Our Current Protocols paper on the UCSC Genome Browser is out!

We teamed with Bob Kuhn of the UCSC Genome Browser group to create a series of pragmatic, useful, and (we hope) effective examples of how molecular biologists can use the UCSC Genome Browser to make their benchwork time more efficient, and to represent their discoveries as custom tracks in the browser as well. And that paper is now out on the Current Protocols site:

http://www.currentprotocols.com/protocol/mb1909 (or the short version: http://bit.ly/413iNw)

cp_paper_UCSC_new

Thanks to my co-authors for their huge contributions and helpful suggestions.  We are happy to take questions here, or over at the CP site.  Or if you have comments/suggestions for future updates we are open to that as well.  We are encouraged by the publishers to update that manuscript periodically, and if something isn’t flowing for you, or you need more information, be sure to holler.

FYI: we have one in the pipeline on Galaxy as well. We’ll let you know when that is available as well.  For now, check out the free tutorial on Galaxy here.


Full reference and abstract: http://www.ncbi.nlm.nih.gov/pubmed/19816931

Curr Protoc Mol Biol. 2009 Oct;Chapter 19:Unit19.9.

The UCSC genome browser: what every molecular biologist should know.

Mangan ME, Williams JM, Kuhn RM, Lathe WC 3rd.

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one’s understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.

PMID: 19816931

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