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> Note that the key competitors to the patented MPEG technology is coming from "benevolent monopolies" like Google. That may be true in the abstract or in the

by jomar 8y ago

> Note that the key competitors to the patented MPEG technology is coming from "benevolent monopolies" like Google. That may be true in the abstract or in the case of MPEG's multimedia technologies. It is not true in this specific case of genomic file formats. The existing formats in use in the field (BAM and CRAM) that MPEG-G is looking to supplant come from the genomics community itself. They have come about in the course of bioinformaticians' work analysing sequencing data or as bioinformatics research [1]. Thus this R&D has primarily been bankrolled as scientific research; the funding comes from scientific charities or other scientific research funding. That is to say, it has come from collaboration. [1] CRAM originates from "Efficient storage of high throughput DNA sequencing data using reference-based compression", published in Genome Research in 2011. <https://genome.cshlp.org/content/21/5/734.long> https://genome.cshlp.org/content/21/5/734.long>

rayiner 8y ago
The work behind that article was done at the European Molecular Biology Lab ("EMBL"), which is a government-supported research lab. I wouldn't call that "collaboration" --it's one of the three forms of R&D spending I mentioned above ("government as benevolent monopoly"). These are my made up definitions of course, so we can argue about what counts as "collaboration." I'd say something like W3C or Linux--companies and individuals working together who aren't bankrolled by either patents, the government, or a quasi-monopoly.
- Tynach 8y ago
  > I wouldn't call that "collaboration" --it's one of the three forms of R&D spending I mentioned above ("government as benevolent monopoly"). The difference between government funding and a 'benevolent monopoly' is that in the first case an entity that does not directly benefit financially is providing the funding, while in the second case the entity providing the funding has a financial incentive to do so. And that's ignoring the fact that they listed the government as one source of funding, the link provided being an example of what they are talking about, not the sole instance. At least according to their comment, some funding for such things also comes from 'scientific charities'.
- jomar 8y ago
  One core part of CRAM originated with that article; more has come later. I'm involved in BAM and CRAM -- it feels like a collaboration to me! These formats are a collaboration between bioinformaticians at a number of research institutes and companies around the world, with various charity, governmental, or other funding. They are maintained under the auspices of GA4GH, which is indeed something like W3C.
- jkbonfield 8y ago
  Firstly, GA4GH has commercial members as well as academics, and all collaborate together to produce file formats, standards and protocols. Secondly you missed out a key part of funding - precompetitive alliances. Eg see the Pistoia Alliance (https://www.pistoiaalliance.org/ https://www.pistoiaalliance.org/) who funded the SequenceSqueeze project into compression of FASTQ (http://www.sequencesqueeze.org/ http://www.sequencesqueeze.org/). The notion here is simple - there are some technologies that are so core they cross all the commercial and academic boundaries. Collaboration rather than competition is considered to be to the mutual benefit of everyone involved. It is this mind set which lead to the Alliance for Open Media (AOM), who are also in direct competitive with MPEG.

by jomar 8y ago

rayiner 8y ago

The work behind that article was done at the European Molecular Biology Lab ("EMBL"), which is a government-supported research lab. I wouldn't call that "collaboration" --it's one of the three forms of R&D spending I mentioned above ("government as benevolent monopoly"). These are my made up definitions of course, so we can argue about what counts as "collaboration." I'd say something like W3C or Linux--companies and individuals working together who aren't bankrolled by either patents, the government, or a quasi-monopoly.

Tynach 8y ago
> I wouldn't call that "collaboration" --it's one of the three forms of R&D spending I mentioned above ("government as benevolent monopoly"). The difference between government funding and a 'benevolent monopoly' is that in the first case an entity that does not directly benefit financially is providing the funding, while in the second case the entity providing the funding has a financial incentive to do so. And that's ignoring the fact that they listed the government as one source of funding, the link provided being an example of what they are talking about, not the sole instance. At least according to their comment, some funding for such things also comes from 'scientific charities'.
jomar 8y ago
One core part of CRAM originated with that article; more has come later. I'm involved in BAM and CRAM -- it feels like a collaboration to me! These formats are a collaboration between bioinformaticians at a number of research institutes and companies around the world, with various charity, governmental, or other funding. They are maintained under the auspices of GA4GH, which is indeed something like W3C.
jkbonfield 8y ago
Firstly, GA4GH has commercial members as well as academics, and all collaborate together to produce file formats, standards and protocols. Secondly you missed out a key part of funding - precompetitive alliances. Eg see the Pistoia Alliance (https://www.pistoiaalliance.org/ https://www.pistoiaalliance.org/) who funded the SequenceSqueeze project into compression of FASTQ (http://www.sequencesqueeze.org/ http://www.sequencesqueeze.org/). The notion here is simple - there are some technologies that are so core they cross all the commercial and academic boundaries. Collaboration rather than competition is considered to be to the mutual benefit of everyone involved. It is this mind set which lead to the Alliance for Open Media (AOM), who are also in direct competitive with MPEG.