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Re: [Gmod-ajax] URL help
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From: Scott C. <sc...@sc...> - 2022-10-19 19:28:55
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The other thing that just occurred to me is relatively low-tech: get a bunch of thumb usb drives (4 or 8 GB ones are pretty cheap) and put the data on them and then just hand them out to your students. On Wed, Oct 19, 2022 at 9:19 AM Scott Cain <sc...@sc...> wrote: > 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... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qQ%2FBysXzDTQOgjR9l53q8l1FrvrNvB5AtbGCBbV%2BGBQ%3D&reserved=0> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8U%2F5MVsNSMnlNjFOa6xapvA2%2FYkziLN0va6%2FSz1NCZE%3D&reserved=0>) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gEWlRGTiBO1%2FKdFHmrdBSBATe1iJkYHYnbcyd8x%2BRIk%3D&reserved=0> >> ) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874605958%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MLajm2JStSdqzyGglrCVDfaLxs9M9vJpTWJXhLCyx70%3D&reserved=0> >> ) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> >> ) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> >> ) >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ef%2FtxFQca4jWYKOCgl2hqUnx8JcY4T66J0aChae6DUs%3D&reserved=0>) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=poog6eHte%2FW3uaKJimk7TjuKm13XNHqP79pnDnoohGQ%3D&reserved=0> >> ) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >> <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fkfJ2bZy0oLsERzABMAzo1VHJ%2Fi6tb5tIiIhxMTKoSo%3D&reserved=0> >> ) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ch%2FVsYa1GkaGMoXsYkZaXEtuT1MsD9klg%2BOYRyeY188%3D&reserved=0> >> ) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/ >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7COlivia_Rasmussen%40student.uml.edu%7C2ccf3ad164b74bcd265008daacd26477%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638012316874762656%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLXzR21K0WtSljMj04HIcISQezKhJT%2BPlHxCzNUvoyM%3D&reserved=0> >> ) >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/) > 216-392-3087 > WormBase Developer (http://wormbase.org/) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/) > VirusSeq Project Manager (https://virusseq-dataportal.ca/) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/) > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Project Manager (http://gmod.org/) 216-392-3087 WormBase Developer (http://wormbase.org/) Alliance of Genome Resources Group Leader (http://alliancegenome.org/) VirusSeq Project Manager (https://virusseq-dataportal.ca/) Human Cancer Models Initiative Project Manager ( https://hcmi-searchable-catalog.nci.nih.gov/) |
