Keine Experimente!

Lange habe ich diese Idee mit mir herumgetragen, jetzt habe ich sie dank Deutschem Historischen Museum und Vector Magic in die Tat umgesetzt. Den Vektorisierungs-Look finde ich sogar ziemlich passend.

Sollte der Witz unverstanden bleiben, hier die Auflösung. Andernfalls das ganze als PDF, zum Ausdrucken oder Editierien (statt Bioinformatik kann man ja auch Theoretische Physik favorisieren).

A seminar on Makefiles!

This blog, my tumblelog, and my Twitter stream are littered with examples of my use of Makefiles. So I was very happy to find this blog post about a whole seminar on Makefiles on FriendFeed. Go and check it out, I learned something new!

Want: Auto-adjust laptop fan speed with motion sensor

Someone should really integrate Fan Control with the MacBook's motion sensor. If the computer didn't move for a long time: It's sitting on a desk, so it can run hotter, but be silent. If the computer is being moved around: I have it on my lap, so turn the fan up and keep the case cool.

Meta-blogging to commemorate the creation of a tumblelog

I am posting a meta-blog entry because I just created a mini-blog at Tumblr to supplement my micro-blog at Twitter which in turn was meant to supplement this (hypo?)blog. So, now my online blogging presence fragments into:

1. this blog
2. delicious bookmarks
   
3. Twitter
4. tumblelog for things too long to tweet
   
5. shared items from Google reader
   

...only to be pulled back together at FriendFeed, which is actually where the discussion happens. Interesting. (Oh, and this is so true. Now, do I re-tweet it or post the quote on Tumblr?)

4th German Conference on Chemoinformatics: ChEMBL

The talks of the first full day of the 4th German Conference on Chemoinformatics are over. Most interesting for me was Christoph Steinbeck's talk about the recently announced data acquired by the EBI. The database will be called "ChEMBL". There will be a monthly update cycle, so the acquisition does not only capture the current state, but the database is going to be extended. There are three parts (although they'll be combined eventually):

• "DrugStore": interactions for 1500 drugs. Christoph says that he doesn't expect this to go much beyond what's already publicly available in DrugBank et al. today.
• "CandiStore": 15,000 clinical leads
• "StARLite": 500,000 medical chemistry leads. This is where most of the novelty (in terms of public data) lies. For this part, there are >5500 annotated targets, >3500 of which are proteins (the rest is e.g. tissues), and 2 million experimental bioactivities. The database contains bidirectional links to the literature on synthetic routes and assays for the ligands and descriptions of the targets.

The data will be first made available as database dumps, more user-friendly interfaces will be added later.

Two URLs of interest that I didn't know before: The ChEMBL blog and John Overington's lab homepage.

Other remarks about today will follow when I have a real internet connection (not just 6 kB/s via Bluetooth/GPRS for 9 ct/min) to do some more background research.

Three presentations down, one to go

I just passed my third annual review, which means that thanks to doing my PhD in Europe I should be done soon (caveat). Everything went fine, now I'll still wait for some results to come back from the lab and then I'll write my thesis—but luckily as cumulative thesis.

Lastly, here's the Wordle digest of my report. I guess the main topic of my research clearly shines through.

Web 2.0 killer app: FriendFeed for scientic papers

This post is inspired by Eva's thoughts on getting scientists to adopt Web 2.0 and Cameron's post on making Connotea a killer app for scientists.

Many people have added their CiteULike or Connotea libraries to FriendFeed, so during the day you can see various new papers flow by. Similarly, journal's TOC updates and saved searches on PubMed create a regular stream of possibly interesting papers. Lastly, after a few weeks or months, papers are processed by ISI Web of Science and can be tracked by citation alerts. In the end, you might see the same paper flow by a couple times.

This situation is far from ideal. You see echos of the same paper and papers arrive via multiple channels: RSS, email, web sites. There are far too many potentially interesting papers, so you have to focus your various alerts in order not to be overwhelmed.

My proposal for the killer app is a central place which tracks all of the above items (i.e., friend's libraries, PubMed searches, journal TOC and citation alerts) and integrates with your personal library. Just like in FriendFeed, there should be a way to rate/like a paper ("Faculty of 1,000,000"?), to prioritize the new papers, and to save papers to your library. The most important and difficult feature would be to merge equivalent entries, i.e. a Connotea link to PubMed needs to be merged with the journal TOC alert etc. So when you already identified something as interesting and filed it, you won't be alerted again if it comes in via another channel.

Of course, there should be a non-mandatory way to tag papers, to have groups, and to recommend papers to specific users (like the "for:" tag in delicious.com).

Bonus points: keep track of comments and blog posts of the paper, plus all the extended literature analysis that Cameron proposed.