Google maps for next-gen facilities

james hadfield · 05-05-2009, 01:40 PM

Hi everyone,
I made a Google Map to try and add the facilities I knew of where there was a next-gen sequencer (and other genomics platforms). It is proving to be interesting to me but I would really like to make it easier for anyone to add content and search for users, always good when you want to find someone local to talk to!
Is there anyone out there who could make a really useful map, post it and then members of SeqAnswers could update it?
James.

Map Title is "Genomics: NextGen sequencers; Illumina (Solexa), ABI SOLiD, Roche/454. Microarrays: Illumina BeadStation, Affymetrix"

gengen · 05-07-2009, 10:38 PM

Your map sounds very interesting and helpful !

If your map is public, please let me know how can I access your map.

Maybe, I could upload some information of Japan

james hadfield · 05-20-2009, 01:46 PM

Unfortunately I cannot get Google Maps to do what I would like and make a publicly accessible map where anyone can add their location and equipment.
Try a google map searh for "Genomics: nextgen", you should find it.

ECO · 05-20-2009, 03:31 PM

I love this idea and am looking into how to make it happen.

(james I got your msg, will respond tonight).

bioinfosm · 05-21-2009, 10:42 AM

this is good guys .. I will watch out for it

not sure if this link will work for people
http://maps.google.com/maps/ms?msa=0...en&ie=UTF8&z=2

David Lovell · 05-21-2009, 08:43 PM

Hi All,
First, big thanks to James for getting this happening. I’ve been thinking about this for a while, so when a colleague emailed me a pointer to this on SeqAnswers, I thought this opportunity to good to miss.

I think geographical view of sequencing (and related) facilities will be a very useful resource, especially as an overview of a very rapidly changing environment. Recently, Ewan Birney (EBI) gave a seminar and workshop series in Australia and, when he asked the obvious question “what sort of ‘omics facilities does Australia have?” it was impossible to give a succinct response.

I’m going to make some suggestions with the aim to create a map resource (or resources) that are (a) easy to search (b) easy to maintain (c) easy for anyone to contribute to.

My suggestions are
1. To use GoogleMaps as the platform, rather than anything more customised
2. To follow GoogleMaps’ approaches to collaborating and sharing
3. To consider having a map per continent, country or region, e.g., Europe, Australia, Oceania to avoid all the admin, setup etc falling on one altruist. One person has to “own” a GoogleMap, even though many others can contribute.
4. To use a labelling approach that’s helpful and consistent across maps

GoogleMaps provides the ability to import one GoogleMap into another (wanna try that James?) so it seems conceivable to create a master map from several others while devolving the responsibility of maintaining and managing different maps.

To explore these ideas a bit further I started a map of Australian 'omics and bioinformatics (with all of four entries).

I’d be interested to know your thoughts about this, or any ideas to make things work better.
Cheers,
David

james hadfield · 05-21-2009, 11:11 PM

http://tinyurl.com/orm8cr

here is a link, ask if you would like to be a collaborator and add your facility or any in your vicinity. I will need your email address to do this.
James.

james hadfield · 05-21-2009, 11:16 PM

David made some great comments and I have opened the map to collaborators and will try to mege our two maps to see how this works out.

3. To consider having a map per continent, country or region, e.g., Europe, Australia, Oceania to avoid all the admin, setup etc falling on one altruist. One person has to “own” a GoogleMap, even though many others can contribute.
In may ways I prefer to add anyone on SeqAnswers to the collaborator list on a single map to prevent things getting lost.

4. To use a labelling approach that’s helpful and consistent across maps
Absolutley, I tried to distinguish three main platforms and it is not easy. What do you do when there is everything in one lab! Your thoughts on this would be appreciated, anyone know how to build icons?

Glad to see this has gotten peoples attention.

ECO · 05-22-2009, 05:59 AM

Nice work gents. James, the pins aren't showing up for the map you set up. David's seems to work.

Edit: Nevermind. Just have to unview and view again. Added LIFE and corrected the location for Illumina's home base.

JasonKTA · 05-22-2009, 10:53 AM

I would add Prognosys Biosciences in La Jolla as an Illumina GAII sequencing center.

505 Coast Blvd. S
La Jolla, California 92037
858-459-2428

This map is a great idea and will be very useful. Thanks!

Terry V · 06-03-2009, 02:55 AM

Great stuff! Im gonna try and create a Google account, cuz I got some more centres to add. Could this be the start of a medical sequencing consortium?

james hadfield · 06-03-2009, 12:29 PM

Hi Everyone,
Several people have contated me about this post and asked to be added as collaborators so they can add facilities. I am more than happy to do this or let go and pass this resource onto someone elses more capable hands. Any volunteers?
I know there are loads of better user created and editable maps out there for other applications so it can be done better. However I will update and manage this creation until something better comes along.
Thanks for the positive response.
James.

Terry V · 06-04-2009, 12:34 AM

Hi James, although I do not have the capacity to come up with a better tool than GoogleMaps (when it comes to computer tools, I am completely dependant on what exists already), but I would be more than happy to take the burden of collecting everything out of your hands. I would be really motivated to expand and complete this thing!

dkoboldt · 08-12-2009, 10:56 AM

James,

I should point out that the markers for WashU are incorrectly located in Seattle, WA (where the Univ. of Seattle is located).

The Genome Center at Washington University is in St. Louis, Missouri.

Address: 4444 Forest Park Blvd, St. Louis, MO 63108 USA.

vialea · 08-12-2009, 11:13 AM

Hi James
Please add Memorial Sloan Kettering Cancer Center (New York,zip code 10065).The Genomics Core Lab has a 454 and a SOLiD.
Thanks

MU Core · 08-12-2009, 11:47 AM

Hello James,

We are a core facility with one GAIIx.

DNA Core Facility
University of Missouri
216 Bond Life Sciences Center
Columbia, MO 65211
http://biotech.missouri.edu/dnacore/

MichaelTippie · 08-12-2009, 12:26 PM

At Eureka Genomics we provide next generation sequencing services on an Illumina GA IIx as well as advanced bioinformatics analysis of next gen data using proprietary algorithms developed by our scientific founder, Dr. Yuriy Fofanov. We have worked for a variety of big pharma, biotech, government and academic researchers. Our next presentation is at the CHI Next Generation Sequencing Conference in Providence, RI on 9/23/09.

In the US, we provide both sequencing and bioinformatics. In the rest of the world we partner with excellent local sequencing providors (e.g. Source Biosciences in the UK, GATC in Germany, Genotypic in India) who do the next gen sequencing and then we perform the bioinformatics analysis.

Best regards,

Michael Tippie
VP, Business Development
Eureka Genomics
750 Alfred Nobel Dr.
Hercules, CA 94547
510-964-0461 (w)
425-830-5805 (cell)
www.eurekagenomics.com

chrisamiller · 08-12-2009, 01:10 PM

Baylor College of Medicine is mislabeled on your map. It's in Houston, TX, not Waco (we're unaffiliated with Baylor University). Here's a map of the correct location:

http://maps.google.com/maps?f=q&sour...3&ie=UTF8&z=17

Thanks, and nice work.

Jarretinha · 08-12-2009, 03:55 PM

Hi James and colleagues,

Found this thread in my GenomeWeb feed. It's really a nice idea to see how this machines spread over the world. Do anyone know where I can find a Heliscope? By the way, I'm marking the next-gen seq center here in Brazil.

LNCC - Laboratório Nacional de Computação Científica
Av. Getulio Vargas, 333
CEP 25651-075, Petrópolis, RJ - Brazil
They have a 454.

Instituto de Biologia
Universidade Federal do Pará
R. Augusto Corrêa, 1
CEP 66075-110, Belém, PA - Brazil
They have a SOLiD

Centro Avançado de Tecnologias em Genômica
Universidade de São Paulo
Av. Prof. Lineu Prestes, 748
CEP 05508-000 São Paulo, SP - Brazil
They have a 454.

There are more of them here, but by now I was unable to track them down.

Best,
Daniel

DNAcowboy · 08-13-2009, 03:16 AM

Nice Work James, congratulation.

Could you let us know the grand total number of instrument you have collected until now?

I read recently this paper:
http://www.genomeweb.com/leerink-rep...-poised-growth
(the whole paper can be found here: http://siliconinvestor.advfn.com/rea...msgid=25756735)
which mentions 900 instrument worldwide. Are we there yet?

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05-05-2009, 01:40 PM	#1
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Google maps for next-gen facilities Hi everyone, I made a Google Map to try and add the facilities I knew of where there was a next-gen sequencer (and other genomics platforms). It is proving to be interesting to me but I would really like to make it easier for anyone to add content and search for users, always good when you want to find someone local to talk to! Is there anyone out there who could make a really useful map, post it and then members of SeqAnswers could update it? James. Map Title is "Genomics: NextGen sequencers; Illumina (Solexa), ABI SOLiD, Roche/454. Microarrays: Illumina BeadStation, Affymetrix"

05-07-2009, 10:38 PM	#2
gengen Junior Member Location: Osaka, Japan Join Date: May 2009 Posts: 4	How can I access ? Your map sounds very interesting and helpful ! If your map is public, please let me know how can I access your map. Maybe, I could upload some information of Japan

05-21-2009, 08:43 PM	#6
David Lovell Junior Member Location: Canberra, Australia Join Date: May 2009 Posts: 2	GoogleMaps for next-gen: Suggestions about how to collaborate Hi All, First, big thanks to James for getting this happening. I’ve been thinking about this for a while, so when a colleague emailed me a pointer to this on SeqAnswers, I thought this opportunity to good to miss. I think geographical view of sequencing (and related) facilities will be a very useful resource, especially as an overview of a very rapidly changing environment. Recently, Ewan Birney (EBI) gave a seminar and workshop series in Australia and, when he asked the obvious question “what sort of ‘omics facilities does Australia have?” it was impossible to give a succinct response. I’m going to make some suggestions with the aim to create a map resource (or resources) that are (a) easy to search (b) easy to maintain (c) easy for anyone to contribute to. My suggestions are 1. To use GoogleMaps as the platform, rather than anything more customised 2. To follow GoogleMaps’ approaches to collaborating and sharing 3. To consider having a map per continent, country or region, e.g., Europe, Australia, Oceania to avoid all the admin, setup etc falling on one altruist. One person has to “own” a GoogleMap, even though many others can contribute. 4. To use a labelling approach that’s helpful and consistent across maps GoogleMaps provides the ability to import one GoogleMap into another (wanna try that James?) so it seems conceivable to create a master map from several others while devolving the responsibility of maintaining and managing different maps. To explore these ideas a bit further I started a map of Australian 'omics and bioinformatics (with all of four entries). I’d be interested to know your thoughts about this, or any ideas to make things work better. Cheers, David

05-22-2009, 10:53 AM	#10
JasonKTA Junior Member Location: San Diego, California Join Date: May 2009 Posts: 1	I would add Prognosys Biosciences in La Jolla as an Illumina GAII sequencing center. 505 Coast Blvd. S La Jolla, California 92037 858-459-2428 This map is a great idea and will be very useful. Thanks! Last edited by JasonKTA; 05-22-2009 at 11:18 AM.

05-20-2009, 01:46 PM	#3
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Unfortunately I cannot get Google Maps to do what I would like and make a publicly accessible map where anyone can add their location and equipment. Try a google map searh for "Genomics: nextgen", you should find it.

05-20-2009, 03:31 PM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	I love this idea and am looking into how to make it happen. (james I got your msg, will respond tonight).

05-21-2009, 10:42 AM	#5
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	this is good guys .. I will watch out for it not sure if this link will work for people http://maps.google.com/maps/ms?msa=0...en&ie=UTF8&z=2

05-21-2009, 11:11 PM	#7
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	http://tinyurl.com/orm8cr here is a link, ask if you would like to be a collaborator and add your facility or any in your vicinity. I will need your email address to do this. James.

05-21-2009, 11:16 PM	#8
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	David made some great comments and I have opened the map to collaborators and will try to mege our two maps to see how this works out. 3. To consider having a map per continent, country or region, e.g., Europe, Australia, Oceania to avoid all the admin, setup etc falling on one altruist. One person has to “own” a GoogleMap, even though many others can contribute. In may ways I prefer to add anyone on SeqAnswers to the collaborator list on a single map to prevent things getting lost. 4. To use a labelling approach that’s helpful and consistent across maps Absolutley, I tried to distinguish three main platforms and it is not easy. What do you do when there is everything in one lab! Your thoughts on this would be appreciated, anyone know how to build icons? Glad to see this has gotten peoples attention.

05-22-2009, 05:59 AM	#9
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Nice work gents. James, the pins aren't showing up for the map you set up. David's seems to work. Edit: Nevermind. Just have to unview and view again. Added LIFE and corrected the location for Illumina's home base.

06-03-2009, 02:55 AM	#11
Terry V Junior Member Location: the Netherlands Join Date: Jun 2009 Posts: 6	Great stuff! Im gonna try and create a Google account, cuz I got some more centres to add. Could this be the start of a medical sequencing consortium?

06-03-2009, 12:29 PM	#12
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Hi Everyone, Several people have contated me about this post and asked to be added as collaborators so they can add facilities. I am more than happy to do this or let go and pass this resource onto someone elses more capable hands. Any volunteers? I know there are loads of better user created and editable maps out there for other applications so it can be done better. However I will update and manage this creation until something better comes along. Thanks for the positive response. James.

06-04-2009, 12:34 AM	#13
Terry V Junior Member Location: the Netherlands Join Date: Jun 2009 Posts: 6	Volunteer nr 1 Hi James, although I do not have the capacity to come up with a better tool than GoogleMaps (when it comes to computer tools, I am completely dependant on what exists already), but I would be more than happy to take the burden of collecting everything out of your hands. I would be really motivated to expand and complete this thing!

08-12-2009, 10:56 AM	#14
dkoboldt Member Location: St. Louis Join Date: Mar 2009 Posts: 62	James, I should point out that the markers for WashU are incorrectly located in Seattle, WA (where the Univ. of Seattle is located). The Genome Center at Washington University is in St. Louis, Missouri. Address: 4444 Forest Park Blvd, St. Louis, MO 63108 USA.

08-12-2009, 11:13 AM	#15
vialea Junior Member Location: New York Join Date: Aug 2009 Posts: 1	addition Hi James Please add Memorial Sloan Kettering Cancer Center (New York,zip code 10065).The Genomics Core Lab has a 454 and a SOLiD. Thanks

08-12-2009, 11:47 AM	#16
MU Core Member Location: Columbia, Missouri Join Date: Apr 2008 Posts: 57	Addition Hello James, We are a core facility with one GAIIx. DNA Core Facility University of Missouri 216 Bond Life Sciences Center Columbia, MO 65211 http://biotech.missouri.edu/dnacore/

08-12-2009, 12:26 PM	#17
MichaelTippie Junior Member Location: Hercules, CA Join Date: Aug 2009 Posts: 1	Please add Eureka Genomics as a site for Illumina GA II At Eureka Genomics we provide next generation sequencing services on an Illumina GA IIx as well as advanced bioinformatics analysis of next gen data using proprietary algorithms developed by our scientific founder, Dr. Yuriy Fofanov. We have worked for a variety of big pharma, biotech, government and academic researchers. Our next presentation is at the CHI Next Generation Sequencing Conference in Providence, RI on 9/23/09. In the US, we provide both sequencing and bioinformatics. In the rest of the world we partner with excellent local sequencing providors (e.g. Source Biosciences in the UK, GATC in Germany, Genotypic in India) who do the next gen sequencing and then we perform the bioinformatics analysis. Best regards, Michael Tippie VP, Business Development Eureka Genomics 750 Alfred Nobel Dr. Hercules, CA 94547 510-964-0461 (w) 425-830-5805 (cell) www.eurekagenomics.com

08-12-2009, 01:10 PM	#18
chrisamiller Junior Member Location: USA Join Date: Jun 2008 Posts: 7	Baylor College of Medicine is mislabeled on your map. It's in Houston, TX, not Waco (we're unaffiliated with Baylor University). Here's a map of the correct location: http://maps.google.com/maps?f=q&sour...3&ie=UTF8&z=17 Thanks, and nice work. Last edited by chrisamiller; 08-12-2009 at 01:10 PM. Reason: typo

08-12-2009, 03:55 PM	#19
Jarretinha Junior Member Location: São Paulo Join Date: Aug 2009 Posts: 3	Hi James and colleagues, Found this thread in my GenomeWeb feed. It's really a nice idea to see how this machines spread over the world. Do anyone know where I can find a Heliscope? By the way, I'm marking the next-gen seq center here in Brazil. LNCC - Laboratório Nacional de Computação Científica Av. Getulio Vargas, 333 CEP 25651-075, Petrópolis, RJ - Brazil They have a 454. Instituto de Biologia Universidade Federal do Pará R. Augusto Corrêa, 1 CEP 66075-110, Belém, PA - Brazil They have a SOLiD Centro Avançado de Tecnologias em Genômica Universidade de São Paulo Av. Prof. Lineu Prestes, 748 CEP 05508-000 São Paulo, SP - Brazil They have a 454. There are more of them here, but by now I was unable to track them down. Best, Daniel Last edited by Jarretinha; 08-12-2009 at 04:18 PM.

08-13-2009, 03:16 AM	#20
DNAcowboy Member Location: france Join Date: Apr 2008 Posts: 31	Nice Work James, congratulation. Could you let us know the grand total number of instrument you have collected until now? I read recently this paper: http://www.genomeweb.com/leerink-rep...-poised-growth (the whole paper can be found here: http://siliconinvestor.advfn.com/rea...msgid=25756735) which mentions 900 instrument worldwide. Are we there yet? Last edited by DNAcowboy; 08-13-2009 at 03:19 AM. Reason: provide full link