Samuel's Tech Blog

Interesting stuff: A new Program in Computational & Systems Biology in Uppsala. I attended the inaugural symposium, and these are some highlights.

The program consists of four groups/labs in Uppsala, working in the fields of bioinformatics, computational biology and/or systems biology. The symposium consisted of talks from each of the four group leaders.

Ok, so on to the talks

Johan Åqvist started off and presented some work they are doing on the ribosome, pppGpp binding etc. The Åquist group is one of two groups working in molecular dynamics, the other group being the one of David van der Spoel, who continued and presented their work on simulating some rather big systems (in terms of no of atoms), like the melting of ice and a full tobacco necrosis virus (approx. 1 million atoms). Quite nice.

Then Johan Elf, whose group is the Systems Biology one of the four, presented their work. They use single molecule imaging(!) to discern the dynamics of transcription factors binding to DNA (among other things) by following the molecules over a time-span, resulting in nice movies of how the molecules move in the cell. Fun! :). It is promosing too, since it gives hope that one day it will be possible to do a bit more full-scale simulations of cellular processes (which requires high quality data on binding dynamics, which is mostly lacking today).

Finally, prof. Komorowski presented their work on feature selection based solely on the data (instead of "guessing in the air" (don't know how to say that in english!)), which was quite interesting as well IMO. As Komorowski also concluded, there is another distinction between the four groups apart from one being in the "systems biology" field (Elf's) and the others' in the computational biology, that Komorowski's bioinformatics group is working in the "discrete world" whereas the others are working in the "continuous world". These two worlds, as Komorowski mentioned, has not yet been bridged in any final way.

Still there are naturally a lot of intersections between the fields of these groups anyway and most probably it will be fruitful with a bit more interactions now through the common program and symposiums.

Congratulations Uppsala, and wishing the people involved all the best with the new program!

Some thoughts on Systems biology

I think Systems Biology is interesting, since it seems that now finally people realize they have to treat biological systems in a more integrated way - that "the whole is more than the sum of it's part". In practice, what is done a lot is that the biological systems are treated as engineered systems (which makes a lot of sense IMO) which has lead people to apply the "old" highly developed fields of engineering (like control theory, mechanics, dynamics, network/circuit theory etc.) to the biological systems, indeed yielding a lot of fruitful results. (The engineered solutions in the biological systems for example far outperform human made ones time after time. Take for example the amazingly robust biological control regulators for maintaining stable circadian (24h) oscillations in the midst of sometimes very noisy in-signals, aso aso.).