Hello,
Is there anything I can do to imprve the speed when using the browser? It has been frustratingly slow as of late.
Thank you,
James T Bennett, MD PhD
Division Genetic Medicine
Department of Pediatrics, University of Washington
Assistant Director, Molecular Diagnostics, Seattle Children's Hospital
Brotman Baty Institute for Precision Medicine
Center for Developmental Biology and Regenerative Medicine
206-884-2324 OFFICE
917-797-8963 CELL
http://depts.washington.edu/cdbrm/wordpress/research-labs/bennett-lab/
OFFICE 1900 Ninth Ave., Seattle, WA 98101
MAIL M/S C9S-5 Room 545,, Seattle, WA 98101
Hello James,
Thank you for writing to the Genome Browser support team about your speed issue.
We will do our best to suggest some speed improvements, but could you please send us one or more Saved Session links with the view(s) that are very slow? Additional information may be helpful too: what type of data do you normally view? Are you using a GBiB or GBiC mirror? To share a session, you can access our Saved Sessions page here:
For general performance increases, we suggest reducing the number of tracks (including Custom Tracks) to a minimum and/or reducing their display to "Dense". If your Genome Browser is pulling data from a variety of large BED or WIG files, visualization may be faster if stored in compressed and indexed bigBed / bigWig formats. Further issues may arise if you host your files to visualize on a server that is slow to respond.
We will certainly do everything we can to help you and we appreciate your cooperation in resolving this problem. Please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.
All the best,
Daniel Schmelter
UCSC Genome Browser
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Thank you for your prompt response.
1) I do not have that many tracks open. I am aware that this can slow things down, but even when I hide almost all of them the browser is still crawling, slow I don’t think that is the solution.
2) I do not know if I am using a mirror or not. I just go to https://genome.ucsc.edu/cgi-bin/hgGateway
3) I am a clinical geneticist. So the tracks I generally use are gene names (ucsc genes and refseq), as well as all the variants (dbSNP, Gnomad, Exac), and some conservation tools (GERP, 64-way). I do like to have the codon numbering on by default. I generally turn off most of the copy number variant data and all the expression data. I like to have COSMIC on too, but have turned that off to try to improve speed.
4) Although I have uploaded custom tracks (BED file), I am not doing that now.
5) I also use in silico PCR and BLAT- they are also extremely slow.
I just created a login (for the first time actually!) to try to make my session public. Here is the link:
Here is a UCSC browser session I'd like to share with you: http://genome.ucsc.edu/s/bennej02/hg19_bennett_test
Thank you for your response, and for your important work on the browser!!
Best,
Jimmy
James T Bennett, MD PhD
Division Genetic Medicine
Department of Pediatrics, University of Washington
Assistant Director, Molecular Diagnostics, Seattle Children's Hospital
Brotman Baty Institute for Precision Medicine
Center for Developmental Biology and Regenerative Medicine
206-884-2324 OFFICE
917-797-8963 CELL
http://depts.washington.edu/cdbrm/wordpress/research-labs/bennett-lab/
OFFICE 1900 Ninth Ave., Seattle, WA 98101
MAIL M/S C9S-5 Room 545,, Seattle, WA 98101
From: Daniel Schmelter <dsch...@ucsc.edu>
Date: Monday, May 3, 2021 at 5:30 PM
To: "Bennett, James" <James....@seattlechildrens.org>
Cc: "gen...@soe.ucsc.edu" <gen...@soe.ucsc.edu>
Subject: Re: [genome] UCSC browser very slow past month
CAUTION: This email originated outside of this organization.
Dear James,
Thank you so much for sharing this session and helping us try to identify what is occurring to slow down your use of the site.
Can you do another step for us and check the results of this link (scrolling to the bottom of the page):
http://genome.ucsc.edu/s/bennej02/hg19_bennett_test?measureTiming=1
That will have some text like the below, that if you can copy and send back to us the text you see when you load this link it may help us understand what may be happening from your location:
track, load time, draw time, total (first window)
User Track, 4, 0, 4
Fix Patches, 72, 3, 75
UCSC Genes, 3, 5, 8
RefSeq Curated, 1, 11, 12Startup (bottleneck 0 ms) : 162 millis
Get cart of 138 for user:907878019_QhT3wCEONSQ2C8MmjQgHpMdqfzF1 session:(null): 0 millis
Time before getTrackList: 6 millis
Time after trackDbLoad : 368 millis
Time after visibilities: 9 millis
parentChildCartCleanup: 17 millis
Time at start of obtaining trash hgt png image file: 113 millis
Time completed writing trash hgt png image file: 102 millis
Done with trackForm: 13 millis
Time at end of doMiddle, next up cart write: 1 millis
Time to write and close cart: 1 millis
Overall total time: 792 millis
For instance, when we load your session we are not seeing a slowdown, although the first loading of the link did take 2 seconds, after that when navigating to new gene locations the response was much more quick (Overall total time: 728 millis).
If you are willing to do this for more than one link it might further help us.
Here is another link with many more tracks similar to the ones mentioned:
http://genome.ucsc.edu/s/dschmelt/hg19.clinicalTracksMentioned?measureTiming=1
Please distinguish which data you are sharing when you give the information found at the bottom of the pages (from "track, load time..." to "Overall total time:...").
Thank you again for reporting this experience and helping us in trying to resolve it.
All the best,
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/FF0FD53E-BE20-40F0-87CB-88EE657EF7CE%40seattlechildrens.org.
Hi Brian,
Thank you very much for your attention to this. I have attached two screenshots of this data, as requested. The first is just the bottom of the link you sent
http://genome.ucsc.edu/s/bennej02/hg19_bennett_test?measureTiming=1
I then zoomed in a bit to this link:
and screenshot the bottom of that (that is the 2nd screenshot)
Is this helpful?
Thanks,
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
We are having issues reproducing your connection issues. Does this slow down happens every time you zoom in on the Genome Browser? Does this issue also occur when you are using other web browsers?
I look forward to your reply. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/598CEA56-89B5-4C61-BE8A-7EF20C863825%40seattlechildrens.org.
Hi Jairo,
The UCSC browser is slow for me all the time. Other websites are just fine- definitely UCSC browser specific. It is not just slow when I zoom in- it is slow everywhere within https://genome.ucsc.edu/
As a specific example, it took a total of 36 seconds to go from screen 1, after clicking on the top RefSeq transcript of FGFR1, to screen 2. See attached.
This is a very long time, and it definitely did not used to be this long for me.
To compare, it is ~3 sec when I click on any article link within https://www.nytimes.com/
Any updates on my issue? Could we do a screen share or something so I can show you?
Thanks,
James T Bennett, MD PhD
Division Genetic Medicine
Department of Pediatrics, University of Washington
Assistant Director, Molecular Diagnostics, Seattle Children's Hospital
Brotman Baty Institute for Precision Medicine
Center for Developmental Biology and Regenerative Medicine
206-884-2324 OFFICE
917-797-8963 CELL
http://depts.washington.edu/cdbrm/wordpress/research-labs/bennett-lab/
OFFICE 1900 Ninth Ave., Seattle, WA 98101
MAIL M/S C9S-5 Room 545,, Seattle, WA 98101
Matthew Speir
UCSC Cell Browser, Quality Assurance and Data Wrangler
Human Cell Atlas, User Experience Researcher
UCSC Genome Browser, User Support
UC Santa Cruz Genomics Institute
Revealing life’s code.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/B536B280-CA87-4147-997F-8B3D702E967F%40seattlechildrens.org.
Hello,
First, thank you all very much for your help with this. As a geneticist I really need fast browser access- I use it almost every day!
Before trying all of what you suggested, I did an experiment. I accessed UCSC browser from my home. Using the exact same computer. And it worked at normal speed.
So I think it has something to do with the wifi connection, or my network, at work. Does this clue help you? I have not heard others at work report on UCSC but will ask. Is it possible the combination of something in my computer/proxies plus my work network are the issue?
Best,
Matthew Speir
UCSC Cell Browser, Quality Assurance and Data Wrangler
Human Cell Atlas, User Experience Researcher
UCSC Genome Browser, User Support
UC Santa Cruz Genomics Institute
Revealing life’s code.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CABJi3aLozc53pXwZX-_gak%2B7898W2OYi62XAi2y-qxdhVAqAUw%40mail.gmail.com.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAHm%3D4fwMjf4M9cQhSTQKj7bRJy83Une2UtOmJ2vSx0of0nLEkA%40mail.gmail.com.
Thank you- I have initiated a ticket with our IT guys on our end, will let you know.