Permission is granted for reuse of all graphics produced by the UCSC Genome Browser website. There is no need to contact us to get permission. If your publisher, notably Elsevier, insists on getting approval, please direct them to this webpage. However, when you use the UCSC Genome Browser in your work, please cite one of our publications.
As far as the UCSC Genome Browser group is concerned, the raw table data and binary files used to create the graphics by the browser is freely available for both public and commercial use. This applies to data that is downloaded as files via http, https, ftp or rsync, and equally when data is accessed through the public MySQL server or via the web API.
Sometimes, the source databases or authors place restrictions on the data. In very rare cases, the genomes come with citation requirements. The README.txt file in the download directory of each assembly shows the original restrictions pertaining to the genome sequence itself by the original authors; most assemblies do not have any restrictions.
Certain genome annotation data, mostly on the human genome and in the domain of clinical genetics, have specific restrictions. Usually the data must be obtained from the source database directly in the original format or licensed, rather from UCSC. Examples are HGMD, LOVD, OMIM, Decipher, Genomenom, Genehancer and COSMIC, as well as any GISAID-derived data on viral genomes. Please see the respective track documentation pages on these assemblies for more details, by selecting the assembly and clicking the track title in the genome browser.
The majority of the Genome Browser source code is available under the MIT license, see the file LICENSE in our source code repository. As such, the Unix command line utilities needed to build tracks and track hub files, or that can be part of computational pipelines except BLAT/liftOver, and our hundreds of tools to filter , sort, rearrange, join and process genome annotation files, can be used by anyone freely and they can be redistributed via package managers and installation tools, even for commercial use. Notable examples are bedToBigBed, wigToBigWig, overlapSelect, featureBits, pslMap, pslFilter and pslCDnaFilter.
-The exception are kent/src/blat, kent/src/jkOwnLib and the -the programs that produce the graphical images and the graphical user interface -for the UCSC Genome Browser, the following subdirectories under kent/src/hg: +The exception are source code directories with special LICENSE files in them. +These are kent/src/blat, kent/src/jkOwnLib and the programs that produce +the graphical images and the graphical user interface +for the UCSC Genome Browser, so the following subdirectories under kent/src/hg:
cgilib das encode hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver
-See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: +See the LICENSE file in the top level of our source code for a listing of +licenses and directories that they apply to: https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE. -
+Directories under non-commercial licenses have LICENSE files in them that start +with the "LicenseRef-proprietary" SPDX tag.When you use the UCSC Genome Browser in your work, please cite one of our publications.
+Non-commercial usage for the Genome Browser graphical interface (primarily the "hgTracks" program), including download and local installation, aka setting up a "mirror", is free. When you use the UCSC Genome Browser in your work, please cite one of our publications.
For commercial use, a license is required for download and local installation of
-certain Genome Browser webserver CGI binaries and source code.
-As specified above, this applies to the following subdirectories and programs under kent/src/hg, these are the
-programs that produce the graphical images and the graphical user interface for the UCSC Genome Browser:
+certain Genome Browser webserver CGI binaries and source code. In the source
+code repository, the respective directories are marked by special LICENSE
+files in them.
+As specified above, this applies to kent/src/blat, kent/src/jkOwnLib and the
+following subdirectories and programs under kent/src/hg, the majority are the programs
+that produce the graphical images and the graphical user interface for the UCSC
+Genome Browser:
cgilib das encode hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver
Also, BLAT and isPCR, if needed, are covered by a separate license (see below). This concerns the source code directories src/blat and src/jkOwnLib.
To purchase a commercial license for Genome Browser source code, LiftOver, GBiB, or GBiC, please visit the Genome Browser store.
We also have an FAQ on licensing questions which may help to clarify questions on how to license the code. We also have documentation on how to choose the best way to install a local installation of the Genome Browser, also called a "mirror".If you would like to purchase more than 20 copies of the Genome Browser source code, please follow these instructions:
Genome Browser licensing questions should be directed to genome-www@soe.ucsc.edu. For information about commercial licensing of the Blat and In-Silico PCR tools, see the Kent Informatics website or contact kent@soe.ucsc.edu.
See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE.
This software includes software made by open-source projects: