GI2012TrackHubsPoster: Difference between revisions

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This page contains links related to the UCSC Genome Browser poster presented by [[User:brianraney|Brian Raney]] at Genome Informatics 2012 [https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296])
This page contains links related to the UCSC Genome Browser poster presented by Brian Raney at Genome Informatics 2012 [https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296])


=Poster: Remote Data Track Storage for Viewing on the UCSC Genome Browser  =
=Remote Data Track Storage for Viewing on the UCSC Genome Browser  =


* Files: [[Media:Hinrichs_BoG2012_GBVariants.pptx|.pptx]], [[Media:Hinrichs_BoG2012_GBVariants.pdf|PDF]]
* Files: [[File:BraneyGI2012.pdf]] [[File:BraneyGI2012.pptx]]


==Parallel downloading, remote access, and caching make for good performance==
= Introduction to Track Data Hubs =
The technology behind the data hubs, and their optimization, is what enables good performance in the browser. Threads allow hub tracks to be downloaded in parallel, avoiding an otherwise large serial internet latency that tends to increase both with distance to the remote hub and with the number of hub tracks visible. The performance of the cache becomes very important once the data has been fetched. Optimizations include a read-ahead buffer for the cache data that speeds up reading by a factor of 30. Browser users typically visit a few favorite genes, and only those small pieces of the large remote data file are fetched. The cache contains a sparse data file as well as a bitmap file that keeps track of cached blocks.  Unix stores files as sparse files, which take up no space for unwritten parts of the file. This results in great disk-space efficiency in the cache. Temporarily inaccessible data hub resources are handled with reasonable timeouts and informative error messages.
Navigate to this URL to get information about track data hubs, including information about how to set one up, and to register it with the UCSC Genome Browser.


==Assembly Data hubs==
[http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html]
To address the increasing need for researchers to annotate sequence for which UCSC does not provide an annotation database, we will be introducing Assembly Data hubs. These will allow researchers to include the underlying reference sequence, as well as data tracks that annotate that sequence.   Sequence will be stored in the UCSC twoBit format, and the annotation tracks will be stored in the same manner as Track Data Hubs.


==How to get help==
=How to get help=
* Search for answers in our mail list archives: [http://genome.ucsc.edu/contacts.html http://genome.ucsc.edu/contacts.html]
* Search for answers in our mail list archives: [http://genome.ucsc.edu/contacts.html http://genome.ucsc.edu/contacts.html]
* Email a new question to our actively monitored list [mailto:genome@soe.ucsc.edu genome@soe.ucsc.edu]
* Email a new question to our actively monitored list [mailto:genome@soe.ucsc.edu genome@soe.ucsc.edu]
* OpenHelix's free training materials: [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml]
* OpenHelix's free training materials: [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml]


==Other posters about the UCSC Genome Browser==
=Other posters and presentations about the UCSC Genome Browser, or by related groups=


* Visually integrating genomic data in the UCSC Genome Browser. Hinrichs AS ''et al.'' HGV 2011 [[HGV2011|genomewiki page]]  [[Media:HGV2011_GenomeBrowser.pptx|.pptx]], [[Media:HGV2011_GenomeBrowser.pdf|PDF]]
[[Presentations]]
* UCSC Genome Browser Data Hubs. Zweig AS ''et al.'' Biology of Genomes, 2011 [http://users.soe.ucsc.edu/~ann/BoG2011.pdf PDF]
 
* Genome-wide ENCODE Data at UCSC. Rosenbloom KR ''et al.'' ASHG, 2010. [[Media:ENCODE_ASHG2010.ppt|PPT]]
[[Category:Technical FAQ]]
* UCSC Genome Browser Tool Suite. Hinrichs AS ''et al.'' Genomics of Common Disease, 2008: [[Media:UCSC_Genome_Browser_GCD_2008.ppt|.ppt]], [[Media:UCSC_Genome_Browser_GCD_2008.pdf|PDF]]
[[Category:Assembly/Track Hubs]]

Latest revision as of 21:08, 23 April 2013

This page contains links related to the UCSC Genome Browser poster presented by Brian Raney at Genome Informatics 2012 [1])

Remote Data Track Storage for Viewing on the UCSC Genome Browser

Introduction to Track Data Hubs

Navigate to this URL to get information about track data hubs, including information about how to set one up, and to register it with the UCSC Genome Browser.

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

How to get help

Other posters and presentations about the UCSC Genome Browser, or by related groups

Presentations

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