Hello Galaxy Folks,
NCBI has received a few requests to provide a mechanism for people browsing the NCBI databases to download the data they have selected into Galaxy, so we are looking into it. I know some other sites have done this, it looks like through a URL based callback mechanism.
However, I know things can change over time, and I'd like to be sure that we are assessing an approach that reflects your current best thinking, whether it turns out to be something well established you are happy with, or if you might be considering moving toward something new, we'd like you to tell us what you think would work best for your users in your environment.
If you can just point me at a URL with the appropriate documentation, that's great. If you'd prefer to dialog a little, we're happy to talk. If there is a particular person we should be talking to, let me know.
Thanks for your help.
Regards, Jim Ostell
James M. Ostell, Ph.D. Chief, Information Engineering Branch National Center for Biotechnology Information, NLM, NIH Bldg 45, Rm 5AN.44A 45 Center Drive Bethesda, MD 20892-6510
Hi Jim,
The preferred method to add external datasources is the URL-based callback mechanism as described in http://www.ncbi.nlm.nih.gov/pubmed/21531983 and http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources. It has proven effective for importing data from various data resources using their native interfaces into any of the many public or private Galaxy instances which exist, based upon the user's starting location.
Please let us know if we can provide additional assistance.
Thanks for your interest in Galaxy,
Dan
On Oct 26, 2011, at 9:00 AM, Ostell, Jim (NIH/NLM/NCBI) [E] wrote:
Hello Galaxy Folks,
NCBI has received a few requests to provide a mechanism for people browsing the NCBI databases to download the data they have selected into Galaxy, so we are looking into it. I know some other sites have done this, it looks like through a URL based callback mechanism.
However, I know things can change over time, and I’d like to be sure that we are assessing an approach that reflects your current best thinking, whether it turns out to be something well established you are happy with, or if you might be considering moving toward something new, we’d like you to tell us what you think would work best for your users in your environment.
If you can just point me at a URL with the appropriate documentation, that’s great. If you’d prefer to dialog a little, we’re happy to talk. If there is a particular person we should be talking to, let me know.
Thanks for your help.
Regards, Jim Ostell
James M. Ostell, Ph.D. Chief, Information Engineering Branch National Center for Biotechnology Information, NLM, NIH Bldg 45, Rm 5AN.44A 45 Center Drive Bethesda, MD 20892-6510
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks Dan,
We will read the docs and follow up. I cc'd 5 folks who are looking into this at NCBI by way of email introduction, in case you get some questions from one of them.
Regards, Jim Ostell
From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Wednesday, October 26, 2011 3:56 PM To: Ostell, Jim (NIH/NLM/NCBI) [E] Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Providing Data to Galaxy Users
Hi Jim,
The preferred method to add external datasources is the URL-based callback mechanism as described in http://www.ncbi.nlm.nih.gov/pubmed/21531983 and http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources. It has proven effective for importing data from various data resources using their native interfaces into any of the many public or private Galaxy instances which exist, based upon the user's starting location.
Please let us know if we can provide additional assistance.
Thanks for your interest in Galaxy,
Dan
On Oct 26, 2011, at 9:00 AM, Ostell, Jim (NIH/NLM/NCBI) [E] wrote:
Hello Galaxy Folks,
NCBI has received a few requests to provide a mechanism for people browsing the NCBI databases to download the data they have selected into Galaxy, so we are looking into it. I know some other sites have done this, it looks like through a URL based callback mechanism.
However, I know things can change over time, and I'd like to be sure that we are assessing an approach that reflects your current best thinking, whether it turns out to be something well established you are happy with, or if you might be considering moving toward something new, we'd like you to tell us what you think would work best for your users in your environment.
If you can just point me at a URL with the appropriate documentation, that's great. If you'd prefer to dialog a little, we're happy to talk. If there is a particular person we should be talking to, let me know.
Thanks for your help.
Regards, Jim Ostell
James M. Ostell, Ph.D. Chief, Information Engineering Branch National Center for Biotechnology Information, NLM, NIH Bldg 45, Rm 5AN.44A 45 Center Drive Bethesda, MD 20892-6510
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Ostell, Jim (NIH/NLM/NCBI) [E]