Solid 4HQ? - Page 2

KevinLam · 10-24-2010, 06:59 PM

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 · 10-25-2010, 12:04 AM

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 · 10-28-2010, 10:57 PM

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 · 11-01-2010, 04:21 PM

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 · 11-03-2010, 06:39 AM

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 · 11-03-2010, 08:21 AM

Quote:

Originally Posted by 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

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...aces-i--c.html

ECO · 11-03-2010, 08:30 AM

Specs for 5500 and 5500xl.

drio · 11-03-2010, 08:45 AM

@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 · 11-03-2010, 08:50 AM

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 · 11-03-2010, 09:37 AM

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

drio · 11-03-2010, 12:59 PM

Is there any documentation about ECC?

colindaven · 01-20-2011, 04:13 AM

Any ideas on real release dates for the 5500XL (solid 4hq) ? Has anyone got one yet ?

"Initial shipments of the 5500xl are planned for December 2010."

Oh that was from the press release at
http://www.lifetechnologies.com/news...aces-i--c.html

KevinLam · 01-20-2011, 05:21 AM

Rumours I have heard is march 2010. Not sure what's the hold up.

pmiguel · 01-20-2011, 05:52 AM

There may be 5500xls in the field, if only as test units. That would fulfill the "initial shipments" claim.

--
Phillip

Enrico Palazzo · 01-21-2011, 02:15 AM

Yes, release date is March/2011. Does anybody know the new output format? I believe it is called XSV or something like this..

bioits · 01-24-2011, 10:12 AM

Quote:

Originally Posted by Enrico Palazzo

Yes, release date is March/2011. Does anybody know the new output format? I believe it is called XSV or something like this..

I believe it is called HDF, which is a standardized file format (single file replaces csfasta, qual, and spch files).

VanessaS · 01-25-2011, 03:15 PM

At the Sequencing at the Tipping Point Conference, back in December, they were saying the new file format would be .xqs (or maybe it was .xsq?)
Its a binary file format, with one file per lane. This is supposed to be why theres no need for a cluster under the machine, its like 60% smaller.

bioits · 01-25-2011, 05:03 PM

Sorry, just remind me. It is called .xsq (eXtensible SeQuence)

drio · 01-26-2011, 05:49 AM

I think the reason for not having a minicluster is the use of FPGAs along with a very powerful machine (like illumina). Anyone has more info about that? I guess we'll find out at AGBT.

pmiguel · 01-26-2011, 09:37 AM

Yes, I have ".xsq" in my notes as the new format name. They were going to be about 30 gigabytes per lane. 12 lanes per "flow chip".

--
Phillip

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10-24-2010, 06:59 PM	#21
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 203	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 __________________ http://kevin-gattaca.blogspot.com/

10-28-2010, 10:57 PM	#23
truthseqr Junior Member Location: In Silico Join Date: Oct 2010 Posts: 1	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/ Last edited by truthseqr; 10-28-2010 at 11:21 PM.

11-03-2010, 08:45 AM	#28
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	@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. __________________ -drd

11-03-2010, 12:59 PM	#31
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	Is there any documentation about ECC? __________________ -drd

10-25-2010, 12:04 AM	#22
SrScientist Junior Member Location: Germany Join Date: Oct 2010 Posts: 5	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.

11-01-2010, 04:21 PM	#24
Chipper Senior Member Location: Sweden Join Date: Mar 2008 Posts: 324	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

11-03-2010, 06:39 AM	#25
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	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

11-03-2010, 08:30 AM	#27
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Specs for 5500 and 5500xl.

11-03-2010, 08:50 AM	#29
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	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

11-03-2010, 09:37 AM	#30
Kingpin31 Junior Member Location: C.de Join Date: Nov 2010 Posts: 2	ECC module means that you run a 6th primer that gives you direct basespace output. Has nothing to do with any additional hardware.

01-20-2011, 04:13 AM	#32
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	Any ideas on real release dates for the 5500XL (solid 4hq) ? Has anyone got one yet ? "Initial shipments of the 5500xl are planned for December 2010." Oh that was from the press release at http://www.lifetechnologies.com/news...aces-i--c.html Last edited by colindaven; 01-20-2011 at 04:13 AM. Reason: add

01-20-2011, 05:21 AM	#33
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 203	Rumours I have heard is march 2010. Not sure what's the hold up. __________________ http://kevin-gattaca.blogspot.com/

01-20-2011, 05:52 AM	#34
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	There may be 5500xls in the field, if only as test units. That would fulfill the "initial shipments" claim. -- Phillip

01-21-2011, 02:15 AM	#35
Enrico Palazzo Junior Member Location: Hamburg, Germany Join Date: Jul 2010 Posts: 9	Yes, release date is March/2011. Does anybody know the new output format? I believe it is called XSV or something like this..

01-25-2011, 03:15 PM	#37
VanessaS Member Location: Dallass Join Date: Nov 2009 Posts: 49	At the Sequencing at the Tipping Point Conference, back in December, they were saying the new file format would be .xqs (or maybe it was .xsq?) Its a binary file format, with one file per lane. This is supposed to be why theres no need for a cluster under the machine, its like 60% smaller.

01-25-2011, 05:03 PM	#38
bioits Member Location: USA Join Date: Aug 2010 Posts: 23	Sorry, just remind me. It is called .xsq (eXtensible SeQuence)

01-26-2011, 05:49 AM	#39
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	I think the reason for not having a minicluster is the use of FPGAs along with a very powerful machine (like illumina). Anyone has more info about that? I guess we'll find out at AGBT. __________________ -drd

01-26-2011, 09:37 AM	#40
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	Yes, I have ".xsq" in my notes as the new format name. They were going to be about 30 gigabytes per lane. 12 lanes per "flow chip". -- Phillip