CHI Next Generation Sequencing, San Diego March 17-19, 2009

natgenex · 01-22-2009, 09:25 AM

CHI's latest Next-Generation Sequencing meeting takes place in San Diego, March 17-19, 2009. Highlights include a keynote from Richard Gibbs, updates from all the major commercial platforms, and one of the first presentations from Complete Genomics (Rade Drmanac).

http://www.healthtech.com/seq/overview.aspx

doxologist · 02-12-2009, 12:46 PM

For those who have been to CHI meetings... what is your experience? From their millions of advertising emails, I have become a little suspicious of the commercial nature of the conference.

natgenex · 02-12-2009, 01:07 PM

I'm biased (being affiliated with CHI) but the Next-Gen Sequencing meetings are among the best attended, fastest growing events. Yes, there's a strong presence of commercial technology suppliers, but most of the audience likes that -- at least for this topic. With the exception of AGBT, this is one of the best places to get information and network.

doxologist · 02-12-2009, 01:51 PM

thanks for the info.

I agree that AGBT is probably the best venue and that commercial involvement is now critical in this field.

BioWizard · 03-02-2009, 10:17 AM

"commercial" nature of the conference is a great feature. For example, in this conference we discovered a new startup which invented technology to perform next gen sequence alignment 100 times faster than any other solution. We don't have the budget for big cluster like some of you big time genome centers. With these guys' tool, we do alignment on one computer, and it cuts our total sample sequencing time by a day. Its nice to hear academics talking about their wonderful science (fiction), but we go to this conference to also pick up the latest technology "real solutions", and for that we need "commercial" vendors. Unfortunately Next Gen sequencing is not main stream enough that we can get the best tools automatically from Microsoft and Intel... no , we rely on small innovative start ups (often formed by professors !!) and the only way we find out about them is these "commercial" shows.

ECO · 03-02-2009, 05:24 PM

Quote:

Originally Posted by BioWizard

"commercial" nature of the conference is a great feature. For example, in this conference we discovered a new startup which invented technology to perform next gen sequence alignment 100 times faster than any other solution. We don't have the budget for big cluster like some of you big time genome centers. With these guys' tool, we do alignment on one computer, and it cuts our total sample sequencing time by a day. Its nice to hear academics talking about their wonderful science (fiction), but we go to this conference to also pick up the latest technology "real solutions", and for that we need "commercial" vendors. Unfortunately Next Gen sequencing is not main stream enough that we can get the best tools automatically from Microsoft and Intel... no , we rely on small innovative start ups (often formed by professors !!) and the only way we find out about them is these "commercial" shows.

BioWizard, again, please see your PM box before posting further about aligners. Thanks!

doxologist · 03-03-2009, 07:40 AM

Quote:

Originally Posted by BioWizard

"commercial" nature of the conference is a great feature. For example, in this conference we discovered a new startup which invented technology to perform next gen sequence alignment 100 times faster than any other solution. We don't have the budget for big cluster like some of you big time genome centers. With these guys' tool, we do alignment on one computer, and it cuts our total sample sequencing time by a day. Its nice to hear academics talking about their wonderful science (fiction), but we go to this conference to also pick up the latest technology "real solutions", and for that we need "commercial" vendors. Unfortunately Next Gen sequencing is not main stream enough that we can get the best tools automatically from Microsoft and Intel... no , we rely on small innovative start ups (often formed by professors !!) and the only way we find out about them is these "commercial" shows.

BioWizard:

I agree that great collaboration must exist between commercial and academic initiatives. It just sometimes, highly commercial talks just end up being advertisement without much discussion of method/development. I think there are a proliferation of open source efforts within the next generation markets which allows for all players to be involved.

BioWizard · 03-10-2009, 08:35 PM

Yes, doxologist, there is "something for everyone".

bioinfosm · 03-11-2009, 09:13 AM

Quote:

Originally Posted by doxologist

For those who have been to CHI meetings... what is your experience? From their millions of advertising emails, I have become a little suspicious of the commercial nature of the conference.

Slightly off topic, but CHI is going a bit extra with their marketing.. I feel so especially after I got the pre-recorded Kevin Davies call close to mid-night asking to consider attending BioIT world Expo and networking with 1500 people .. blah..blah..

vruotti · 03-16-2009, 11:05 AM

Hello,
I will be attending the CHI conf in San Diego and for the ones that are interested in aligners I would like to propose a small group discussion in between talks.
Date and time will be determined soon. Will anyone be interested on getting together to share ideas re the storm of aligners and the short read headache we all tend to deal with?

Victor

mchaisso · 03-16-2009, 08:11 PM

I'll be there and am interested in hearing of short read aligning headaches, but I'll only be around intermittently since this is a very busy month for me. I'll follow this thread to find out where to meet.

2007lab · 03-17-2009, 09:24 AM

Would there be some kind of Video Archive for us to peek into after the conference is over? like AACR for e.g.?

mchaisso · 03-17-2009, 09:54 AM

My guess is no, but I'll post my slides online (still trying to cram one or two in though now).

vruotti · 03-17-2009, 03:39 PM

If there is enough interest... How about getting together tomorrow Wed. There is a question-answer session at 5:40. Maybe after this session?

If this doesn't work perhaps Thursday during lunch?
Victor

vruotti · 03-17-2009, 09:23 PM

Interesting Panel discussion today.
A representative from Illumina, Roche, Solid and Helicos were all side by side answering questions from the audience.

The common problem was scalability. All four are working on trying to use a little sample as possible (well as Helicos) and make easier to run more samples. Gel/PCR free protocols are on the way.
Have not heard of a GAIII yet from Illumina. I did hear from the 1.4 pipeline.
It supposed to do a better job extracting intensities from images. So, do we save the images after all?

victor

strob · 03-18-2009, 12:11 AM

Can you give us a status regarding the Helicos package?

doxologist · 03-19-2009, 07:55 AM

Quote:

Originally Posted by 2007lab

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)

Genomatix · 03-19-2009, 04:01 PM

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...

joa_ds · 03-26-2009, 08:03 AM

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...

swbarnes2 · 03-26-2009, 08:40 AM

Quote:

Originally Posted by joa_ds

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
My experience at Xgen conference in San Diego, CA March 2011	analyst	Events / Conferences	14	05-23-2011 11:35 AM
FREE pass to CHI conference next week in San Diego, CA	ECO	Events / Conferences	8	03-15-2010 08:24 AM
CHI NGS Data Analysis - Sept 2009	bioinfosm	Events / Conferences	19	09-18-2009 08:17 AM
Live Blogging from the CHI Next Gen Conference! (San Diego, CA): Updated Day 2	ECO	Events / Conferences	21	04-30-2008 07:57 PM
CHI: Next Gen Sequencing Technologies (April 23 - 24, San Diego, CA)	ECO	Events / Conferences	3	04-23-2008 03:41 PM

01-22-2009, 09:25 AM	#1
natgenex Member Location: Boston Join Date: Nov 2007 Posts: 11	CHI Next Generation Sequencing, San Diego March 17-19, 2009 CHI's latest Next-Generation Sequencing meeting takes place in San Diego, March 17-19, 2009. Highlights include a keynote from Richard Gibbs, updates from all the major commercial platforms, and one of the first presentations from Complete Genomics (Rade Drmanac). http://www.healthtech.com/seq/overview.aspx

03-16-2009, 11:05 AM	#10
vruotti Member Location: US Join Date: Feb 2008 Posts: 13	Small Group Gathering regarding aligners Hello, I will be attending the CHI conf in San Diego and for the ones that are interested in aligners I would like to propose a small group discussion in between talks. Date and time will be determined soon. Will anyone be interested on getting together to share ideas re the storm of aligners and the short read headache we all tend to deal with? Victor

03-17-2009, 09:23 PM	#15
vruotti Member Location: US Join Date: Feb 2008 Posts: 13	Conference update. Interesting Panel discussion today. A representative from Illumina, Roche, Solid and Helicos were all side by side answering questions from the audience. The common problem was scalability. All four are working on trying to use a little sample as possible (well as Helicos) and make easier to run more samples. Gel/PCR free protocols are on the way. Have not heard of a GAIII yet from Illumina. I did hear from the 1.4 pipeline. It supposed to do a better job extracting intensities from images. So, do we save the images after all? victor

02-12-2009, 12:46 PM	#2
doxologist Member Location: USA Join Date: Jan 2009 Posts: 96	For those who have been to CHI meetings... what is your experience? From their millions of advertising emails, I have become a little suspicious of the commercial nature of the conference.

02-12-2009, 01:07 PM	#3
natgenex Member Location: Boston Join Date: Nov 2007 Posts: 11	I'm biased (being affiliated with CHI) but the Next-Gen Sequencing meetings are among the best attended, fastest growing events. Yes, there's a strong presence of commercial technology suppliers, but most of the audience likes that -- at least for this topic. With the exception of AGBT, this is one of the best places to get information and network.

02-12-2009, 01:51 PM	#4
doxologist Member Location: USA Join Date: Jan 2009 Posts: 96	thanks for the info. I agree that AGBT is probably the best venue and that commercial involvement is now critical in this field.

03-02-2009, 10:17 AM	#5
BioWizard Member Location: Houston, TX Join Date: Mar 2009 Posts: 27	"commercial" nature of the conference is a great feature. For example, in this conference we discovered a new startup which invented technology to perform next gen sequence alignment 100 times faster than any other solution. We don't have the budget for big cluster like some of you big time genome centers. With these guys' tool, we do alignment on one computer, and it cuts our total sample sequencing time by a day. Its nice to hear academics talking about their wonderful science (fiction), but we go to this conference to also pick up the latest technology "real solutions", and for that we need "commercial" vendors. Unfortunately Next Gen sequencing is not main stream enough that we can get the best tools automatically from Microsoft and Intel... no , we rely on small innovative start ups (often formed by professors !!) and the only way we find out about them is these "commercial" shows.

03-10-2009, 08:35 PM	#8
BioWizard Member Location: Houston, TX Join Date: Mar 2009 Posts: 27	Yes, doxologist, there is "something for everyone".

03-16-2009, 08:11 PM	#11
mchaisso Member Location: Seattle, WA Join Date: Apr 2008 Posts: 84	I'll be there and am interested in hearing of short read aligning headaches, but I'll only be around intermittently since this is a very busy month for me. I'll follow this thread to find out where to meet.

03-17-2009, 09:24 AM	#12
2007lab Member Location: NYC Join Date: Mar 2009 Posts: 14	Would there be some kind of Video Archive for us to peek into after the conference is over? like AACR for e.g.?

03-17-2009, 09:54 AM	#13
mchaisso Member Location: Seattle, WA Join Date: Apr 2008 Posts: 84	My guess is no, but I'll post my slides online (still trying to cram one or two in though now).

03-17-2009, 03:39 PM	#14
vruotti Member Location: US Join Date: Feb 2008 Posts: 13	If there is enough interest... How about getting together tomorrow Wed. There is a question-answer session at 5:40. Maybe after this session? If this doesn't work perhaps Thursday during lunch? Victor

03-18-2009, 12:11 AM	#16
strob Member Location: Belgium Join Date: Nov 2008 Posts: 79	Can you give us a status regarding the Helicos package?

03-19-2009, 04:01 PM	#18
Genomatix Registered Vendor Location: Ann Arbor, MI Join Date: Feb 2009 Posts: 12	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...

03-26-2009, 08:03 AM	#19
joa_ds Member Location: belgium Join Date: Dec 2008 Posts: 52	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...