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Finally after three weeks of recovery, I give you my write up of the Noalpoint European Tour. I had a great time in The Netherlands at Advances in Microarray Technology, visiting the Sanger Center in Cambridge and I also had the opportunity to catch up with Alf Eaton and Euan from postgenomic over a few pints in London. Both Alf and Stew are now working for Nature's web technology group, the people behind Connotea.

The meeting

Advances in Microarray technology 2006 was a very boutique, business oriented conference touting the latest in arraying and microfluidics. I didn't do any live coverage of the talks as no provisions were made for attendees to have internet access either. Commercial internet access at the Amsterdam Hilton was outrageously expensive and the pricing plans were equally insane. Having been at meetings with internet access it does tend to be a distraction. Of the talks I have notes on, most are informatics focused. There were many other interesting talks on cell-arrays, extra-cellular matrix arrays, microfluidics devices and protein arrays.

Day one

Day one was focused on microfluidic arrays and bioinformatics. Despite the presenters suggestions that the talks were focused on the science the many turned out to be thinly veiled advertisements for the companies the speakers represented. I don't have a problem with companies getting their message out, just don't try and pretend otherwise.

All manner of microfluidic arrays were presented, I was especially impressed with Martin Dufva's home made thermal gradient array for genotyping. The system was designed to overcome the problem that for precise single base discrimination it is impossible to have a group of oligos that all hybridize optimally at the same temperature. The three bioinformatics talks were sketchy, Alvis Brazma gave an overview of the EBI efforts to bring order to public microarray data storage (i.e. ArrayExpress), other than that he mentioned that data integration was a problem and wasn't sure what to do about it. I asked during question time whether he thought the semantic web might have an impact on this and his comment was that any future data standards are likely to be spreadsheet based. It seems Excel's dominance is compete. Thomas Werner of Genomatix showed convincingly that a systems biology approach to data analysis is more revealing than simply listing the top ten upgregulated genes on a chip, of course the best way to do this is using his company's tools, no surprise there. Eytan Domany gave an informative talk on finding a unique diagnostic gene list for brest cancer. The message was simple: diagnostic gene lists for cancer don't overlap because the studies use insufficient samples. His claim was that for a 50% overlap you need to do 2200 microarray experiments.

Day two

Day two was all protein arrays. All of the protein arrays presented were variations on the theme of minaturized elisa assyas (i.e. spotting antibodies). The only talk I'll mention was from Sabine Flitsch on Glycochips. The importance of protein glycocylation is poorly understood. Prof. Flitsch and collaborators are trying to understand the processing in more detail using chips of spotted carbohydrates.The problem is carbohydrates are very trick to synthesize and work with. The chip is still very much in development but progress is being made.

Day three

Day three was all DNA microarrays. Winston Kuo gave a talk on sequence based comparison of data from different microarray platforms. I had the opportunity to talk to Winston during the meeting, and he told me that he had been working on platform comparisons for miroarray data since 2000-2001. Problem was he was just one guy, and had just become aware of a huge consortium, Microarray Quality Control (MAQC) was in the processes of publishing similar work. He ended up finishing the paper and getting published in Nature biotech two months before MAQC, not bad. Finally there were a two talks relevant to my current work on microarray probe design. Catherine Putonti discussed a method for host-blind probe desing for virus identification. Host-blind in this case means that the probes will not bind to host sequences. Sascha Todt presented his PhD work on binding energy profiles and their effect probe hybridization efficiency.

The Sanger Center

People I know who have visited Hinxton described it as a sleepy little village. That would be an understatement. About 30-40 minutes by bus from Cambridge there is literally nothing of interest there other than the Sanger Center. The genome campus is nonetheless an impressive place, excellent facilities, the best people in Genomics and Bioinformatics from all over Europe work there and the area itself is very beautiful. The highlight of the visit was a tour through the sequencing center, I can't recall the name of the center manager, but he was very enthusiastic and a huge fan of Linux. All-in-all worth a visit, but I don't know if could work there.