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Open Standards and Resources in Systems Biology: collaborative scale-up toward virtual life
Correspondence: (Login to view email address)
- EMBL–EBI, Wellcome-Trust Genome Campus, Hinxton, United Kingdom
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- Document Type:
- Presentation
- Date:
- Received 30 November 2006 13:26 UTC; Posted 30 November 2006
- Subjects:
- Biotechnology
- Abstract:
The practise of Systems Biology relies on interfaces. Interfaces
between the entities we study: the paradigm moved from a physical
object centric view toward a relationship-centric one; interfaces
between tools: From the retrieval of the primary data to the fine
analysis of a model’s behaviour, one uses many tools, more or less
well connected; interfaces between individuals: To build any
non-trivial mechanistic model requires to merge existing work and
gather external expertise.If we want these interfaces to be generic enough to allow for anybody
to leverage on existing toolkits, a fundamental requirement is the
existence of community-developed well supported standards, but also
open resources where to find the “lego” blocks. Over the last
half-decade, several efforts have been launched in that direction,
whether concerning encoding format, ontologies or databases. Some of
them are now well-established in the field and play a significant role
to improve its coherence but also to increase the size and the quality
of quantitative models.- Presented at:
- BioScope-IT annual meeting, 24 November 2006
Discussion
- Votes:
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7 votes
- Comments:
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3 comments
What I meant in the presentation by “systems-biology is scale-free” was much simpler than that. I just meant that being the study of the dynamic relationships between many components, the same formalism can be applied, whether those components are molecules, cells or organisms. While in the recent years, systems biology has been the playgrown of biochemists, it has not always been the case. Cf. Dennis Noble and Peter Hunter or the whole community of theoreticians in developmental biology.
May be you wish to say that it is multi-scale rather than scale-free.
“Scale-free” is an abusively used in many articles. I think it originally meant to be
some patterns are self-similar so that similar patterns emerge independent of scale.
now, many says id distribution is power-law that is scale-free. the definition that I think is too lose… - (Login to share with a colleague)
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- License:
- This document is licensed to the public under the Creative Commons Attribution 2.5 License
- How to cite this document:
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Le Novere, Nicolas. Open Standards and Resources in Systems Biology: collaborative scale-up toward virtual life. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2006.10.1> (2006)
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Michael Hucka on 20 January 2007 06:29 UTC
I like the summary of systems biology and its goals, and especially the 3-part sequence physiology->molecular bio->systems bio.
However, I don’t know what is meant by “systems biology is scale-free”. Do you mean the same thing that some people mean by “biological networks are scale-free”?
The notion that biological networks are scale-free has been popularized and repeated by many people, but the idea has been and can be disputed. Scale-free theory assumes that the nodes of a network are homogeneous (i.e., that it doesn’t matter what their characteristics are, only their connectivity) and the principle prediction of scale-free theory is that the connectivity obeys a power-law relationship, with some being hugely connected and consequently the potential source of catastrophic network failures. I suspect the assumption and the prediction together are false for biomolecular interaction networks. The argument (not invented by me, but my interpretation of it) goes like this. First, surely we can agree that one of the most obvious features of molecular networks is that there are thousands upon thousands of unique molecules playing roles in a cell; they are not undifferentiated nodes. Removing one leads to unique failures of the overall system. Second, a power-law scaling effect in biological networks would mean that, on the one hand, that the majority of molecules only interact with one other molecule, and on the other hand, there are a few molecules that are “connected” to an incredibly vast number of other molecules, in the sense that they react with a myriad of different molecules in the cell. Are either of these last points true?