Update: it appears that conference domain name http://www.icsb-2008.org/ was not maintained after the conference, so I had to remove all the links to that website (which now appears to be owned by someone not related to ICSB). However, there seems to be a mirror of ICSB-2008 at http://www.gmm.gu.se/groups/icsb08test/.

Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

I took part in almost all the conference events, starting with pre-conference tutorials and finishing with post-conference workshops, and including the Viking Dinner.

On August 22 (the tutorials day), I attended the tutorials by SBW team, Chris Myers (iBioSim), and CellDesigner 4. Out of these, I liked iBioSim tutorial the most: it had a balanced combination of presented theory and hands-on experience using the program. iBioSim is positioned as (and actually appears to be) a gene-network computer-aided construction software (or, gene regulatory network CAD – GRN CAD). I recommend reading through the Myers group homepage, installing the iBioSim tool (I had problems running it on Linux, but on Windows and Mac it works fine – as long as your saved project’s path has no non-latin symbols and spaces), and reading through the tutorial which is included in the iBioSim tool (in the help menu, choose Help, then scroll down the opened page, and click Tutorial).

CellDesigner’s tutorial was also good, and referring to my older post on choosing cell modelling software, it is clear that CellDesigner is getting better with the new versions; it does include SBW inter-connectivity feature, and also can use COPASI for modelling. The SBW tutorial was probably somewhat outside the field of my experience, though I did gain some tool use experience and did learn the purposes for which the SBW package can be used. It should be noted that SBW isn’t only a “workbench” now, as it includes reaction modelling and simulation tools itself, so it can be used without the conjunction with external tools (as it was initially intended).

On the 23rd of August, there were two more tutorials – Introduction into parameter estimation with COPASI (see also here), and Reaction Network theory for systems biology. To me personally, these were not as exciting as iBioSim :), but nevertheless useful.

Here’s ICSB tutorials program.

During the main conference event (on August 23-27), we had a number of parallel sessions on various SB-related topics. As from my point of view, there were two strongly exposed main topics: quantitative systems biology (actually, I was really impressed by the number of high-quality QSB studies presented), and… funding! The FUNDING topic took about 25-30% of the time of discussions; it was also tightly intertwined with the needs of the pharmaceutical industry (there was a dedicated session on this, too, and it was also somewhat about funding). It should be noted, that AstraZeneca and Novo Nordisk were the Platinum sponsors of the ICSB conference. Also, funding opportunities seem to be relatively good in Europe, especially for the integrative German projects – such as a probably well-known HepatoSys project (the results of which, unfortunately, are not publicly available – at least yet). However, in addition to the already known HepatoSys, I learned about a number of other large Systems Biology projects being carried out – such as ENFIN, APO-SYS, SYBILLA, UNICELLSYS and many others (see the full ICSB conference program for details).

For me personally, the main (and the most easy to comprehend) bits of information were obtained from the posters devoted to the reconstruction of GRNs. I’ve found around 15 [potentially] interesting posters – all of which were scrupulously photocopied for further referencing (our systems biology group has just started working on the GRN reconstruction problem).

Also, there was some interest in the tool I presented – the COTRASIF. Although it is not strictly systems-biology (actually, it is pure genomics tool), there were several people interested, and also providing valuable suggestions and feedback. To summarize:

1. we’d better put in TFBS enrichment statistics – showing how strongly is each promoter “enriched” with the sought TFBS (the higher the enrichment – the higher chances that that gene does respond to the TF; this parameter is a higher-level statistic than a plain old score)
2. we need to release the standalone (non-web) binary of the HMM finder tool. This was suggested by the ChIP-seq practitioner – such a tool would allow to better define the boundaries of the experimentally identified binding sites. Clearly, if it were to be used as ChIP-seq-tool, it would better have some good I_c filter to cut off non-informative sequence flanks, and also an internal filter of the resulting Markov matrix I_c
3. we do need to increase the pre-defined promoter size. Actually, we’ll increase the upstream-from-TSS part to 2kb (from the current 800b). And closer to the end of October we’ll introduce the whole-genome search option
4. we need to publish an article comparing PWM method to HMM method, and providing the FP/FN statistics for both methods as implemented by our tool, plus the FP/FN statistics after applying orthology filtering. Actually, we are working on that, and an article should be re-submitted at the beginning of October

We also had social program – an excursion through the Archipelago to the Island of Marstrand, followed by the Viking dinner at the Carlsten Fortress – one of the best-preserved stone fortresses of the Northern Europe. The 2.5h boat travel was pleasant – especially thanks to the unusually warm and sunny weather, which lasted for the whole conference (it only got somewhat colder on the final workshops day). I liked the dinner, although 3 meat dishes is too much even for such a seasoned meat-eater as I am You can see some excursion photos in my gallery.

The next ICSB-2009 will be held at Stanford in California, USA; ICSB-2010 is scheduled to be held in Edinburgh, Scotland, UK. The place for ICSB-2011 is already being negotiated (it’s getting similar to the Olympic Games country scheduling procedures).

I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

This yet has to be fixed somehow.

If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:

- first, install all the necessary packages:
aptitude install build-essential libxml2 libxml2-dev python-dev

- then configure, make and install libsbml:
./configure ––with-python (execute from the directory where the downloaded libsbml archive was extracted to)
make
make install
ldconfig

- then check if installation was successful:
python
and when the python prompt >>> appears, run from libsbml import * – if there are no warnings/errors, then you are done!