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.

Mendeley = Mekentosj Papers + Web 2.0 ?

Via Ricardo Vidal: Mendeley seems to be a Windows (plus Mac/Linux) equivalent of Mekentosj Papers (which is Mac OS X only, and has been described as "iTunes for your papers"). In addition to handling your PDFs, it has an online component that allows sharing your papers and other Web 2.0 features (billing itself as "Last.fm for papers").

Here, I'm reviewing the Mac beta version (0.5.6). I am focusing most on the desktop side and compare it to Papers, because I have a working solution in place and I would only switch to Mendeley if the experience is as good as with Papers. (I.e., my main problem is off-line papers management, Web 2.0 features are icing on the cake.)

By Mac standards, the app is quite ugly. Both Mendeley and Papers allow full-text PDF searches, which is important if you want to avoid tagging/categorizing all your papers. Papers can show PDFs in the main window, copy the reference of the paper and email papers. Mendeley in principle can also copy the reference, but special characters are transformed to gibberish in this beta version. Papers allows you to match papers against PubMed, Web of Science etc., while Mendeley only offers to auto-extract often incomplete meta-data. This matching feature is extremely useful as you get all the authorative data from the source, and most often Papers can use the DOI in the PDF to immeadiately give you the correct reference. Update: Mendeley also uses DOIs to retrieve the correct metadata, if available. (Thanks, Victor for your comment.)

The beta version is quite rough, I just had to kill it because I found no way to close the "about" window. Extraction of meta-data and references doesn't always work, but this might be more of a problem of the information that's stored in the PDFs.

Of course, once there's a critical mass of people using Mendeley, there'll be all the Web 2.0 features that Papers doesn't have. Judging from the talk I think they might be trying to do too much: Connotea/CiteULike plus Dopplr plus LinkedIn. For me, a simple way to export new references from Papers to Connotea/CiteULike would be enough. More modularity is better, because it allows you to choose the best tool in each layer.

More info by the Mendely folks: Short demo, a little longer talk.

CiteWeb: Following citations made easy

One good way to keep up with the literature in a field is to track which new papers are citing seminal papers of the field. Each Friday, I get lots of citation alerts from ISI Web of Science, but often enough I see the same paper again and again (citing different papers that are on my watch list). So I set out to write an app that would take ISI's RSS feeds, coalesce them, and give them back to you. For example, in the screenshot one review paper is citing five of my tracked papers:
If you're using citation alerts from Web of Science, then give CiteWeb a try at citeweb.embl.de. If you find a bug, you can either comment here, or grab the source code and fix it. :-)

I started working on this to try out if Google App Engine was useful. It turned out that downloading many items from a remote host leads to time-outs from App Engine, so I ported the app to Django. The source code is released under the MIT License.