Remotely plotting with IGV, even without X11 server

IGV is a convenient program to visualize data and results from next-generation sequencing experiments, be it raw BAM files or genotype VCFs.

In order to facilitate inspection of hundreds or even thousands of sites, IGV has a built-in batch mode. A batch control file can look as simple as this:

new

genome /data/ref/hs37.fasta
load /data/patient1.bam
load /data/patient2.bam

goto 1:28000000
snapshot /path/to/file.png
...

(Reference genome and BAMs should of course be indexed). Executing such a batch file is also straightforward:

/path/to/igv.sh --batch /path/to/batch/file

Now this will work fine if the computer you are executing this command on can provide a graphical user interface (GUI): IGV requires a GUI, even in batch mode.

This generally doesn't case problems under Windows or on Linux and Mac workstations. Linux servers, however, do not always readily provide an X server (and of course you would want to plot your 10,000 positions on your server rather than on your workstation).

So what to do if your server does not provide an X11 server? There are at least two possibilities:

• Use SSH to tunnel the X11 communication to your local workstation, and run a local X11 server.
  
  Under Windows, for example, start by installing the X11 server Xming. I assume that you use Putty for SSH. Open the "Putty Configuration" dialogue, go to Connection -> SSH -> X11, activate "Enable X11 forwarding". Now start Xming, establish the SSH session with Putty and X11 should work. For a first test, try to start the program xterm. A terminal window should become visible on your Windows desktop.
  
  IGV should work under this setup. However, latency can become a bit of a problem - IGV really insists on sending the data to properly display a particular position to your local X11 server before moving on to the next position.
  
  This is why I generally try to avoid this situation, unless I just want to quickly manually check one or two positions.
  
• Install an X11 server that does not care whether any real display hardware is available.
  
  Xvfb, for example, does this job: it provides a virtual display which IGV will happily accept as a basis for batch-mode plotting.
  
  It should usually be possible to install a precompiled Xvfb package for your distribution.
  
  If you are lacking sufficient privileges, it is also straightforward to install a local version.
  
  Xvfb is part of the XFree86 project, so go to http://ftp.xfree86.org/pub/XFree86/4.8.0/binaries/, navigate into the appropriate subfolder (depending on your distribution and LIBC version) and download Xvfb.tgz and Xfnts.tgz.
  
  In my case, for example, I had to download
  
  ftp://ftp.xfree86.org/pub/XFree86/4.8.0/binaries/Linux-x86_64-glibc23/Xfnts.tgz
  
  and
  
  ftp://ftp.xfree86.org/pub/XFree86/4.8.0/binaries/Linux-x86_64-glibc23/Xvfb.tgz
  
  Now do a tar -xvzf on both files. (Sources are, of course, also available, but installation is perhaps a bit more cumbersome. Refer to XFree86 for more details).
  
  Let's assume that you extracted the Xfnts file into /path/to/lib/X11/fonts/ (the latter part of the path is determined by the tar file), and the Xvfb into /path/to/xvfb.
  
  Navigate into /path/to/xvfb, and type
  
  ./Xvfb :0 -nolisten tcp -fp /path/to/lib/X11/fonts/misc
  
  (Note the added 'misc' for the -fp parameter!).
  
  You might receive a complaint about lacking security data, which we are happily going to ignore for the moment. This nowithstanding, the program should continue execution without terminating.
  
  You can now start the terminal server in the background, typing
  
  ./Xvfb :0 -nolisten tcp -fp /path/to/lib/X11/fonts/misc &
  
  The last remaining task is to tell IGV that it is to utilize display port :0. In order to do so, simply type
  
  DISPLAY=:0
  
  immediately before starting IGV, e.g. with
  
  /path/to/igv.sh --batch /path/to/batch/file
  
  ... and enjoy high-speed plotting on your server!

World-class MBA in Dusseldorf

The Economist, our favourite magazine, has produced a worlwide ranking of Executive MBA programmes - and the Kellogg-WHU program comes seventh.

This is nice for a couple of reasons.

The WHU's good position gives some international credibility to at least one German business school, finally. (I had long held the WHU in high regard, but always assumed, maybe wrongly, that it would not be a match for the top international schools. Perhaps this is changing now).

Second, a substantial part of the German arm of the course takes place in Dusseldorf, on the newly acquired Schwanenhöfe Campus of the WHU. The Schwanenhöfe is a former industrial area, now redeveloped with a strong cluster focus on high-value services, education and innovation. It is located in the hip Flingern district, home to many nice cafes, bars and galleries.

StartupDorf

A new website which aims at connecting entrepreneurs in the Dusseldorf area has gone online recently, largely unnoticed: StartupDorf.

At the moment, the functionality is limited to a mashup which displays startups in the area on a map of Dusseldorf.

This idea is of course not novel: There are already quite a couple of sites (and maybe this, although not limited to startups) trying to maintain a catalogue of interesting startups in the area (not to forget this wonderful blog post, of course).

However, none of these existing sites are complete, and StartupDorf seems to offer quite a nice list. More community can clearly do no harm. And, finally, I love the name StartupDorf and the way their logo plays with the city's official new logo.

"Tech" companies

 Apparently, "tech" has become synonymous with web startups.

Frankly, I think that this is bullshit.

Admittedly, successful web startups sometimes require a fair amount of technological knowledge and expertise. Is is not for nothing that Google hires some of the best software engineers, and some of the scientific research and engineering coming out of Google is amazing. The same applies to Facebook.

However, in most cases, the real technological challenges only come with success. Most web startup business models are easily bootstrapped. And the average retail web business, even if successful, will hardly venture into unexplored technological areas. Recommendation engines? User clustering? Get a copy of Machine Learning for Hackers or Programming Collective Intelligence and get over it - these things have been solved, at least up to the second or third approximation (and check out the Netflix Prize for the fourth and fifth).

"High tech", or just "technology", in their true meanings, comprise much more than just web technology. What about gene sequencing technologies, biocatalysis, solar cells, power transmission, electric cars, flying into space?

Of course these companies qualify as "high tech", much more so than many companies actually labelled as "tech".

I would like to suggest that the true tech companies are those with business models built on a fundamental extension, or improvement, of existing technology.

So why is it that the web sector has so successfully claimed the label "tech"? I don't have an answer to this question -- but I would like to note that there is a vested interest of web startups, and indeed web startup clusters, in suggesting that the sets of "technology startups" and "web startups" are mostly identical.

So why is it that the public (replace with"many journalists"/"bloggers", if desired) has (have) accepted this confusion of terms? Two factors, in my opinion, are

• Technological complexity. It is much more complicated to evaluate the prospects of a true tech company than the business model of an arbitary pseudo-tech online retailer.
  
  True tech investment often requires a bet on the odds of success of an unproven technology. You better have some solid technical understanding if you want to be successful in these bets.
• Scalability, consumer-centric. A successful online shoe retailer can easily scale to millions of customers (or so the thinking goes). If this works out, there are going to be huge returns for the investors.
  
  For true tech companies, things are often not that clear. Scalability arguments often assume a certain uniformity on the customer side of things. High-tech customers, however, do not tend to be particularly uniform in their needs and desires.
  
  (Potentially, however, there are huge returns for investors too, partly driven by the potential monopolization of ideas due to patents.)

In summary, web technology startups promise easier returns than true technology startups, and simplicity is a big driving force behind reporting and perception. There are not many people, apart from those who already know better, who have an interest in pointing out that web tech != tech.

Note that I am not in any way against web startups - rather to the contrary. However, the (primarily societal and secondarily financial)  returns from tackling a big problem - such as cancer, renewables, etc. - are probably much bigger than the returns of tackling a small problem - such as creating an efficient online marketplace for shoes.

We should all keep on trying to make small improvements - such as efficient online markets for everyday goods. However, this should not prevent us from focusing on the more important stuff at times.

Radioactivity, guys - stay tuned!

Interesting Dusseldorf tech companies / startups

Not all German tech is in Berlin. The following list is just based on sampling the news and some Google searching - if something is missing, please let me know. I do, however, not aspire to be complete - I am only going to list things which I find interesting.

Another criterion for inclusion is that there is some (or seems to be) tech development happening in Dusseldorf. So R&D, research and programming qualify, whereas a merely sales-orientied European headquarter (of which there are plenty in Dusseldorf) doesn't count. Sometimes I am not sure, and this will then be mentioned.

Big success stories

• Trivago - majority stake acquired for $632M by Expedia. Easily the biggest German tech buy-out in 2012.
• Qiagen - not really a recent one, but still the only large German biotech company (well, 'large' only by German standards, but still with a market capitalisation of a couple of billion Euros). Slightly strategically troubled by the emergence of 'next-generation' sequencing technologies, of which it now (after acquiring Intelligent Bio-Systems and their sequencing technology) hopes to profit more strongly. Let's see how this goes...

Community

• 1stMOVER - Germany's first incubator focusing on mobile apps and development. Just set up a couple of months ago (as of March 2013), so a bit too early to judge.
• K-LAN - (Co-)working space with an inclination for tech and mobile apps. Home to 1stMOVER, and quite close to the Vodafone Germany campus in Oberkassel.
• GarageBilk - another notable co-working space in another part of town, maybe not so much focused on (rapidly scalable) tech. coworkingloft also gets mentioned, for the nice views.
• Business with Soul -  Community event including talks and drinks. Seems to be nice but never managed to attend one.
• StartupDorf - is going to be an online community for startups in Dusseldorf. At the moment, however, it only offers a map of startups in town.

Aspiring

• Auxmoney.com - consumer-to-consumer lending, apparently the German market leader. Recently closed a $12M round with Union Square Ventures and Index Ventures.
• Evocatel - biocatalysis and custom-made enyzmes. Just completed a round B of EUR 3.5M.
• Rheinfabrik - company behind the reasonably successful time-management app Eisenhower.  One of the founders, Andreas Kwiatkowski, also has an interesting blog.

Interesting novel

• Emmas Enkel - the traditional German corner store ("Tante Emma Laden") beamed into the 21st century, online shop included. I am not at all convinced that this model will work, but I am going to watch quite closely!
• Springlane.de - apparently an online shop / magazine mashup, all about cooking and culinary quality lifestyle. According to the founders, already team of >= 40 people.  
• Just Spices - create your own spice cocktail.

Interesting established

Some established companies, included purely on subjective judgement.

• E.ON Global Commotidies - the energy trading arm of E.ON, once (maybe before the Energiewende) the world's largest invester-held utility (or eletrical utility? People cite multiple slightly different versions of this claim, but E.ON was - and still is - big).
  

The mobile tech cluster
Dusseldorf is home to the (German) headquarters of a substantial fraction of mobile companies  (some of those are actually home-grown - Vodafone Germany was, for example, created from the take-over of Mannesmann of Dusseldorf, which at this point was the second-largest mobile network operator in Germany).

The city markets this under the Mobile Capital brand. The website also has a list of the companies present in Dusseldorf, which I am not going to reproduce here.

Why Kraftwerk are (still) amazing

1. The albums have a theme, but no message.
2. The themes are futuristic, realistic, and important.
3. The song is the theme - the music is the description.
4. They mix long melodies and short rhythms in the right way.

Notes:

1. It is more important to say what is or will be than what should be (or at least equally important).  Musicians should not aspire to be philosophers. When they try message (or moral), they often sound silly.
   
   (The notable Kraftwerk exception here is of course "Radioactivity", and the message - "Stop Radioactivity" - is certainly well-intentioned and less certainly - philosophically, scientifically - up to their standard).
   
2. (The unity of) Europe, (the influence of) computers, radioactivity (or maybe the importance of physics). Biology and biotechnology do sadly not appear.
   
   Many of these songs have interestingly turned out to be anticipating the future (again, only in a descriptive, not in a normative way). But even from the perspective of a realized future (i.e. now), they are still quite futuristic. Quasars? Still cool. The Man-Machine? Still expected to make its appearance in ca. 50 years' time.
   
3. "Metal on Metal" and "Trans Europe Express"sound like a train travelling through Europe. "We are the robots" sounds like work-singing robots. The music is the essence of the description, and vice versa. (To a limited extent, this also applies to the visuals displayed on concerts).
   
4. Kraftwerk songs have long-running background melodies and short-lived electronic elements that appear and re-appear throughout the song, so carefully mixed that the songs appear hypnotic and are fun to listen to. In the 1970s and 80s, their music (the mere composition of their music) was revolutionary. Even today, "Radioactivity" (in its Minimum-Maximum version) can claim to contain some of the finest electronic tunes ever played.
   
5. And indeed, there is an element of humour to Kraftwerk. Haha.

Dusseldorf Steet Art: Best of 2012

Sebastian from Streetartmag has posted his 77 personal favourites from 2012 - check it out!

Artist: Naegeli. Photo credits: Sebastian Hartmann