Google maps for next-gen facilities - Page 2

dulcinea · 08-13-2009, 07:05 AM

There is one GAIIx at the University of Wisconsin - Madison

University of Wisconsin Biotechnology Center Sequencing Facility
425 Henry Mall, Madison, WI 53706

MarcoG · 08-14-2009, 05:52 AM

Hello James,

There are further 2nd Generation Sequencing devices.

machines:
2x GAIIx
1x GS FLX

address:
Fritz Lipmann Institute
Leibniz Institute for Age Research
Genome Analysis
Beutenbergstr. 11
07745 Jena
Germany

URL:
http://genome.fli-leibniz.de

Cheers,

Marco

Yang Zheng · 08-16-2009, 09:51 PM

Hi James,
It's a great work you've done to integrate the information of sequencing centers world wide.
For Beijing Genomics Institute in China, the headquater has moved to Shenzhen since May, 2007. We have 30 Illumina GAII, 1 ABI SOLiD, 1 Roche 454.

Beijing Genomics Institute at Shenzhen
Shenzhen, Guang Dong, China
www.genomics.org.cn

Thanks again for your effort.

Laurence Game · 08-18-2009, 07:38 AM

Hi James, we have 1 GAII and 1 SOLiDv3. The Roche 454 was sent back!
Laurence

lcollado · 08-26-2009, 08:46 PM

Hello,

Great map!

We have 1 GAII at UUSM from UNAM, Mexico.
http://uusm.unam.mx/

It's new for us, so the website is not complete right now, but at least there is the contact info.
Greetings,
Leonardo

caddymob · 08-26-2009, 10:45 PM

2 GAIIs and 5 SOLiDs at TGen in Phoenix (www.tgen.org). Home of Craig et al, Nature Methods 2008 (bar-coded multiplexed sequencing).

445 N. 5th Street
Phoenix, AZ. 85004

lcollado · 08-27-2009, 11:28 AM

Just a detail about UUSM. It's located at Cuernavaca and not Mexico City.
Thanks for adding it

Leonardo

jillwbrown · 09-22-2009, 01:31 PM

Stanford has a Heliscope in Steve Quake's department.

Christelle · 09-23-2009, 01:31 AM

Hi James,

We are a core facility with 1 GAII at MGX (3 GAII in november)
http://mgx.transcriptome.eu

Montpellier GenomiX (MGX)
Institut de Génomique Fonctionnelle
141 rue de la cardonille
34094 Montpellier Cedex

Cheers,

Christelle

james hadfield · 09-30-2009, 09:14 AM

Nope, the map does not allow this kind of info to be easily extracted. There are almost 150 sites listed as having next-gen sequencers. Most of these have multiple instruments and some have upwards of 40. I would guess the map captures around 400+ instruments, maybe more.

Keep on adding stuff everyone!

kopi-o · 09-30-2009, 07:58 PM

Six Illumina GA machines
One SOLiD
One Roche 454

(there may be more, not sure)

Genome Institute of Singapore
60 Biopolis Street
#02-01 Genome
Singapore 138672

james hadfield · 11-20-2009, 07:24 AM

Thanks to everyone for looking at the GoogleMap and adding information,
there have been over 100,000 views! There is now an updated and improved
version which you can find at http://pathogenomics.bham.ac.uk/hts/

The old version is now locked for future edits but will be periodically
updated from the new database. The new site allows you to add new sites,
update sites with platforms and capacity and correct any errors you find
on the map yourself.

The new map has a number of new features. Sites are clustered together
to make it easier to navigate high-density regions. You can filter by
individual platform, for example "show me all sites which have Illumina
& SOLiD". There is more information held about each site. All
the work on the new map has been done by Nick Loman at University of
Birmingham, I really must thank him for taking my idea and making it
much more user friendly. We'd be grateful for any feedback if you find
any small problems or have suggestions for improving the interface further.

The map was put together in the first place to show how many places had
installed systems. I think when I first made it there were about the
same number of Illumina's world-wide as Broad has currently. There has
been phenomenal growth in next-gen technologie.

And of course, for those interested in the question of which platform is
in the lead, we will be putting league tables up shortly. But we wanted
to give the community some time to help get the map as accurate as
possible. Look out for the tables next week.

Hopefully this map can help you find someone close to you to collaborate
with, ask questions or just go to the pub and join in nerdy
conversations about your first sequences being 350bp on an autorad. DNA
bp is the next MB of Ram!

nickloman · 11-20-2009, 07:34 AM

Thank you James! I really hope you all like the new site. Please do take the time to check the entry for your institute is as up-to-date as possible, and add missing facilities if you know about them. We'd be keen to get feedback on the usability and any features that would improve the site further. Obviously league tables are the next thing to implement!

Michael.James.Clark · 11-20-2009, 03:27 PM

I tried adding our site to the map, but right-clicking the map did nothing. I'm using Firefox 3.0.15 on a Macbook Pro.

nickloman · 11-21-2009, 12:48 AM

Thanks for the feedback. I gave it a try on Firefox 2.0 on the Mac and it seemed to work. Did you try CTRL-CLICK on the map? I have found some references to there being a possible bug in Firefox 3 and right-click handling so perhaps that's the issue (http://code.google.com/p/gmaps-api-i.../detail?id=377). Anyway, if you still have problems try going directly to http://pathogenomics.bham.ac.uk/hts/add/ and dragging the marker to the correct place (you'll need to zoom out a bit).

brjordan · 11-23-2009, 05:24 AM

Yes, the map is very nice and very useful. It is also still very incomplete, at least for two countries I know fairly well i.e. France and Taiwan (there are at least five second-gen systems in Taiwan that I know of). I'll be collecting the information with the correct institution names for you.
Cheers,
Bertrand

nickloman · 11-23-2009, 06:12 AM

Great, thank you Bertrand!

Dushyant · 11-26-2009, 04:53 AM

Dear James,

Appreciate if you could add Xcelris Labs from Gujarat, India in your Google map too. We are using ABI SOLiD v3 and Roche 454 for Whole genome sequencing studies. Congratulations for such an excellent work................
Regards,
DSB

james hadfield · 11-26-2009, 04:55 AM

Dear All,
Please try and add updates and new labs yourself. This is the intention of the new map, it is interactive and does not require effort by a single person.

James.

james hadfield · 12-21-2009, 03:40 AM

The new link for the google map is now, http://pathogenomics.bham.ac.uk/hts. You can add stuff and sort by instrument here now.
Enjoy.

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08-13-2009, 07:05 AM	#21
dulcinea Junior Member Location: Wisconsin Join Date: Apr 2009 Posts: 1	addition There is one GAIIx at the University of Wisconsin - Madison University of Wisconsin Biotechnology Center Sequencing Facility 425 Henry Mall, Madison, WI 53706

08-14-2009, 05:52 AM	#22
MarcoG Junior Member Location: Germany Join Date: Aug 2009 Posts: 1	further sequencing devices Hello James, There are further 2nd Generation Sequencing devices. machines: 2x GAIIx 1x GS FLX address: Fritz Lipmann Institute Leibniz Institute for Age Research Genome Analysis Beutenbergstr. 11 07745 Jena Germany URL: http://genome.fli-leibniz.de Cheers, Marco Last edited by MarcoG; 09-04-2009 at 02:39 PM.

08-16-2009, 09:51 PM	#23
Yang Zheng Junior Member Location: Shenzhen, China Join Date: Aug 2009 Posts: 1	Please edit information of Beijing Genomics Institute Hi James, It's a great work you've done to integrate the information of sequencing centers world wide. For Beijing Genomics Institute in China, the headquater has moved to Shenzhen since May, 2007. We have 30 Illumina GAII, 1 ABI SOLiD, 1 Roche 454. Beijing Genomics Institute at Shenzhen Shenzhen, Guang Dong, China www.genomics.org.cn Thanks again for your effort.

08-26-2009, 08:46 PM	#25
lcollado Member Location: Baltimore, MD Join Date: Jun 2009 Posts: 65	Hello, Great map! We have 1 GAII at UUSM from UNAM, Mexico. http://uusm.unam.mx/ It's new for us, so the website is not complete right now, but at least there is the contact info. Greetings, Leonardo __________________ L. Collado Torres, Ph.D. student in Biostatistics.

08-18-2009, 07:38 AM	#24
Laurence Game Junior Member Location: London, UK Join Date: May 2008 Posts: 5	Hi James, we have 1 GAII and 1 SOLiDv3. The Roche 454 was sent back! Laurence

08-26-2009, 10:45 PM	#26
caddymob Member Location: USA Join Date: Apr 2009 Posts: 36	2 GAIIs and 5 SOLiDs at TGen in Phoenix (www.tgen.org). Home of Craig et al, Nature Methods 2008 (bar-coded multiplexed sequencing). 445 N. 5th Street Phoenix, AZ. 85004

08-27-2009, 11:28 AM	#27
lcollado Member Location: Baltimore, MD Join Date: Jun 2009 Posts: 65	Just a detail about UUSM. It's located at Cuernavaca and not Mexico City. Thanks for adding it Leonardo __________________ L. Collado Torres, Ph.D. student in Biostatistics.

09-22-2009, 01:31 PM	#28
jillwbrown Junior Member Location: Spokane WA Join Date: Mar 2008 Posts: 1	Stanford heliscope Stanford has a Heliscope in Steve Quake's department.

09-23-2009, 01:31 AM	#29
Christelle Junior Member Location: France Join Date: Feb 2008 Posts: 1	Hi James, We are a core facility with 1 GAII at MGX (3 GAII in november) http://mgx.transcriptome.eu Montpellier GenomiX (MGX) Institut de Génomique Fonctionnelle 141 rue de la cardonille 34094 Montpellier Cedex Cheers, Christelle

09-30-2009, 09:14 AM	#30
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Nope, the map does not allow this kind of info to be easily extracted. There are almost 150 sites listed as having next-gen sequencers. Most of these have multiple instruments and some have upwards of 40. I would guess the map captures around 400+ instruments, maybe more. Keep on adding stuff everyone!

09-30-2009, 07:58 PM	#31
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	Six Illumina GA machines One SOLiD One Roche 454 (there may be more, not sure) Genome Institute of Singapore 60 Biopolis Street #02-01 Genome Singapore 138672

11-20-2009, 07:24 AM	#32
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	New GoogleMap, search by platform and other features... Thanks to everyone for looking at the GoogleMap and adding information, there have been over 100,000 views! There is now an updated and improved version which you can find at http://pathogenomics.bham.ac.uk/hts/ The old version is now locked for future edits but will be periodically updated from the new database. The new site allows you to add new sites, update sites with platforms and capacity and correct any errors you find on the map yourself. The new map has a number of new features. Sites are clustered together to make it easier to navigate high-density regions. You can filter by individual platform, for example "show me all sites which have Illumina & SOLiD". There is more information held about each site. All the work on the new map has been done by Nick Loman at University of Birmingham, I really must thank him for taking my idea and making it much more user friendly. We'd be grateful for any feedback if you find any small problems or have suggestions for improving the interface further. The map was put together in the first place to show how many places had installed systems. I think when I first made it there were about the same number of Illumina's world-wide as Broad has currently. There has been phenomenal growth in next-gen technologie. And of course, for those interested in the question of which platform is in the lead, we will be putting league tables up shortly. But we wanted to give the community some time to help get the map as accurate as possible. Look out for the tables next week. Hopefully this map can help you find someone close to you to collaborate with, ask questions or just go to the pub and join in nerdy conversations about your first sequences being 350bp on an autorad. DNA bp is the next MB of Ram!

11-20-2009, 07:34 AM	#33
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Thank you James! I really hope you all like the new site. Please do take the time to check the entry for your institute is as up-to-date as possible, and add missing facilities if you know about them. We'd be keen to get feedback on the usability and any features that would improve the site further. Obviously league tables are the next thing to implement!

11-20-2009, 03:27 PM	#34
Michael.James.Clark Senior Member Location: Palo Alto Join Date: Apr 2009 Posts: 213	I tried adding our site to the map, but right-clicking the map did nothing. I'm using Firefox 3.0.15 on a Macbook Pro.

11-21-2009, 12:48 AM	#35
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Thanks for the feedback. I gave it a try on Firefox 2.0 on the Mac and it seemed to work. Did you try CTRL-CLICK on the map? I have found some references to there being a possible bug in Firefox 3 and right-click handling so perhaps that's the issue (http://code.google.com/p/gmaps-api-i.../detail?id=377). Anyway, if you still have problems try going directly to http://pathogenomics.bham.ac.uk/hts/add/ and dragging the marker to the correct place (you'll need to zoom out a bit).

11-23-2009, 05:24 AM	#36
brjordan Member Location: Marseille France Join Date: Jan 2009 Posts: 23	Yes, the map is very nice and very useful. It is also still very incomplete, at least for two countries I know fairly well i.e. France and Taiwan (there are at least five second-gen systems in Taiwan that I know of). I'll be collecting the information with the correct institution names for you. Cheers, Bertrand __________________ Bertrand Jordan Marseille-Nice Genopole Luminy Science Park 13288 Marseille, FRANCE

11-23-2009, 06:12 AM	#37
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Great, thank you Bertrand!

11-26-2009, 04:53 AM	#38
Dushyant Junior Member Location: India Join Date: Dec 2008 Posts: 7	NextGen Sequencers in India Dear James, Appreciate if you could add Xcelris Labs from Gujarat, India in your Google map too. We are using ABI SOLiD v3 and Roche 454 for Whole genome sequencing studies. Congratulations for such an excellent work................ Regards, DSB

11-26-2009, 04:55 AM	#39
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Dear All, Please try and add updates and new labs yourself. This is the intention of the new map, it is interactive and does not require effort by a single person. James.

12-21-2009, 03:40 AM	#40
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	The new link for the google map is now, http://pathogenomics.bham.ac.uk/hts. You can add stuff and sort by instrument here now. Enjoy.