[pmiguel]

Sorry Phillip (go Boilers!), but I'm not joking or mistaken. During the talk of the Life Tech. sequencing platforms, there was a slide showing both instruments w/ the new names, and he said that we were one of the first groups of people to hear that new info. The speaker was Michael Rhodes, Senior Manager - Sequencing, from Life Technologies.

Well, I still have my doubts about the SOLiD being "de-branded" to be called something like the "5500". Not that I would necessarily mind. This "brand" meme that hit industry pundit around a decade ago, is now impacting Purdue. In fact, last weekend was the launch of our new brand-thing "makers-all". Some sort of post-modern play on "boilermakers". Probably would need an introductory course in semiotics to understand all that is in play here. But I digress...

--
Phillip

[pmiguel]

A haiku for Phillip:

Another benefit of dumping the "solid" brand for a numeric one. Impossible to write haikus about it.

[daughart]

A little bird told me that the SOLiD 4HQ will NOT be an upgrade, it will be a completely new machine. I suspect that the computing hardware will remain the same (basically the bottom half of the main machine and the computer module, which holds some buffers in a cabinet below), but the top half of the sequencing machine will be completely replaced. I have heard word of improvements to the slide loading system and other improvements to fix slide issues and fluidics. New imaging, new robotics.

EDIT: Also, first post!! Been reading seqanswers for the last 18 months, it's been really helpful!

[SrScientist]

I´ve seen that presentation about these new instruments now too. Indeed, two new instruments. Cooperation with Hitachi. Nice robotics; much faster than previous solids; new slides (more flexible); higher accuracy (and keeps on increasing); and more.

[KevinLam]

I have seen the presentation as well.
They do mention it is upgradeable although I think its more like a trade in

I DO NOT see the computer cluster anymore, that's something I am curious about.
it is named 5500XL and 5500 solid system
which is your 4 HQ and PI

One can only fathom their obession with these 4 digits judging by similar instruments named
AB Sciex Triple Quad 5500 and the AB Sciex QTrap 5500

Honestly the 5500 numbers are of no numerical significance AFAIK.

Finally we are at 75 bp though

[KevinLam]

Oh there was a brief mention of the Ion Torrent at the presentation as well but nothing of great significance. I do wish they marketing fellows will push ion torrent out faster but i think they are trying to streamline production by testing if invitrogen kits can replace the ones at ion torrent. I do hope they do not sacrifice compatibility over performance

[SrScientist]

regarding "performance of Ion Torrent" in that seminar they´ve also mentioned that the accuracy of the PGM is increasing and could reach q40 at launch (e.coli; ~2-6x coverage).
In terms of speed one can go for up to 4 runs per day.
Application number will increase too because of the R&D-man-power behind LifeTech compared to Ion Torrents.

[truthseqr]

SOLiD @ ASHG

AB is premiering two new instruments at ASHG next week.

Mobile ASHG calendar: http://m.appliedbiosystems.com/ashg/

Twitter account: @SOLiDSequencing

SOLiD Community: http://solid.community.appliedbiosystems.com/

More info soon at: solid.appliedbiosystems.com/solid5500/

[Chipper]

Looks promising. Up to 230 M fragments per lane and possibility to run 1 lane in one day.

* Pay-per-use reagents for cost-effective
consumable usage

* 1 day for 35 bp, 1 lane

* Nanobeads: Up to 300 Gb or greater than 4.8 B tags (paired-end or
mate-paired runs)

* Reference-free analysis with Exact Call Chemistry Module

[pmiguel]

From the In Sequence article, link, but login is required:

"Real-time data processing means no compute cluster is necessary."

Any idea how this could be possible when a cluster is required to run a solid v4 and it does data processing on the fly, if not exactly "in real time"?

--
Phillip

[KevinLam]

From the In Sequence article, link, but login is required:

"Real-time data processing means no compute cluster is necessary."

Any idea how this could be possible when a cluster is required to run a solid v4 and it does data processing on the fly, if not exactly "in real time"?

--
Phillip

I recall speculation that V4 to HQ cannot be upgraded as its entirely different.
In the preview launch they did allude to the fact that instead of slides it is now 6 lanes of microfluidic on a flowchip (which still looks like a slide to me though)

and the highly advertised fact that "Developed and manufactured with long-standing partner Hitachi High-Technologies, the 5500xl delivers on the promise of the SOLiD 4hq"

So based on this I am guessing the optics and fluidics are changed. Hence perhaps that's the main reason behind not requiring a on instrument cluster.

however, if you asked me, I really feel that the cluster was provisioned so that users may run at least bare minimal analysis on the data, without having to buy an offline cluster. The running time of the cycle scans are probably long enough to process the images with a desktop computer. granted it has enough storage.

just my two cents.
btw for those that do not have access to genomeweb try the official press release.

http://www.lifetechnologies.com/news-gallery/press-releases/2010/life-techologies-lauches-ew-solid-sequecer-to-drive-advaces-i--c.html

[ECO]

Specs for 5500 and 5500xl.

[drio]

@Kevin
Is it possible they follow the illumina way? To use a powerful machine for the
image processing and base calling. They don't mention details of the onboard
machine, other than runs windows.

Notice how in the brochure (thanks ECO) saids that the ECC feature requires a module.

[pmiguel]

We actually had occasion to repeat image analysis on a completed run of one full slide (~500 million usable beads). (This is not "primary analysis", that occurs after image analysis.) The instrument was otherwise idle. Our solid v4 linux cluster was pegged at 100% load on all 4 nodes for the duration. It took about 1.5 hours/base processed. That is >5 days of wall clock time for a run that completed in about 2 weeks. So that works out to about 40% of the capacity of the cluster had the full 2 weeks to run. Since the solid has 2 flowcells, it might be called upon to do image processing on the fly for both at the same time.

This suggests that the cluster is slightly over provisioned ( by about 25%).

The 5500xl has 2 flowcells like the v4 and will have to process more beads. So no relief there for our console computer.

Perhaps the computation becomes simpler because a sample will be divided across 6 discrete lanes per flow cell? But it seems more likely there has been some break through in the process that has drastically reduced the computational resources required to do image processing.

--
Phillip

[Kingpin31]

ECC module means that you run a 6th primer that gives you direct basespace output. Has nothing to do with any additional hardware.