Usage of Kent Utils Code

Christopher Gibb

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Jul 5, 2016, 11:31:15 AM7/5/16

to genome...@soe.ucsc.edu

To the UCSC Genome Informatics Group,

My name is Christopher Gibb, I am a Research Assistant with the Thunder Bay Regional Research Institute in Canada. I am currently involved in the development of an in house data analysis tool. I'd like to eventually release this as an open source project. We are primarily interested in a few of the data format conversion functions found in your own project. I see your license allows non-commercial redistribution and use of the genome browser itself but does not necessarily make mention of any of the utilities it uses. (i.e. Kent Utils). Would it be permissible for us to integrate some source code from Kent Utils? That is, provided proper citation of course. I look forward to your reply.

All the best,
Chris

Christopher Lee

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Jul 18, 2016, 12:47:42 PM7/18/16

to Christopher Gibb, genome...@soe.ucsc.edu

Hi Chris,

Thank you for your question concerning usage of the Kent Utils code. Is it possible for you
to provide a little more information about your plans? Which tools will you be using? Will
you be charging a fee for use of your program? Will you be using the pre-compiled binaries
or will you be compiling the source yourself? How do you plan on integrating our programs
into yours?

You can reply to me directly if you do not want to include the list in your response.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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Christopher Gibb

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Jul 18, 2016, 4:33:38 PM7/18/16

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Hi Chris,
The program will be free, open source. Potentially MIT licensed. License has not yet been decided upon yet. The tool we are particularly interested in is faToTwoBit. We would like to distribute the binary form of faToTwoBit with the program. I have compiled faToTwoBit on Linux for distribution. Further, I would like to port faToTwoBit to Windows for use in a Windows port of the application.

All the best,
Chris

>>> Christopher Lee <chm...@ucsc.edu> 07/18/16 12:48 PM >>>

Christopher Lee

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Jul 19, 2016, 1:06:02 PM7/19/16

to Christopher Gibb, genome...@soe.ucsc.edu

Hi Chris,

faToTwoBit is entirely open source and free to use by anyone, feel free to distribute the binary
with your project as you wish. If you have any feedback on our utilities or make any improvements
please let us know so we can support them too!

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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