on my personal experience. Please keep in mind that my main task is the data analysis itself, not the general tool development. Some of the points are not so relevant for people mainly developing software.

Maybe you are already inspired by general classical literature such as "Getting things done", "Seven habits of highly effective people" and the new kid on the block "The-4-hour-work-week" and are following blogs such as lifehacker.

Set up a proper tool box containing ...

... a programming language (or several) that suits your needs and lets you write functional and readable code quickly, e.g. Python
... the knowledge of the most important/used Unix commands
... a powerful editor (hot tips here: syntax-highlighting and completion)
... a reference management system like Connotea/citeulike or JabRef
... a browser equipped with handy extentsions
... a proper version control system for your code and documents - CVS or Subversion might be the options that come to your mind first, but if you would ask Linus Torvalds, he would recommend git.

The habit of proper documentation

Think about your future ego that will thank you for the possibility to travel back in time.
Write a lab journal/book

I highly recommend a blog or wiki based system, but for sure flat files or even a hand written notebook *cough*no*couch*way!!!*cough* might do the job.
Write down what you did, how you did it, why you did it, and where the input and output are stored. Also some of your key graphics, article summaries, and overviews of the results should be placed in there.
By articulating the thoughts in your head you define aims and become aware of them ("Begin with the end in mind" as Stephen R. Covey says).

Document your code

A short description at the beginning of the program is the minimal documentation.
Give meaningful names to functions and variables. If you cannot find a proper name, you don't know what the thing really does.

Use clear file names, file headers and folder structures to find things easily

I do this by putting the date in the beginning of folders where I organise my analyses e.g. 2007-05-28-foo_analysis_in_bar_data.
I put a master shell script into these folders which contains all the calls and sometimes, as a comment, the names of the resulting files.
The output files of my programs have a short header that tells by which program they were created, at which time and with which parameters the program was called (I use a little library for that).

Empathy and compassion

Think about which information in your head could be needed by other people in your lab or in your scientific community. A wiki for example can be an excellent tool for organizing generally needed knowledge and avoiding the drain of it if somebody leaves the lab.

Other small tips:

Be aware that demands will change so program from the beginning on in a way that make it easy to extend/adapt the program.
As soon as there is the smallest possibility that a function might be used twice write a proper library.
Often flat files are a handy format for data, and grep and others are good companions. If data sets are constantly changing and built of many components a proper database might be a better solution. For many purposes you don't need a client-server-based database like MySQL but a simple library based one e.g. SQLite that does the job without server set up and user management.
Code your graphics, as this will give you more control. Especially if you have graphics that consist of different panels, it will save you a lot of time if changes will be needed (and this will be the case). I personally create primarily SVG files and convert them to other formats if needed.
If you set up a web-server think not only about functionality but also about security. Make the internet a safer place and don't feed the spam/botnet industry with your server.
Regarding sustainability: We are not evolved to work for hours in the same position in front of a computer. Know when to take breaks, stretch, and try to focus as often as possible at distant objects. Hopefully this will help to maintain proper eyesight long enough until neuronal interfaces are on the market.

James Watson is sequencend

2007-06-01T10:25:00.000+02:00

EN: The next step to the personal genome: Yesterday James Watson, one of the discoverers of the DNA structure, got the sequence of his genome. It was sequenced by 454 in two month and cost less than $1 Million. Watson will make parts of his genome public soon.

More information can be found in the press release.

[via Technology Review]

Today is World No Tobacco Day

2007-05-31T07:00:00.000+02:00

EN:

You can find information at the WHOs World No Tobacco Day page.

German Open Access information platform

2007-05-30T14:08:00.000+02:00

EN: open-access.net is a new platform with the aim to spread information and give advice about Open Access with a focus on the German scientific community. It is funded by the German Research Foundation.

[Via netzpolitik.org]

9th International EMBL PhD Student Symposium

2007-05-28T11:31:00.000+02:00

EN: If you are a PhD student in life sciences the 9th International EMBL PhD Student Symposium might be the right place for you to listen to stimulating talks from many different fields and meet other young scientist. The topic will be "Patterns in Biology - Organisation of Life in Space and Time". It will take place from the 25th to 27th October, 2007 in Heidelberg, Germany. As it is well funded all/most of the expenses of the selected participants are usually reimbursed.

Pac-man phylogenetic tree

2007-05-24T10:20:00.000+02:00

EN: Inspired by the pac-man pie chart I created a pac-man phylogenetic tree using iTOL.

This
work is licensed under a
Creative Commons Attribution-Share Alike 3.0 License.

Pimp my Genome - Google Tech Talk

2007-05-08T12:43:00.000+02:00

EN: Andrew Hessel gave a cool Tech Talk at Google called "Pimp my Genome! The Mainstreaming of Digital Genetic Engineering". It is an introduction for non-biologists (well, not only) to Synthetic Biology and Open Source Biology. I have not stumbled over iGem before this talk, which looks quite interesting.

OpenBSD 4.1 released

2007-05-01T23:50:00.000+02:00

EN: Puffy Baba arrived. Our favorite operating system OpenBSD is now available in version 4.1. To see what's new check out the release notes.

Running out of oil

2007-05-01T14:10:00.000+02:00

EN: What would happen if we run out of oil today? World Without Oil, an alternate reality game, simulated this scenario. Different online media like blogs, podcast and videos are used to create this made-up reality and draw a picture of the peak oil situation. Hopefully it stimulates thoughts about the topic and real action, too.

[vie O'Reilly Radar]

Alternative machine-interfaces

2007-04-27T12:05:00.000+02:00

EN: If you sitting in front of a computer keyboard and mouse usually are the interfaces to communicate with the machine. On mobile phones and PDAs the data input it is more tricky. A recent Google Tech Talk shows a cool solution: Dasher. It is hard to describe the interface, but it feels like browsing through the text you want to enter. It has a probabilistic language model under the hood to make this possible. With this Java applet you can test the concept without installing Dasher locally.

Chinese and other languages with many symbols are supported, too. For disabled people Dasher can be a good solution for communicating.

Although the basic implementation is already some years old, there are new features to add. The video shows how to control it just with head, eyeball or breathing muscles movements. As the Wii seems to inspire cell phone producers to build in senors for motion and rotation the tilting of a handheld device could be used to control Dasher.

Some link I wanted to post already for a while and that fit into that topic: Liquid browsing for displaying and browsing multiparametric data and Octomatics, a very intuitive way of displaying numbers and calculating with them.

Wiki paper - an experiment

2007-04-25T13:25:00.000+02:00

EN: Kevin Kelly proposed in the article Speculation of the Future of Science wikis as a tool for collaboratively creating scientific articles that will constantly grow. Maybe this is a further step into that direction: As Jean-Claude Bradley announced on Useful Chemistry, he has started an experiment in which he uses an open wiki to write a publication on the Uki reaction. He hopes the way of writing will not hamper the acceptance of the final paper by a publisher.

After my presentation at the Allen Press Emerging Trends in Scholarly Publishing Seminar a seminar participant who is working for a publishing company told me what he sees in wikis: For him not the the collaboration is in the focus, but the version control system. In his company a paper was accepted once but after some month the authors wanted to change/add a little part, which was not possible.

Today these little but interesting pieces that are not worth an own publication might be lost. The usage of wikis for publications could save them. When citing such wiki articles the version is an essential part of the citation.

Mal langsam, Herr Innenminister

2007-04-19T20:24:00.000+02:00

DE: Mann, in letzter Zeit kommt man einfach nicht mehr hinterher mit der Bloggerei, wenn es um Überwachung von Seiten Vater Staat geht. Unser ~~Überwachungs~~Innenminister Schäuble hat montan einen Kreativitätsschub wie ein junger Picasso. Die Jungs von dataloo sind daraufhin ebenfalls kreativ geworden und haben ein Stasi 2.0 Bild zusammengebastelt.

EN: Hmm, no time to explain all this in english. Our current Interior Minister goes crazy and thinks loudly about a lot of surveillance... read more at these english pages to get the background.

(Dank an Michael für den Link!)

Report - Emerging Trends in Scholarly Publishing - Update

2007-04-13T04:02:00.000+02:00

EN: Ted Freeman from Allen Press invited me to give a talk (slides) at the 2007 Allen Press Emerging Trends in Scholarly Publishing Seminar in Washington (D.C.). It was a very stimulating meeting and I will try to give a small report on some of the contributions. The foci of the talks might be in some cases different than the points I mention, but the slides of all talks will be online soon so you might can figure them out for yourself.

Our session called With a Little Help From My Friends: Online Scholarship 2.0 was started with an interesting talk by Richard Akerman (he will also blog about the meeting, so maybe we will complement each other). Some of his messages were that if publishers don't give the platform for communities those will be built by the communities themselves. In his opinion open peer review doesn't scale well. He advised the publishers to make more use of semantic web technologies to make it easier for the readers to handle the articles. Josh Greenberg presented Zotero, a Firefox extension that helps to manage research sources. There will soon be (summer of this year) a server set up to share Zotero content with others. Also the API will be improved soon. Josh hopes that in future there will be more meta data added by the content providers so that less reverse engineering has to be done. Dean Giustini showed the impact of Web 2.0 on the medical world and mentioned examples like Ask Dr Wiki. I gave an introduction to wikis and their application is science, after that I discussed the experiences of the First EMBL online PhD Symposium.

The keynote was given by Jaron Lanier who is generally quite skeptical regarding the Web 2.0 paradigms (see e.g. his article Digital Maoism). For me personally it was sometimes hard to follow his line of thought as he jumped a lot and mixed many different, unconventional ideas. I guess that is the way a visionary has to think :). In my opinion the bottom line was that the anonymity of the web brings out the worst in people. The tendency to bad behavior was there before, but the web just enables this more efficiently. So complete open systems might not be the solution for things like peer reviewing. Hmm, I think that there were many other points here that I don't remember properly.

From the session Here, There, and Everywhere: The Great Promise of Research Data Commons I would like to mention John Wilbanks' talk who introduced us to Science Commons. He stressed that delayed data publishing blocks the whole process of science that takes place later in the pipeline and he encouraged publishing data as soon as possible to increase the speed of research. In his opinion scientific literature should also be treated as a scientific data source and should be made available as completely and accessibly as possible. This would increase the power of data mining enormously.

The third session We Can Work It Out: Peer Review, Dynamic Documents and the Wisdom of Crowds was a panel discussion chaired by Irv Rockwood with Jaron Lanier, Chris Surridge and David Baldwin. On one side David defended the classical peer review process, on the other side Chris, managing editor of PloS ONE, tried to sell the advantages of the open peer review approach.One point he especially mentioned that I wasn't aware of before: reviewing articles consumes a lot of researcher's time. As many journals are very proud of their rejection rate, a lot of man power is wasted when scientists submit the same paper from the top down through the prestige hierarchy of journals. If journals would somehow exchange the comments of referees quite some labor could be saved. But this is not the case.

This was just a quick overview of the impression I got. I am a little bit jet lagged so maybe I will improve this posting later or will post separately about some of the points. As mentioned, keep an eye on Richard's blog as he will report about the meeting, too. If anybody thinks I got something wrong please post a comment.

Update: As Chris Surridge noticed the talk slides and videos of some parts of the seminar are online now.

Lack of water

2007-04-04T13:00:00.000+02:00

EN: The lack of water is already a major problem in certain areas of the world and as the world's population and living standards increase, the situation will aggravate. An interview in the ZEIT (german) with the CEO and president of the advisory board of Nestlé Peter Brabeck-Letmathe gives more insight into that topic. Brabeck-Letmathe explains that water should be considered as a fossil resource and why it does not make sense in many parts of the world to produce biofuels. The reason for this is that the crops necessary to produce biofuels require the water (and other resources) that would otherwise be used to grow food crops. It is mentioned that agriculture consumes 93% of all fresh water used and that one vegetable calorie needs around 50 liters in production while one animal calorie needs 500 liters. Brabeck-Letmathe proposes less wasteful technologies, genetic engineering and higher water prices to improve the situation.

I assume a reduced consumption of animal products and the industrial usage of organisms that naturally uses less water would also help. Algae like Spirulina might be candidates as they require less water than common crops. If you have a better/newer/contradicting source please let me know. More proposals?

R.i.P Paul Watzlawick

2007-04-03T08:28:00.000+02:00

EN: Paul Watzlawick, mostly famous for his communication theories (e.g. one cannot not communicate), died at the 31st of March, 2007. I enjoyed reading some of his books (The Pursuit of Unhappiness is highly recommended) as he had a wonderful, humorous way of communicating his thoughts.

Waiting for WikiProteins

2007-03-30T11:07:00.000+02:00

EN: I am asking myself when WikiProfessionals will launch WikiProteins. In a news post [1] ( alternatively check this ars technica article) it was claimed to be online in March 2007. At the moment the website only shows the demo video of the protein annotation wiki. It will have strong Semantic Web functionality under the hood and will be followed by similar wikis like WikiAuthors, WikiChemicals and WikiClinical. Well, that's the plan at least.

[1] Key biology databases go wiki, Nature 445, 691 (15 February 2007) | doi:10.1038/445691a; Published online 14 February 2007

23C3 media online

2007-03-27T16:44:00.000+02:00

EN: Quick link - As announced the video and audio files of the 23rd Chaos Communication Congress (23C3) are online now. Same for the official proceedings.

Citizendium launched

2007-03-26T15:46:00.000+02:00

EN: The Citizentdium, a Wikipedia forked that was announced on the Wizard of the OS 4, is finally online. It is based on contributions of selected, known by name experts. This means the mechanism for generating high quality articles is quite close to the one of Scholarpedia ("the free peer reviewed encyclopedia written by scholars"). Not sure if they will attract enough manpower to really compete with Wikipedia.

The real danger of drugs

2007-03-23T14:39:00.000+01:00

EN: Just a short notice. David Nutt et al. published an article [1] in The Lancet with a wholistic view on the danger of drugs including physical harm, addiction potential, and social effects. Bottom line is that some legally available substances like alcohol and tabaco are more dangerous than illegal ones like cannabis, LSD, ecstasy, if you use the proposed scale for ranking.

[1] Development of a rational scale to assess the harm of drugs of potential misuse, David Nutt, Leslie A King, William Saulsbury, Colin Blakemore, The Lancet, 2007; 369:1047-1053

Google improves privacy protection

2007-03-15T08:35:00.000+01:00

EN: Google announced a change of their privacy policy. Some months ago I mentioned a posting by fred's house with a proposal of a service named "Google Data Privacy (GDP)" (Pedro liked that idea, too). Google seems now to be aware of the community's wish of better privacy protection and will adapt their systems in the near future. From the announcement:

Unless we're legally required to retain log data for longer, we will anonymize our server logs after a limited period of time. When we implement this policy change in the coming months, we will continue to keep server log data (so that we can improve Google's services and protect them from security and other abuses)—but will make this data much more anonymous, so that it can no longer be identified with individual users, after 18-24 months.

The first steps into the right direction. Thanks Google!

The Sorcerer II Global Ocean Sampling Expedition

2007-03-13T09:44:00.000+01:00

EN: Even if you are usually not interested in Metagenomics - the pure size of the Global Ocean Sampling Expedition results is impressive. The Craig Venter Institute published a collection of papers (and other media) about that was expected already for a long time ago. Seems like this huge amount of data and other technical issues were hard to handle. But now the first part of the the ocean sequencing trip analysis is out.

These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp).

The number of interesting biological observations and novelties is lower than expected for such a giant project (Roland once mentioned this discrepancy for metagenomic studies) but there is still much potential in the data for further analyses.

Update: The video of the press conference is online now. Pedro followed it live and blogged some comments. This publication brought up again some voices questioning the (expensive) general metagenomic method. Working with this noisy data I can tell that it is often quite a pain. But to get the big image even if it would just show us we have seen already everything we have to go that way. Hopefully improving technologies - I once mentioned single-cell sequencing combined with microfluid separation systems - will make it easier for us to explore the unknown wold out there.

Freebase - semantic web for the community

2007-03-10T19:36:00.000+01:00

EN: This looks very promising - Freebase combines the Web 2.0 (community based data generation/maintenance) and semantic web (using meta data for making information better "understandable" for machines) philosophy in one application. It's the first child of the company Metaweb (nomen est omen) and will be Creative Commons licensed (nice!). Tim O'Really wrote a helpful introduction (that was bashed because of an "outdated view" about the semantic web). bbgm mentioned briefly the potential for science. At the moment you have to be invited to sign in, however you should keep an eye on it.

Update: Freebase has now a blog called Freebasics.

Secured computers - no SPAM

2007-03-06T14:10:00.000+01:00

EN: O'Reilly Radar has a interesting discussion about the technologies to fight e-mail SPAM. But I am not sure if fighting SPAM alone makes the world a better place. SPAM is a symptom that shows that (1) there are too many unsecured computers connected to the net and (2) there is enough criminal energy out there that makes use of them. If the SPAM problem is solved somehow (some proposals are mentioned in the article) both points aren't solved. It might lead to an increase of other computer crimes like blackmailing companies with DDOS attacks using botnets. Crime is partly the result of missing options of legal work for the people committing the crimes, but well ... that's hard to solve. Increasing general security of computers is easier. Unfortunately the focus in most companies/communities seems to be on implementing as much features as possible while increasing complexity and reducing security.

Using an unsecured machine in the net is like driving drunk ... you don't endager only yourself but also others. My personal solution is using OpenBSD (but sure there are others ;)).

Chaos Communication Camp 2007

2007-02-23T13:11:00.000+01:00

EN: For those who haven't heard about it so far: There will be a Chaos Communication Camp this year which will takes place from the 8th - 12th August in Finowfurt (close to Berlin). If you are interested in Open Source, IT, hacking, art, knowledge distribution, science and the whole world this might be the right place for you to find more people of your kind. A lot of well known projects will be there and usually the program offers a lot of interesting talks. To get an impression how the camps look like you can watch a documentary video (around 20 mins) of the camp in 2003.

Update: The CCC event blog announced the call for participation which includes a list of the topics on the camp.