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).

Here is formal definition:

high-throughputomics

the term is used to denote/mention any or all of the modern high-throughput techniques (in all of, but not limited to: genomics, transcriptomics, proteomics, …), together with derived/applicable data-processing approaches. All the “networks” things also conveniently fall into the high-throughputomics definition

As this is a general term, it might be even suitable as a conference title (but NOT for ICSB, which I’m waiting for eagerly).

For a shorter and informal (spoken-only) term, putomics can be used:

putomics

spoken-only, informal short form of high-throughputomics

Putomics is also conveniently similar to “computation” (computomics):

computomics

application of computer hardware and software for the analysis of massive amounts of data, obtained using high-throughput methods; this is a research sub-field of high-throughputomics

P.S.
For easier citing:

Tokovenko, Bogdan. New bioinformatics term: high-throughputomics. 2008-07-16. URL:http://bogdan.org.ua/2008/07/16/new-bioinformatics-term-high-throughputomics.html. Accessed: 2008-07-16. (Archived by WebCite® at http://www.webcitation.org/5ZMD9DITU)

The International Conference on Bioinformatics of Genome Regulation and Structure is the bi-annual event. It features several bioinformatics sections, which IMO cover most of bioinformatics sub-fields.

The Sixth conference, BGRS-2008, was well-organized and had something to offer to everyone. By far the largest section was Genomics and Transcriptomics (at least if judging by the abstracts book and by the posters presented; talks given were distributed more equally between sections). As I did some work in genomics (namely, our COTRASIF tool), I had quite a load of info to digest, and many new potentially fruitful contacts to establish (which I did quite good).

The second section on my scale of priorities was “COMPUTER ANALYSIS AND IMAGE RECOGNITION IN SYSTEMS BIOLOGY”, which had several interesting researches presented in the field of spatial/developmental modelling. There was a very good talk on model reduction (with an actual example) for the purposes of both comparing different models and decreasing the model complexity without sacrificing model-predicted outcomes.

As for the other sections, I didn’t find them interesting enough. Fortunately, there were social program events scheduled for every day, so I visited the Novosibirsk zoo and the Archaeological museum. I did not do as many pictures as I usually do at conferences/schools, because there were two photographers at the conference, and their photos can be freely seen here and here.

Most of the conference participants could speak Russian (I’d estimate the group of Russian-speaking participants at 90% of the number of participants), even though they were coming from e.g. Singapore or USA. But the official conference language was English, and the 10% of non-speakers were far not underprivileged, which goes well with the international status of the conference.

After the conference, there was a BGRS-2008 summer school. As I stayed for some extra days, I managed to attend up to 90% of the school’s events (including the guided tour to Novosibirsk ). For me, summer school was somewhat less useful than the conference, but nevertheless such presentations as on Petri nets and about SABIO-RK/Sycamore were informative and will be used in my future work.

There were 3 prizes for the student presentations; winners are at the end of the page.

Certificates were given after successful school completion. As I wasn’t registered, I can now only print out the empty certificate, which is to signify that I did not attend the last day of the school and thus was disqualified .

Just found that there are also some photos from the organizers.

There was also a football (soccer) game between the ICG team and the school participants team. I’m a fan of neither watching nor playing football, so I skipped this event altogether.