Make Newbler Open Source: an update

My petition to ask Roche/454 Life Science to make the Newbler software open source, as announced on this blog, has so far yielded 124 signatures. Thanks to all who signed!

It is not to late to add your signature!

Please do this before Thursday February 13th. On that day, at the Advances in Genome Biology and Technology (AGBT) meeting, I have been given the opportunity to hand over the petition results to two Roche representatives: Dan Zabrowski, Head of Roche Sequencing Unit and Paul Schaffer, Vice President of Roche 454 Sequencing Business. The fact that Roche opens up for me meeting these people makes me very happy!

Finally, here are some of the comments added by people who signed the petition. I anonymised them, but if you see your comment and would rather not I repeat it here, let me know (lex dot nederbragt at ibv dot uio dot no). Thanks for these wonderful comments on the Newbler assembly:

Roche has an excellent opportunity of publicit their commitment with science making their fantastic product Newbler open-source

I would like to runProject forever!

Newbler source code is very valuable to the sequencing community. Roche will be doing a service to the scientific community by making the Newbler source code available after the 454 shutdown.
Goodwill from making this OS is best value Roche can get for this code
This is way overdue. James Knight has done wonderful work but Newbler may fall through the cracks if it is not opened up to the community.

The newbler is great assembler for paired end data.
Please make it opensource, and I would be happy to contribute to it’s development.

Open source is a friend to science aiding reproducibility and allowing future developers to learn from existing work. Please do not limit science by preventing our access.

The Newbler suite has been remarkably useful and should continue to be so. I hope Jim Knight sees this and pushes for his creation to be made open source

I strongly support this petition and note there is a precedent for a commercially-developed assembler to be made publicly available under an open source license – the Celera assembler – much to the benefit of the scientific community.

Newbler was the basis for contig assembly of MiSeq data for me. An excellent piece of software.

Newbler was always my favorite thing about 454. It deserves to live on.

3 thoughts on “Make Newbler Open Source: an update

  1. Typically, large corporations might be willing to open source things, but might also need a partner to actually make it happen. Open sourcing is not for the feint of heart, and they might want to have a place or a community to give the project to. Our chances might be better if we could come up with such a community!

      • The Apache Software Foundation has done it, for example, for Oracle/Open Office. Open sourcing is scary enough for a company with strong intellectual property roots. They’ll want to have someone screen out and replace the bits they don’t want to release (for example, areas they might not have rights to, or bits that reflect badly on their quality control). I don’t know Newbler too well, but I do know the issues in open sourcing formerly closed source code!

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