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HHMI to Enforce HMMER Trademark, Sparks Debate


A recent decision by the copyright holder of the widely used HMMER software to enforce its trademark has prompted some discussion in the bioinformatics community about forking the software and its commercial use.

This spring, the Howard Hughes Medical Institute obtained a trademark from the US Patent and Trademark Office for the freely distributed, open source HMMER, named for its use of profiling hidden Markov models.

HMMER developer Sean Eddy, a bioinformaticist at HHMI's Janelia Farm campus, explains on his blog that the trademark is intended to help enable "a single open source HMMER codebase."

As a result, he says, he is asking developers who use the HMMER name for their software to ensure that it is a true implementation of the HMMER code, and that they contribute to the codebase. Those who don't comply will be asked to change the name of their software.

"There are several different 'HMMERs' out there, some of which have forked HMMER code, some of which say they are independent implementations, and some of which aren't very clear what they are," Eddy says. "I don't think this confusion around the name is useful for the community, and frankly, I find it somewhat annoying that people are forking rather than working together."

He adds that Janelia Farm "will soon start enforcing the HMMER trademark with some friendly letters, if needed — these letters will be requests to work together on a common codebase."

Eddy cites HMMoC, a compiler for hidden Markov models developed by Gerton Lunter at the UK's Medical Research Council, as an example of a name that "no one is going to confuse" with HMMER. However, he also named several commercial packages that are using the HMMER name improperly, in his view: Progeniq's BioBoost Accelerated HMMer, Logical Depth's LD-HMMer, and CLCbio's HMMer.

Eddy noted that none of these companies distributes the code under the open source GPL license, as HMMER is.

— Vivien Marx

Bioinformatics Notes

The David H. Murdock Research Institute licensed Rosetta Biosoftware's suite for translational research projects that involve high performance 'omics applications. The institute will use the company's Rosetta Resolver system for gene expression analysis, Elucidator for proteomics and metabolomics analysis, and Syllego for genotyping analysis.

Penguin Computing has signed an OEM agreement with Life Technologies' Applied Biosystems business unit under which it will bundle its Scyld ClusterWare cluster management software with ABI's SOLiD sequencer. According to ABI's most recent specification sheet for the SOLiD, the system comes with a head node and three compute nodes running 64-bit Linux.


$2 million
Amount out of a total $2.4M in severance and recruiting fees associated with Accelrys CEO Mark Emkjer's departure.

Funded Grants

$313,578/FY 2009
Computational Analysis of Nucleosome Positioning Signals in Eukaryotic Genomes
Grantee: Zhiping Weng, University of Massachusetts Medical School
Began: May 15, 2009; Ends: Apr. 30, 2010

This grant will go toward the development of predictive models of the packing of DNA within eukaryotic cells. Weng's goal is to have models of nucleosome formation that can be used to design DNA sequences that form stable nucleosomes in vivo. Algorithms, software, and data sets from the project will be made freely available.

$135,390/FY 2009
Ultrafast Monte Carlo Simulation of Molecules with Electronic Embedding, and Novel Basis Sets for Intermolecular Interactions
Grantee: Peter Pulay, University of Arkansas
Began: Jun. 1, 2009; Ends: May 31, 2010

According to the grant abstract, these funds will be used to develop algorithms to reduce the computational cost of ab initio quantum/molecular mechanics Monte Carlo or molecular dynamics free energy calculations of molecules electronically embedded in a solvent or protein matrix.

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