Re: [Gmod-ajax] URL help

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Hi Olivia,

How much control do you have over the students' learning environment? If
you have access to the machines to set them up before the students use them
and there aren't too many (or you had a good network admin), you could just
place the data files on each computer's hard drive, or if the files are too
big to do that, you could mount the one drive on each of the computers as a
local drive (I googled for directions for how to do that and it looks like
it would probably be doable for Windows and Mac at least).

If you don't have easy access to the students' machines, then you need to
be able to give them a URL to load data. I have had lots of success with
Amazon Web Services S3 buckets, where I configured the bucket to allow CORS
requests (cross origin resource sharing--required by web servers as a way
to protect against malicious websites from getting dangerous things to your
computer without you knowing it) and then set the data in the S3 bucket as
publicly readable. If you want to go down that route, we can help you with
the details, and I suspect since this is a research project involving
teaching students, you could probably get some S3 storage space from AWS
for free.

I know that it is also possible to do all of the above (CORS, public read
data, and a URL) with Google Cloud, but I don't know how to do it; I only
know it's possible because I have a track in WormBase's JBrowse that pulls
data from a researcher who put his data in a public Google Cloud space. And
it is possible that you could do all of this with OneDrive, but I don't
know how to do that either.

The last thing you could do would be to ask the IT staff at UML to set up a
small web server for your project where you could put the data or set one
up yourself if you're allowed by the university; if you wanted to go down
that route, we can help with that too.

Good luck with your choice,
Scott

On Wed, Oct 19, 2022 at 5:45 AM Rasmussen, Olivia <
Oli...@st...> wrote:

> Hello,
> Thanks so much for getting back to me and sorry for the delayed response.
> This is helpful information to know. It seems like the problem is
> definitely that it is not public. I was wondering if there is any sort of
> work around for this? It's okay if not we are just trying to understand the
> best way to approach this based on what we are trying to do with the
> research. Open to using something that isn't one drive. That just is where
> it is stored at the moment
>
> Olivia
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Thursday, October 13, 2022 12:21:13 AM
> *To:* Rasmussen, Olivia <Oli...@st...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] URL help
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> Hi Olivia,
>
> I wrote a bunch of stuff below, but then went back and reread your email,
> so maybe I can ask more useful questions. I'll keep the other stuff below a
> line so you can read it if you want :-)
>
> So you have some BAM and BAI files on a Microsoft One Drive and want to
> use the data on that to load into JBrowse. I've never used one drive. Is it
> mounted locally so that it "looks like" a local drive, or is it a cloud
> drive that you have to use some other mechanism to access the data (for
> example, can you/do you want to access the data via a URL)? If it's a
> mounted drive and you can load it like it's a local file, I would expect
> that would work. If you've tried that and it doesn't work, please open the
> browser's developer tools/javascript console to see if there are any errors
> and send them to us.
>
> If you have to access the data on one drive via a URL, it gets a little
> trickier. It would make life easier if the data were accessible publicly
> (meaning you don't need a password or other credential to get it), but that
> might be possible to work around. Additionally, binary data like BAM have
> to be accessed via http using a web server that supports range requests,
> and I have no idea whether one drive does. If you want to give us access to
> the data, we can try to see if we can sort it out. Again, if you try it and
> nothing happens, look in the javascript console for error messages.
>
> Networking technology aside, do these files load correctly if the files
> are local on your computer? Things like naming chromosomes the same as your
> reference sequence frequently trips people up, since "1" is not the same as
> "chr1" which is also not the same as "Chr1". Just something to look into.
>
> Anyway, that's a lot of stuff to get started with.  Let us know where to
> go from here.
>
> Scott
>
>
>
>
> ------------------------
>
> Maybe you can tell us a little more about what you want to do. As Colin
> wrote this morning, JBrowse doesn't really "upload" any data at all. If you
> load local data into the jbrowse instance, it stays on your computer and
> the web browser just accesses the data locally.  If you need to upload
> something (like so one person can share a view with someone else of data
> they have on their computer), you have to sort out some way outside of
> JBrowse to make that happen.  If the users are all local to one another,
> that could be as easy as a shared network drive where the data are placed,
> or if the users aren't all on the same local network, you could put the
> data in a cloud resource like AWS S3 (if this is for a student project, you
> might be able to get a grant from Amazon to supply you with some S3
> space).  But this is all hand-waving until we really know what you want to
> do.
>
>
>
> Scott
>
>
> On Wed, Oct 12, 2022 at 12:14 PM Rasmussen, Olivia <
> Oli...@st...> wrote:
>
> Hello,
> Yes I am. Sorry I sent both! It’s probably easier via email if that’s
> alright. I’m just wondering if it’s possible to upload the links directly
> to jbrowse via a url or if it’s not possible and the data set just needs to
> be downloaded. I've tried and nothing happens. Uploading the downloaded set
> from my computer works fine but because the files are large it's not
> sustainable for the type of project I'm trying to accomplish.
>
> Olivia
>
> Get Outlook for iOS
> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2Fo0ukef&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ObNBohaz0uGMCcWmxsmCahCYVqWT1WUgOaAT5cNlQvQ%3D&reserved=0>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Wednesday, October 12, 2022 3:06:58 PM
> *To:* Rasmussen, Olivia <Oli...@st...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] URL help
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> Hi Olivia,
>
> I'm wondering if you are the same person who asked a similar question on
> gitter. Either is fine with me; you're welcome to have the discussion
> anywhere you want :-)
>
> Scott
>
>
> On Wed, Oct 12, 2022 at 12:05 PM Rasmussen, Olivia <
> Oli...@st...> wrote:
>
> Hello,
> My name is Olivia and I am a student at Umass Lowell, currently working on
> a research project which involves teaching high school students how to use
> Jbrowse.
> I am wondering gif there is a way to upload data directly from a URL?
> Currently the data is on a one drive account and I have tried many times to
> upload the links into the new track box but nothing ever works. We are
> using BAM and BAI links. Wondering if you have any insight.
>
> Thanks,
> Olivia
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
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> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
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> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
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VirusSeq Project Manager (https://virusseq-dataportal.ca/)
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https://hcmi-searchable-catalog.nci.nih.gov/)