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.

Google integrates Scholar into main page

I don't know if it's just me (sitting inside a research institution), but when I search for something that returns a paper, I get info from Google Scholar:

(See also the complete screenshot with notes on Flickr.) However, the order of the results is different: Google Scholar seems to weight by citations, Google by page rank.

ISMB 2008: "Career Paths in Bioinformatics and Computational Biology"

A panel discussion about "Career Paths in Bioinformatics and Computational Biology" was part of Friday's Student Council Symposium during ISMB. The four panelists were from academia: Philip E. Bourne (group leader at University of California San Diego), Alfonso Valencia (group leader at the Spanish National Research Council), Jong Bhak (director of the Korean BioInformation Center) and Richard Wintle (Assistant Director at The Centre for Applied Genomics). (Only RW had spent a longer time [6 years] in the industry at start-up companies.)

[All quotes are paraphrases based on the notes I took.]

Perhaps unsurprisingly, they couldn't offer real comforting answers to the questions of young researchers: "Isn't there a high chance that at the age of 40 you'll be highly trained and specialized, but without a job?" – "There's no job security in academia anyway; I'm not sure if academia is more competitive than industry" (AV). "After the initial boom in bioinformatics positions, will the fraction of grad students who become PIs approach biology with 5 to 10%?" – "Biology will morph into bioinformatics, so there will be more jobs." (JB)

However, I could take away some positive advice. In short: follow your heart, be passionate about something, don't do what everybody else is doing, start you own sub-field if you have to. From my perspective, this is both reasonable and encouraging. As I enter the last phase of being a PhD student, I begin to wonder how I can combine working in science and caring for my family. I guess I hope by staying motivated and by being effective in what I do I can have a chance to grow in my career and by there for my family. (I think this is a great advantage of computational biology: You can't make gels run faster, so to say, but you can be effective in programming and analyzing data.)

Another good insight was that a lot of basic, technological advances will come from industry in the future. Dr. Bhak cited the example of CPU development: The huge increases in processing power we see today is being implemented at Intel and AMD (although I cannot judge how much they rely on basic research by academia). My addition to this might be that part of bioinformatics will become more of an engineering discipline. So, for people interested in this, there will be a big job market in the future.

Similarly, the panelists expected that every biology lab will have embedded computational biologists in the future. I agree, but I think these will be mostly post-doc (i.e. non-permanent) positions.


Some of the questions and answers in more detail:

What will be the big opportunities in the next five years? The current generation of students will lead the bioinformatics industry, like the previous generation is currently leading in academia (JB). There will be many more embedded bioinformaticians (see above, AV). Hybrid skills (wet-lab and computational biology) will become more important (RW). The greatest opportunities are cross-disciplinary approaches that tackle as much complexity as possible (PB).

To stay motivated, and find out what you want to do: Always follow your heart in career decisions; create your own sub-division if you have to (PB). Don't do something just because it's trendy; what you like to do might change over time (at one point, industry might be appealing, later academia) (RW).

To find your spot in academia: Find influential people (RW). Diversify: try to do something that not everyone else is doing (AV).

Micro-blogging ISMB

As Pablo announced, several people including me are micro-blogging about ISMB on FriendFeed and to a lesser extent on Twitter.

Invoking TextMate from a remote machine

I edit all my script files via TextMate, but they live on remote drives (mounted via sshfs). I'm always logged in to the remote machines to run scripts etc. Usually I'll open remote files via Quicksilver, but when I create a new file this isn't an option yet and so it's tedious. Anyway, I've cooked up a quick script (with some help) to open TextMate from a remote machine.

Try it, YMMV:

#!/bin/bash

cd $(dirname $1)

PWD=`/bin/pwd`

BASENAME=$(basename $1)

ssh pasadena "osascript -e \
'tell app \"Terminal\" to do \
shell script \"/usr/local/bin/mate /Volumes/emil$PWD/$BASENAME\"'" >& /dev/null &

pasadena = name of my Mac OS X machine
/Volumes/emil = sshfs mount point

Update: I removed the "-w" option (I didn't want TextMate to wait for the file to be closed) and redirected all the garbage to /dev/null.

Update 2: Support arbitrary (i.e. also absolute) paths.

Update 3: this is broken on Snow Leopard :(

Update 4: Here's a workaround, although it's a bit ugly as you need to invoke sudo.

Unison is great for syncing files

I've already tagged Unison, but I find it so very useful that I just have to write this short blog post to praise it. If you work on two computers and want to keep a set of files in sync, you should try Unison. It's open-source, cross-platform, and the newest version works great on Mac OS X (fink's version was broken when I tried it).

In contrast to other syncing or backup programs, Unison is bidirectional. For example, I just edited some slides for a talk I'm giving tomorrow on my laptop, while I made some changes in the report on my main computer. Then I ran Unison, and it sent the files in the appropriate direction.

Minor gripe: I've tried to sync a huge folder with it and it failed (20 GB / 8600 files+folders), but it works fine and is fast for my normal syncing (350 MB / 1200 files+folders). However, in the first case I really wanted to make a backup, so I just used SuperDuper for this one folder.