70ac948e82b41ef316523635c04e5e2c4a89c417 mspeir Fri Sep 4 16:57:54 2026 -0700 trackLists: give the variant frequency projects their own table, move the page to goldenPath/help/mirrorTracks.html, add the otto cron line, refs #37781 Half the restricted list was national sequencing cohorts sitting under varFreqs and phasedVars, and in one alphabetical table they buried the tracks people actually write in about, OMIM, HGMD and DECIPHER. Those cohorts now get a table of their own below the rest. The split is read off the trackDb parent chain, so the next cohort added under varFreqs lands in the right table with no edit here. The page moves off the htdocs root to goldenPath/help/mirrorTracks.html, beside mirror.html, which now links to it. That link goes in src/product/README.txt, the pandoc source mirror.html is generated from. The licensing page link follows the move, and the page title changes with the file name. Also adds the weekly otto line, placed above the HGDB_CONF that would otherwise apply to it, and keeps the job from listing itself as a self-updating track. Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/htdocs/license/index.html src/hg/htdocs/license/index.html index fcda259756c..d9f10a1da27 100755 --- src/hg/htdocs/license/index.html +++ src/hg/htdocs/license/index.html @@ -1,219 +1,219 @@

Website: No license or permission is needed to use the website, API and public MySQL server for academic, commercial or any other use

This is a public website. There is no license or permission needed to use the website and any services (API, etc) on it. You can also load your own data onto our website and look at it there, and use track hubs or custom tracks to configure how it is displayed, regardless of whether you are a commercial, non-commercial or any other type of entity. However, when you use the UCSC Genome Browser in your work, please cite one of our publications.


Graphics: No permission is needed to reproduce a graphic produced by the Genome Browser

Blanket permission for reuse of all graphics produced by the UCSC Genome Browser website is hereby granted to everyone. 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.


Data: No license is needed for the data files and database tables used by the Genome Browser

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. One exception is the liftOver chain files, which can be linked, downloaded, used and redistributed, but only for non-commercial use; see the liftOver README. A further set of exceptions, for certain clinical genetics tracks, is described below.

Sometimes, the source databases or authors place restrictions on 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. For some of these, we are not allowed to make the data available. Usually the data must be obtained from the source database directly in the original format or licensed, rather than from UCSC. Examples are HGMD, LOVD, OMIM, Decipher, Genomenon, GeneHancer and COSMIC. For viral genomes, any GISAID-sequences or any data -derived from GISAID sequences cannot be shared by us. See this list +derived from GISAID sequences cannot be shared by us. See this list of tracks that we cannot distribute for the exact set. 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. They usually list or link to the exact license conditions. Files for these tracks are not available from our download servers, please contact us for questions or if you need a pointer to the respective conversion scripts in our Github code repository.


Command-line tools: Most command-line tools and directories are freely available for all uses

The majority of the Genome Browser source code is available under the MIT license, see the LICENSE file in our source code repository. As such, the Unix command line utilities needed to build tracks, track hub files, computational pipelines, and our hundreds of tools to filter, sort, rearrange, join, and process genome annotation files can be used and redistributed freely via package managers and installation tools, even for commercial use (except BLAT/LiftOver). Notable examples are bedToBigBed, wigToBigWig, overlapSelect, featureBits, pslMap, pslFilter and pslCDnaFilter.

The exceptions are source code directories with special LICENSE files in them. These are kent/src/blat, kent/src/isPcr, kent/src/jkOwnLib, and the programs that produce the graphical images or user interface for the UCSC Genome Browser. This includes the following subdirectories under kent/src/hg:

cgilib 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: 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.


Graphical browser software: Download and installation of the graphical Genome Browser software and access to the source code is free for non-commercial uses but not commercial usage

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. 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/isPcr, kent/src/jkOwnLib, and the following subdirectories and programs under kent/src/hg. The majority of license protected files are the programs that produce the graphical images and the graphical user interface for the UCSC Genome Browser:


cgilib 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 kent/src/blat, kent/src/isPcr and kent/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 option for a local installation of a Genome Browser "mirror".

If you would like to purchase the Genome Browser source code without going through our store, please follow these instructions:

  1. Read and sign the licensing agreement.
  2. Email a signed copy of the license agreement to the UCSC Office for IP Management (genome-browser-store-group@ucsc. edu).
  3. Follow the instructions in the license agreement for submitting the signed original copy and payment.
  4. After your license application has been processed, you will receive instructions for downloading the browser software and data.

Genome Browser licensing questions should be directed to genome-browser-store-group@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.


Fonts

Atkinson Hyperlegible: Designed by Braille Institute, Applied Design Works, Elliott Scott, Megan Eiswerth, Linus Boman, Theodore Petrosky
Copyright 2020 Braille Institute of America, Inc. This Font Software is licensed under the SIL Open Font License, Version 1.1 . This license is copied below, and is also available with a FAQ at: https://openfontlicense.org SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007

Lexend: Designed by Bonnie Shaver-Troup, Thomas Jockin, Santiago Orozco, Héctor Gómez, Superunion
Copyright 2018 The Lexend Project Authors (https://github.com/googlefonts/lexend), with Reserved Font Name “RevReading Lexend”. This Font Software is licensed under the SIL Open Font License, Version 1.1 . This license is copied below, and is also available with a FAQ at: https://openfontlicense.org SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007


Acknowledgements

This software includes software made by open-source projects: