HMMER policy on trademark, copyright, patents, and licensing

There are two ways of spreading light: to be the candle or the mirror that reflects it.

— Edith Wharton, Vesalius in Zante

On April 14, the US Patent and Trademark Office awarded us a trademark on HMMER. This is a good moment to explain how we plan to deal with intellectual property.

HMMER is scientific software, and its methods are described in journal publications. That means that it must be made available in a form that enables any scientist to understand, reproduce, and extend — like any other result of a scientific paper. For software, this is essentially the same as what people mean by “open source”. Our intent is to make HMMER widely and freely available to the entire scientific community as open source code. At the same time, we have to recognize that HMMER is a large, growing, and increasingly valuable codebase, not just a one-off result, so we’re taking steps to make sure we can sustain it as a long term, coherent open source project. Continue reading →

Computational challenges in the future of large-scale sequencing


I’m preparing a plenary talk on Computational Challenges in the Future of Large-Scale Sequencing that I’ll give at a workshop on The Future of the Large-Scale Sequencing Program, which the NIH National Human Genome Research Institute (NHGRI) is convening in two weeks (Bethesda, 23-24 March 2009). This is part of a long range planning process for NHGRI. This will be the one talk at the workshop that focuses on computational biology’s future needs, so I’m aiming to present a community consensus view as guidance to NHGRI, not just my own view.

What do you think NHGRI should hear?
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