[niceday]

it's a combination of a badly written protocol and 4 1/2 hours of hexane/butanol breaking and enriching. lots of spinning.

[bioits]

The new protocol is just out and no hexane anymore.

[niceday]

I'll have a look. the onetouch should eradicate all of this aparently.

[MissDNA]

Over all do you guys are liking the machine? Is it worth?
We currently have a 454 GS FLX and are looking into the PGM in order to have a different technology at a smaller cost.

[niceday]

we like it. we will love it if and when we get the onetouch. the chance to turn emulsions around quickly makes a big difference in comparison to 454. if it really gets to 1Gb by the end of the year or even half of that it will be worth investing in.

[MissDNA]

We are so behind here in Brazil. On Monday I am going to an event where they are going to present the technology. Apparently the first machines sold here will arrive only in July. What is the difference from the onetocuh to what you have now? I am assuming they are going to sell the new technology here but is always good to know.

[niceday]

If you think about the time it takes to break and enrich a 454 emulsion. Also the time you spent setting up the emulsion pcr. onetouch should be able to do the emulsion, break and enrich. It should produce the final enriched library. It will be similar to SOLiD EZ bead but as a one machine system. It won't be available until 3rd quarter so finding out about it in july will be perfect.

[krobison]

When I saw the brochure for the first time, the iPod caught my attention. What is it used for?

Mostly it is window dressing, though I think they have an app to monitor the machine.

[IonTorrent]

Regarding the very obvious iTouch that is shipped with each ION PGM Sequencer - We had a prototype app running on iOS to perform system monitoring. We decided that it really didn't do what everyone wanted it to do. As time progressed, it became more important to focus on other things than fix this app. ION will be revisiting system monitoring on iOS later this year. But Torrent Server does host PHP web pages hosted with Apache. These pages render nicely in Safari on iOS (iphone/itouch), so the functionality to monitor progress via iOS is there - just not wrapped in an iOS application specific interface. If you want to find out if your run is complete on your iPhone from your chair at home, you can do that. Open Safari and point it to your instance of the Torrent Browser web pages. Recline chair further, drink beverage, etc.

Learn more about Ion Torrent at ioncommunity.iontorrent.com

[epistatic]

Does the one-touch produce enriched beads or just beads for enrichment? My Life Rep didn't know.

[niceday]

from what I can gather it should produce sequence ready spheres. I'm assuming that's enriched spheres.

[epistatic]

Life Rep confirmed spheres still need enrichment. One touch does the emPCR and breaking, still quite nice for the price point.

[cdry7ue]

Dont celebrate till you actually have the data.
Things to look for would be
-the output from your PGM.(How many 50Q17 and 100Q17 reads)
-errors as a function of read depth. Data will become kind of noisy as you approach read end.
-Also look at the coverage across the templates of interest.

[epistatic]

Analysis?

I just met with the Life rep and got the six runs per day, quick turn time to sequence data. I couldn't get information on how fast the ioncompute would analyze those six runs. Is everything in real-time and data in fastq when run is done? That was the impression she had but I found a bit hard to believe.

[cdry7ue]

Computation is not the hard part, with 100K reads one can map those out really fast few minutes tops.
I dont see how you would get 6 runs done in a day unless you are running a sweatshop where people work 18hr days. 4 runs/day is more normal.
Yes you should be able to get fastq from the ion server web interface, it is very convenient. The A,B,C,D beads produce SFFs, which need conversion to fastq's. I use an old world program called sff2fastq which seems to work reasonably.