Designing the Microbial Research Commons Proceedings of an International Symposium (2011) / Chapter Skim
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20. Microbial Commons: Governing Complex Knowledge Assets
20. Microbial Commons: Governing Complex Knowledge Assets
Pages 145-160
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From page 145... ...
It is not just a matter of public sector participants. When my colleagues and I from the University of Waterloo and Wilfrid Laurier University studied 39 open-source initiatives developed after the completion of the Human Genome Project, we found that in many cases private-sector participants were involved, and a few actually catalyzed the formation of those initiatives.
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From page 146... ...
It is important to examine not only the issue of shared implementation from open-source software development and fair access to technology or biotechnology development, but also the way in which a commons serves to enable collaborative knowledge production. For example, in the pharmaceutical industry, the complexities associated with drug discovery are very intense.
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From page 147... ...
The transition point is defined as the point in discovery research when researchers come to believe that unilateral gains from private management of knowledge including appropriation activities are greater than shared gains from open or shared knowledge with the subsequent outcome exit from the commons. Therefore, from a strategic perspective, we need to look at when appropriation will take place -- when materials will be removed and no longer deposited.
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From page 148... ...
With BioBricks we are moving into what I consider the convergence paradigms, as now it is necessary to manage the complexities associated with synthetic biology. BioBricks makes DNA parts available to the public free of charge via MIT's registry of standard biological parts.
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From page 149... ...
Managing the Data Materials Management Downstream Microbial Commons Assets MannDB; WFCC; EcoPatent Commons; Example: GBIF; BioBricks AlgOS Helicos Microbial Data High complementary, High complementary, Non- High complementary, Knowledge Non-substitutable, substitutable or Non-substitutable or Characteristics: High applicability Substitutable, Substitutable, High applicability High applicability Open Access; Open Access; Non-Assertion Clauses; Knowledge Governance Strategy: Use of Supporting Open MTAs; Green Licensing; Access Tools License Agreements GNU-General Public Licenses TABLE 20–1 Governing the Microbial Commons 149
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From page 150... ...
We need to keep in mind that as scientists, information technology professionals, and other experts work together, they each have differing conventions regarding knowledge dissemination and appropriation. Some of them may find value in pure disembodied knowledge.
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From page 151... ...
As of September 2009, there were 4,319 microbial -- in particular, archaeal and bacterial -- genome projects under way around the world. As shown in Figure 21–1, five big sequencing centers are responsible for more than 50 percent of the world's production.
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From page 152... ...
For bioinformatics, of course, this is not true. There the limiting factor is always the quantity of data.
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From page 153... ...
And why do we keep on sequencing the same things? By analogy with what we heard yesterday about the brain, up to this point we have been seeing mainly genomics driven by medical applications or by energy and environmental applications, not by to the need to understand the whole diversity of nature.
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From page 154... ...
A year later, the Human Gut Microbiome Initiative started. And just a year after that, the National Institute of Health launched the Human Microbiome Project with a goal of sequencing 1,000 microbes isolated from different parts of the human body.
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From page 155... ...
If we consider the environmental studies, including only what is publicly available; we have approximately 30 million genes. If we add the environmental studies that we know are ongoing and the Human Microbiome Project studies, we expect that we will have at least 300 million genes over the next 3 years.
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From page 156... ...
We are therefore collapsing all of those different strains of a single species to a single organism, which we call Staphylococcus aureus pan-genome. Originally, the idea was to do this in order to save both in disc space and computation.
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From page 157... ...
Its mission is to implement new genomic standards, methods of capturing and exchanging metadata, standardization of metadata collection, and analysis efforts across the wider genomics community. The consortium's first major publication, which appeared last year in Nature Biotechnology, was a demonstration by the working group of achieving standards and representing metadata using what is called the Minimum Information about a Genomic Sequence (MIGS)
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From page 158... ...
Instead of having a single sequencing center, such as JGI, or even four sequencing centers, as is the case with the Human Microbiome Project, we want to organize a bigger international effort and ask the different countries of the world to contribute to an international genome project. What will that project be?
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From page 159... ...
The key partners in the project will be the GSC, which is definitely the major partner; culture collection centers, which will provide all the biological material for the project; representatives from Grand Challenge projects, including the Genomic Encyclopedia of Bacteria and Archaea, Terragenome, and the Human Microbiome Project; and other participants from large sequencing centers and country members. The response so far has been enthusiastic.
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