Make Newbler open source: the Roche response and the future of Newbler

Earlier this year, I started a petition to ask Roche/454 Life Sciences to make the Newbler software (gsAssembly, gsMapper and Amplicon Variant Analyzer) open source. See this post for the background to the petition.

Source: Wikimedia Commons, by Marcus Quigmire

Source: Wikimedia Commons, by Marcus Quigmire

When I closed the petition, 162 people had signed it, see the PDF on figshare. During the Advances in Genome Biology and Technology (AGBT) meeting in Florida, I handed over the results of the petition to two Roche representatives, Dan Zabrowski, Head of Roche Sequencing Unit and Paul Schaffer, Vice President of Roche 454 Sequencing Business, see my blog post on the conversation I had with them.

Dan Zabrowski and Paul Schaffer promised me an official Roche response, and here it is (exclusively released through this blog):

We want to thank Lex Nederbragt and the 162 signatories, for bringing the Newbler (GS De novo Assembler and GS Reference Mapper) open source request to our attention. We recognize the value of Newbler across all sequencing platforms and that’s why we make the software available to the field, free of charge, through download on our website (http://454.com/contact-us/software-request.asp).
We also look to the community to inform us of any enhancement requests or software bugs. We track all of your feedback in a database and attempt to incorporate as many of your requests into the next commercial software release. Each of these is prioritized at the start of the next project. Please contact your local Roche technical support and provide your feedback to them.
Roche has made a significant investment in the development and maintenance of Newbler and recognizing it is highly-regarded, we will continue to integrate it into our future sequencing platforms, including those we develop internally and those we acquire externally. Roche remains committed to sequencing and will continue to make the software available to the field, free of charge, through download on our website.

So, there you have it:

  • Roche will continue to make Newbler available through a relatively simple registration form
  • Roche will not make Newbler open source (they don’t say that, but that is the obvious conclusion)
  • Roche appreciates community input to Newbler (bug reports, feature request)
  • In a teleconference I had with Paul Schafer and others from Roche, Paul sad that Roche doesn’t see a huge advantage of making Newbler open source, because its free

I keep asking myself, where does this leave us, what have we achieved, if anything, with this petition. My conclusion is that not much has been achieved. Yes, Roche has gotten a clear signal from the community that we would like Newbler to become open source. Many researchers expressed support, for which I am again grateful. Yes, Roche have expressed a commitment to continue to provide access to the software (Newbler will not disappear anytime soon). But the commercial interests of Roche are just too big. Roche is such a big player in this field that, even though they will shut down the 454 sequencing business in 2016, of course they are working towards a new sequencing platform, be it developed internally or acquired. Beyond their collaboration with Pacific Biosciences, it is yet a total secret what else they have in the pipeline. We will just have to wait for rumours and/or press releases to find out. Roche intends to adjust the Newbler program to accommodate this new platform. That gives them plenty of reasons to not make the program open source.

What did I get out of it personally? It was very rewarding to see the massive support for this initiative, I clearly struck a chord with people. It was an interesting experience to talk to the Roche managers. But, I have to be careful not to get frustrated with Roche. I am a big fan of the software as it still is one of the best programs for working with 454 data. We have been, and still are, using it successfully for the Atlantic cod genome assemblies. It would have been a wonderful thing to have the software available open source, and see a community being built around it, leading hopefully to increased usage and further improvements. I didn’t really think this petition would change anything, but of course I did have some faint hope.

I have reopened the petition, so people who missed their chance can still add their name by following this link.

Finally, I once again want to express my thanks to all the petition signer, to Roche for allowing me to personally hand the results over, and for taking the time to formulate a response. I’ll close by encouraging you all to give Newbler a try, and keep an eye out for the next release. I have it from good sources there are some nice surprises coming!

Feel free to add your own thoughts in the comments section!

One thought on “Make Newbler open source: the Roche response and the future of Newbler

  1. “Roche appreciates community input to Newbler (bug reports, feature request)”

    That’s encouraging, because when I submitted a bug in Newbler 2.6 http://seqanswers.com/forums/showthread.php?t=15443 through my local representative, I never got a response other than that it would be passed on. It appeared to be fixed in the next version, but it would have been nice to hear absolutely anything back, because I tended to assume that they didn’t care.

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