Our institute now has an official postdoctoral association. The opening lecture took place last night. Reinhard Fässler, the Institute's managing director, gave a talk on the situation of the postdocs in the Max Planck Society (good news: there will be formal group leader positions; bad news: there will be no career positions at Max Planck except for department heads and maybe a single person per department; I will write a bit more about this later.)

Our homepage is still rudimentary, but as soon as I have access to the new content management system, we will try to flesh it out.

I am just back from a trip to the US, talking to quite a few people in image processing and computational biology. The one thing I noticed that is now markedly different between research in the US and in Europe is that the US is now heavily investing in platform research. The US has a national program, mostly by the NIH, the DoE and to a smaller extent the NSF, to just do research. Money is spent both on actual research projects, many of them aimed at medical research, and on establishing platform technologies to support this research. Quite a lot of the people I talked to in the US were paid by the National Center for Research Resources (NCRR) of the NIH. This organization establishes centers at universities and research institutions which build and provide tools to other researchers. For a computational biologist like me, this is natural; after all, most of our work is creating tools for the colleagues in the wet lab.

Unfortunately, Europe is not doing that. The biggest difference is that most funding here is tied to training (both of students and postdocs) and community goals such as enhancing mobility, and these grants are usually short-term and tied to a certain stage in your career. Beyond that, it gets very difficult. The result is that Europe is indeed producing excellent Ph.D.s and postdocs, who then do basic research in the US, the UK, or Scandinavia (I think Finland has a significantly larger bioinformatics community than Germany).

One result of having a postdoctoral association is that we got informed (at last) of what our Institute is planning for us in the future. And it is not good.

If you do not know the German research ecosystem, the Max Planck Institutes, together with the National Research Centers (Großforschungseinrichtungen), are the National basic research organizations. Since the German universities are perpetually cash-starved, notoriously resistant to reform, and dependent on capricious state governments, who provide their funding, the MPG (as the society running the Institutes is known) is the major organization in Germany for large-scale basic research.

Unfortunately, as we now have learned, there will probably only a very limited number of permanent research positions in the Institute in the future - on the order of one per department (not including the Director). Instead, the Institute will focus on employing Junior Research Groups for a limited period under the assumption that the leaders of these groups will proceed after around five to six years to a position at one of the Universities.

While the establishment of formal junior research groups is nice for those just finishing their Ph.D. or their first postdoc, it still means that a large number of permanent research positions are being eliminated in this way.

A few years ago, when I worked in computational particle physics at MIT, Albrecht Wagner, the head of DESY in Hamburg, gave a talk on the linear collider project. At the very end, he showed a few slides about biological applications by turning one of the two accelerators into a free-electron laser, producing extremely intense X-ray radiation that could, in theory, be used to image single molecules in the very short timespan before they disintegrate in the beam. It was obvious that this would be a revolutionary application, but it was obvious that they would not highlight this too much as this revolutionary device would still be so much cheaper than the linear collider.

By now, the linear collider project in Hamburg has all but died, DESY will shut down its particle physics program at HERA (for which I wrote part of my Ph.D. thesis) this year, and physics with photons is the new thing. And indeed, in this month's edition of Nature Physics, Chapman et. al. report on first images they have taken with the experimental FLASH facility. The resolution is still in the area of around 60nm, but they were able to record and reconstruct a 3D image (basically a hologram) using a 25fs X-ray pulse. They say, this "points" to the possibility of imaging non-crystalline and non-periodic objects at atomic resolution - basically the holy grail for molecular imaging.

Salon.com has an article on "Dreaming in code", a new "anthropological" book (Engineers dans la brume) on how a a team develops an large piece of software over a period of four years. When I read the review, ot immediately reminded my of "The Soul of a New Machine", Tracy Kidder's book about an engineering team at Data General in the late 70s. The sad thing is that the hardware engineers did not have to contend with people on their teams whose technical training consisted of reading "Visual Basic for Dummies" and re-installing Windows a dozen times. Okay, I am dramatizing, a lot of the people I see "writing programs" unfortunately never read any programming book...

Nature Methods just published a "clarification" on their policies about software used in new methods or processes. It basically says they will require that custom-made software components which are of significant importance to the reported results must be made available to the public in a suitable form, and that this may best be achieved by using an open-source development model.

The most revolutionary part of this small article is in the remarks about the inherent advantages of the open-source model in fields - such as microscopy - in which users will often need to customize software. Open-source software is not so much a hobbyist approach to computing, as some people may think, but a very deliberate and professional decision about licensing work that depends on other people works. If I invest time in extending and customizing (or even learning how to install and maintain) a piece of proprietary software, my investment becomes hostage to the owner of this software. If he changes it (or even fails to adapt to new environments), my investment might be lost.

In our lab, the typical examples are MATLAB and Amira on the proprietary side, and Python/Scipy, Chimera, and VTK on the open side. Both MATLAB and Amira are significantly lagging in development (MATLAB has a horrible C interface and nothing for C++, while Amira still uses Tcl as a scripting language and does not expose enough API to add significant functionality).

One ironical thing that shows the progress of the open-source development model is that there are probably more programmers being paid to extend the open software than the commercial software, as both Chimera, Python/Scipy, and VTK are heavily supported by US research institutions (Chimera is being developed through NIH funding, while Python tools have been developed by the Space Telescope Science Institute and the Computational Crystallography Initiative at LBNL, and VTK is prominently used at LANL supercomputers).