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.

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.)

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.

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.

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!

Let's try to keep some privacy

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 2 - DNA hacking and web security ooopses

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:

Google teaches how to enhance privacy

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 ...

Wikipedia license update

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).

Miro - open internet tv

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

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.

Semantic web logos

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





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

Listen to Wikipedia

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

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.

Spreading the spirit of openness

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

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 - 3 - BookCrossing

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!

No support of Nature Precedings by Connotea

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.

Nature Precedings

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.