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  • #16
    Can you give us a status regarding the Helicos package?

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    • #17
      Originally posted by 2007lab View Post
      Would there be some kind of Video Archive for us to peek into after the conference is over? like AACR for e.g.?
      They sell DVDs of their recordings... I believe it's a very high price. (correct me if I'm wrong)

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      • #18
        CHI is a bit overwhelming, but thought the event well run and with some very high quality presentations, albeit some were "commercial" in nature. Since I come from that side, I'm probably a bit prejudiced, but thought even the vendor presentations good without too much flag waving. Some great science as well, including several presentations on the "next-next" generation of machines. FWIW...

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        • #19
          well, this was my first conference ever as i only started my PhD some months ago. Being transatlantic alone in the Hilton, well it aint that bad, but it is kind of 'woooowing'.

          I thought it was very interesting to see what is coming in the next-next gen field. Kinda disapointing as well, makes you feel small. We had the biggest academic cluster installed of Western Europe (6000 cores) and then you see Complete genomics announcing a plan for a 60k cluster with 15 PB storage !!! We are back to eating the crumbs of the bread.

          I was only a bit disapointed with the data management and data analysis part of the conference. There was a talk on Gene Wiki, which is nice to see, but i could have made that also. For the rest there was some commercial talks on data storage systems and file systems, but no real data analysis explanation. I can belief you store a single 454 run in an excel sheet, but what then? No one is using DB systems that were created in houes? No one has build custom pipelines?

          We all know sample prep and downstream processing are the hardest part. The sample prep was widely discussed on the conference, the sequencing itself also, but what then? And then i saw a lot of nice figures and results. But between the sequencing and the figures there is a big dark hole for me. I don't belief that anyone is actually using AVA software for a titanium run? or is manually blatting all the 454 sequences... Would have been nice to see some pipeline or custom solutions.

          Maybe the organizers felt the same? and are therefore planning to split the sequencing in rhode island in 'sequencing and 'data analysis', which makes it very tempting to go again in another 6 months...

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          • #20
            Originally posted by joa_ds View Post
            I can belief you store a single 454 run in an excel sheet, but what then? No one is using DB systems that were created in houes? No one has build custom pipelines?
            I remember that talk. Those grapevine virus people got suckered by GenomeQuest. They could have done most almost everything they wanted to in Access. Because Access is a database program, and Excel isn't. They could have gotten a MySQL database too, but Access is nice and safe and familiar, and they almost certainly already had the license. But they didn't even understand the difference between a spreadsheet and a database.

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            • #21
              Please visit the vendor forum. There are "analysis solutions", but agree they were not well represented at the conference. No commercial announcement here...

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              • #22
                Pardon if this is a repeat. Please visit the vendor forum There are "analysis solutions" available, but agree they were not well represented at the conference. Much talk about the front end (sample prep) etc. Lots of talk about the numbers...very little talk about the analysis and the BIOLOGY that the experiment was done for in the first place.

                That's what we are all about...

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                • #23
                  well, in my opinion you cannot develop a commercial package for next-gen sequencing that is so versatile that you can use it as THE analysis tool for your sequencer.

                  I agree you can make a system that stores and annotates, even maps, your sequences. But automating your complete analysis or conclusion is almost impossible.

                  What if you do a transcript counting run in january, a bisulfite run in february, SNP discovery run in march and a de novo run in april? I hardly doubt that a commercial package can do all this work.

                  So you will need to work modular and automate the modular selection of certain packages. We are working on that here. Trying to think outside the box and always thinking 'can this part of the pipeline be used in other types of experiments'. This is the kind of things I missed in the conference.

                  The grapevine virus was quite interesting, because it was one of the few examples that showed that a specific question combined with a sequencer can generate interesting results that are immediately usable. I have a bit the feeling that the we are evolving to a situation where genomes are sequenced and people are trying to figure out what to do with the sequenced genomes.

                  The other examples were also interesting, but they explained the front prep, the sequencer and then skipped to the results and in the end they say 'data analysis is a very hard task'. I know cancer is a major research field, i know transcript counting is a major research field, but everyone knows that, no? but how to get those results?

                  And all the fancy companies offering fancy data storage is ok for me. I can imagine a Venter institute or Broad institute or CompleteGenomics can use that, but when I see that a new grapevine virus can be discovered using only spreadsheets, i was quite amazed. I would have liked to see more of those analysis pipelines.

                  My guess is that:
                  a) people are letting specialised groups do the data analysis?
                  b) the analysis pipelines are secret?
                  c) analysis is still underway?

                  I was quite surprised because whenever you read a sequencing paper, the analysis pipeline is always mentioned in a nice figure and they always mention some basic metrics such as %mapped, %unmapped, %mixed, avg length...

                  I don't know, might be me, this was my first conference ever. No idea what is like on other conferences

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                  • #24
                    Actually, it is possible, and we do it, but this is not the right thread for that kind of post. I will put something out on the vendor forum shortly. Have a look.

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