Performance of UCSC genome browser

[asma.m...@yahoo.com]

I am very interested in knowing several thing about UCSC genome browser like the following:

What is the biggest data set that was used in this genome browser? What is the size of it?

How many concurrent user can your genome browser handle??

How fast is the navigation and uploading functions?

How many tracks can be shown? Is there an upper limit?

Best Regards

Asma Mistadi

[Jonathan Casper]

Hello Asma,

Thank you for your question about the performance of the UCSC Genome Browser. Exactly which single track is the largest one is hard to measure, but certainly one of the contenders would be the 100-way multiple alignment that we provide for the human hg19 genome assembly. The collected .maf files that provide the data for that track consume about 1.5 terabytes.

Our concurrent user limit is hard to test - we certainly don't want to bring down our live server by testing the limits! If it helps though, the UCSC Genome Browser receives over 1.3 million hits per day. So it's at least that much.

I am not sure how to measure the speed of nagivation. How quickly a page loads depends a great deal on the bandwidth and latency of the connection between our servers and the user. Upload speed is similarly limited - our systems sit behind a 10GB connection, but in practice other factors will likely limit it to much less.

The only upper limit on the number of displayed tracks is from the timeout that we apply to our CGIs. If the Genome Browser has not finished drawing all of the tracks after 5 minutes, it stops trying because there is just too much data. That said, there are some locations where it is possible to view, for example, all 180 tracks of the hg19 human genome assembly. Please note that the number of tracks for hg19 is 180 at the time of my writing, but it will likely go up again in the near future.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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